[gmx-users] NVT simulation and mdp file

Discussion:

teklebrh

2010-03-03 17:37:08 UTC

Dear Gromacs Users,

I have encountered the following issues while I was running my MD
simulation. Can anybody comment on what the meaning of these notes
are. Is there anything I could do to avoid them.

NOTE 2 [file PAP.top, line unknown]:

The largest charge group contains 12 atoms.

Since atoms only see each other when the centers of geometry of the charge

groups they belong to are within the cut-off distance, too large charge

groups can lead to serious cut-off artifacts.

For efficiency and accuracy, charge group should consist of a few atoms.

For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.

My SOLVENT IS TOLUENE --- the PRODRG gave me a topology file with only
one group charge only.

NOTE 1 [file nvt.mdp, line unknown]:

The Berendsen thermostat does not generate the correct kinetic energy

distribution. You might want to consider using the V-rescale thermostat.

NOTE 3 [file aminoacids.dat, line 1]:

The optimal PME mesh load for parallel simulations is below 0.5

and for highly parallel simulations between 0.25 and 0.33,

for higher performance, increase the cut-off and the PME grid spacing

In addition to the above notes I have also some questions about the
NVT and NPT simulation.

1)I am using toluene as a solvent to simulate my polymer, do I need to
use the compressibility of toluene which is 9.2e-5 or the default
value 4.5e-5 1/bar.
2)What about the dielectric constant (the dielectric constant for
toluene is 2-2.4), but the default value is 80 ( I assume this is for
water- am I right).
3)Is always rvdw = 1.4 nm for GROMOS96. As a result I have to
increase my box size of the solute at the beginning to a min of 2*1.4
=2.8 ( min image convection). Is this the right way to do!
4)I run an NVT simulation to equilibrate my system for 100 ps. When I
checked my simulation at the end (successfully completed) I noticed
that the shape of my simulation box looks CIRCULAR! some how the
rectangular shape looks distorted. What does this tell! Do you guys
think something is wrong in my simulation.
5)I included the polar and aromatic hydrogens in my simulation (
ffG43a1.itp ? GROMOS96.1 in PRODRG). Does these hydrogen influence my
result as the force field is a united atom force field. Or How can I
get rid of them if I want. With or without the aromatic hydrogen gave
good results ( besides lower computational cost). Does Gromos96 model
correctly aromatic-Aromatic interaction.

For more information I am posting my full NVT.mdb file below.

I really appreciate your feedback and help in advance.

thank you

Rob

#include ""
;

; File 'mdout.mdp' was generated

;
;

; LINES STARTING WITH ';' ARE COMMENTS

title = NVT equlibration ; Title of run

cpp = /usr/bin/cpp ; location of cpp on linux

; The following lines tell the program the standard locations where to
find certain files

; VARIOUS PREPROCESSING OPTIONS

; Preprocessor information: use cpp syntax.

; e.g.: -I/home/joe/doe -I/home/mary/hoe

include =

; e.g.: -DI_Want_Cookies -DMe_Too

define = -DPOSRES

; RUN CONTROL PARAMETERS

integrator = md

; Start time and timestep in ps

tinit = 0

dt = 0.002

nsteps = 50000

; For exact run continuation or redoing part of a run

; Part index is updated automatically on checkpointing (keeps files separate)

simulation_part = 1

init_step = 0

; mode for center of mass motion removal

comm-mode = Linear

; number of steps for center of mass motion removal

nstcomm = 1

; group(s) for center of mass motion removal

comm-grps =

; LANGEVIN DYNAMICS OPTIONS

; Friction coefficient (amu/ps) and random seed

bd-fric = 0

ld-seed = 1993

; ENERGY MINIMIZATION OPTIONS

; Force tolerance and initial step-size

emtol = 100

emstep = 0.01

; Max number of iterations in relax_shells

niter = 20

; Step size (ps^2) for minimization of flexible constraints

fcstep = 0

; Frequency of steepest descents steps when doing CG

nstcgsteep = 1000

nbfgscorr = 10

; TEST PARTICLE INSERTION OPTIONS

rtpi = 0.05

; OUTPUT CONTROL OPTIONS

; Output frequency for coords (x), velocities (v) and forces (f)

nstxout = 100

nstvout = 100

nstfout = 100

; Output frequency for energies to log file and energy file

nstlog = 100

nstenergy = 100

; Output frequency and precision for xtc file

nstxtcout = 100

xtc-precision = 1000

; This selects the subset of atoms for the xtc file. You can

; select multiple groups. By default all atoms will be written.

xtc-grps =

; Selection of energy groups

energygrps =

; NEIGHBORSEARCHING PARAMETERS

; nblist update frequency

nstlist = 10

; ns algorithm (simple or grid)

ns-type = Grid

; Periodic boundary conditions: xyz, no, xy

pbc = xyz

periodic_molecules = no

; nblist cut-off

rlist = 0.9

; OPTIONS FOR ELECTROSTATICS AND VDW

; Method for doing electrostatics

coulombtype = PME

rcoulomb-switch = 0

rcoulomb = 0.9

; Relative dielectric constant for the medium and the reaction field

epsilon_r = 1

epsilon_rf = 1

; Method for doing Van der Waals

vdw-type = Cut-off

; cut-off lengths

rvdw-switch = 0

rvdw = 1.4

; Apply long range dispersion corrections for Energy and Pressure

DispCorr = no

; Extension of the potential lookup tables beyond the cut-off

table-extension = 1

; Seperate tables between energy group pairs

energygrp_table =

; Spacing for the PME/PPPM FFT grid

fourierspacing = 0.12

; FFT grid size, when a value is 0 fourierspacing will be used

fourier_nx = 0

fourier_ny = 0

fourier_nz = 0

; EWALD/PME/PPPM parameters

pme_order = 4

ewald_rtol = 1e-05

ewald_geometry = 3d

epsilon_surface = 0

optimize_fft = no

; IMPLICIT SOLVENT ALGORITHM

implicit_solvent = No

; GENERALIZED BORN ELECTROSTATICS

; Algorithm for calculating Born radii

gb_algorithm = Still

; Frequency of calculating the Born radii inside rlist

nstgbradii = 1

; Cutoff for Born radii calculation; the contribution from atoms

; between rlist and rgbradii is updated every nstlist steps

rgbradii = 2

; Dielectric coefficient of the implicit solvent

gb_epsilon_solvent = 2.4

; Salt concentration in M for Generalized Born models

gb_saltconc = 0

; Scaling factors used in the OBC GB model. Default values are OBC(II)

gb_obc_alpha = 1

gb_obc_beta = 0.8

gb_obc_gamma = 4.85

; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA

; The default value (2.092) corresponds to 0.005 kcal/mol/Angstrom^2.

sa_surface_tension = 2.092

; OPTIONS FOR WEAK COUPLING ALGORITHMS

; Temperature coupling

tcoupl = Berendsen ; NVT

; Groups to couple separately

tc-grps = PAP TOL

; Time constant (ps) and reference temperature (K)

tau-t = 0.1 0.1

ref-t = 300 300

; Pressure coupling

Pcoupl = No ; no presure coupling in NVT

Pcoupltype = Isotropic

; Time constant (ps), compressibility (1/bar) and reference P (bar)

tau-p = 1

compressibility = 9.2e-5

ref-p = 1

; Scaling of reference coordinates, No, All or COM

refcoord_scaling = No

; Random seed for Andersen thermostat

andersen_seed = 815131

; OPTIONS FOR QMMM calculations

QMMM = no

; Groups treated Quantum Mechanically

QMMM-grps =

; QM method

QMmethod =

; QMMM scheme

QMMMscheme = normal

; QM basisset

QMbasis =

; QM charge

QMcharge =

; QM multiplicity

QMmult =

; Surface Hopping

SH =

; CAS space options

CASorbitals =

CASelectrons =

SAon =

SAoff =

SAsteps =

; Scale factor for MM charges

MMChargeScaleFactor = 1

; Optimization of QM subsystem

bOPT =

bTS =

; SIMULATED ANNEALING

; Type of annealing for each temperature group (no/single/periodic)

annealing =

; Number of time points to use for specifying annealing in each group

annealing_npoints =

; List of times at the annealing points for each group

annealing_time =

; Temp. at each annealing point, for each group.

annealing_temp =

; GENERATE VELOCITIES FOR STARTUP RUN

gen-vel = yes ; assign velocities from Maxwell
distribution (MXD)

gen-temp = 300 ; temperature for MXD

gen-seed = 173529 ; used to initialize random
generator for random velocities

; OPTIONS FOR BONDS

constraints = all-bonds

; Type of constraint algorithm

constraint-algorithm = Lincs

; Do not constrain the start configuration

continuation = no

; Use successive overrelaxation to reduce the number of shake iterations

Shake-SOR = no

; Relative tolerance of shake

shake-tol = 0.0001

; Highest order in the expansion of the constraint coupling matrix

lincs-order = 4

; Number of iterations in the final step of LINCS. 1 is fine for

; normal simulations, but use 2 to conserve energy in NVE runs.

; For energy minimization with constraints it should be 4 to 8.

lincs-iter = 1

; Lincs will write a warning to the stderr if in one step a bond

; rotates over more degrees than

lincs-warnangle = 30

; Convert harmonic bonds to morse potentials

morse = no

; ENERGY GROUP EXCLUSIONS

; Pairs of energy groups for which all non-bonded interactions are excluded

energygrp_excl =

; WALLS

; Number of walls, type, atom types, densities and box-z scale factor
for Ewald

nwall = 0

wall_type = 9-3

wall_r_linpot = -1

wall_atomtype =

wall_density =

wall_ewald_zfac = 3

; COM PULLING

; Pull type: no, umbrella, constraint or constant_force

pull = no

; NMR refinement stuff

; Distance restraints type: No, Simple or Ensemble

disre = No

; Force weighting of pairs in one distance restraint: Conservative or Equal

disre-weighting = Conservative

; Use sqrt of the time averaged times the instantaneous violation

disre-mixed = no

disre-fc = 1000

disre-tau = 0

; Output frequency for pair distances to energy file

nstdisreout = 100

; Orientation restraints: No or Yes

orire = no

; Orientation restraints force constant and tau for time averaging

orire-fc = 0

orire-tau = 0

orire-fitgrp =

; Output frequency for trace(SD) and S to energy file

nstorireout = 100

; Dihedral angle restraints: No or Yes

dihre = no

dihre-fc = 1000

; Free energy control stuff

free-energy = no

init-lambda = 0

delta-lambda = 0

sc-alpha = 0

sc-power = 0

sc-sigma = 0.3

couple-moltype =

couple-lambda0 = vdw-q

couple-lambda1 = vdw-q

couple-intramol = no

; Non-equilibrium MD stuff

acc-grps =

accelerate =

freezegrps =

freezedim =

cos-acceleration = 0

deform =

; Electric fields

; Format is number of terms (int) and for all terms an amplitude (real)

; and a phase angle (real)

E-x =

E-xt =

E-y =

E-yt =

E-z =

E-zt =

; User defined thingies

user1-grps =

user2-grps =

userint1 = 0

userint2 = 0

userint3 = 0

userint4 = 0

userreal1 = 0

userreal2 = 0

userreal3 = 0

userreal4 = 0

Justin A. Lemkul

2010-03-03 18:02:52 UTC

Permalink

Post by teklebrh
Dear Gromacs Users,
I have encountered the following issues while I was running my MD
simulation. Can anybody comment on what the meaning of these notes are.
Is there anything I could do to avoid them.
The largest charge group contains 12 atoms.
Since atoms only see each other when the centers of geometry of the charge
groups they belong to are within the cut-off distance, too large charge
groups can lead to serious cut-off artifacts.
For efficiency and accuracy, charge group should consist of a few atoms.
For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.
My SOLVENT IS TOLUENE --- the PRODRG gave me a topology file with only
one group charge only.

That's almost certainly wrong. See, for instance, the PHE side chain in the
relevant .rtp entry for a more reasonable charge group setup. If you're using
PRODRG defaults, then the charges are probably unsatisfactory, as well.

The rationale for the charge group size is summed up here:

http://lists.gromacs.org/pipermail/gmx-users/2008-November/038153.html

Post by teklebrh
The Berendsen thermostat does not generate the correct kinetic energy
distribution. You might want to consider using the V-rescale thermostat.

See the literature about this one, as well as the numerous list archive
discussions. For initial equilibration, a weak coupling scheme is probably
fine, but you can also use V-rescale. Also of interest:

http://www.gromacs.org/Documentation/Terminology/Thermostats

Post by teklebrh
The optimal PME mesh load for parallel simulations is below 0.5
and for highly parallel simulations between 0.25 and 0.33,
for higher performance, increase the cut-off and the PME grid spacing

This all depends on the size of your system, how much of the work is distributed
between the real-space Coulombic interaction and PME.

Post by teklebrh
In addition to the above notes I have also some questions about the NVT
and NPT simulation.
1)I am using toluene as a solvent to simulate my polymer, do I need to
use the compressibility of toluene which is 9.2e-5 or the default
value 4.5e-5 1/bar.

Well, 4.5e-5 corresponds to water, which you aren't using...

For NVT, this won't matter since the box is fixed, but for NPT, the
compressibility will affect the response of your system to pressure. The
differences may be minimal, but if you know the right value, why accept a wrong one?

Post by teklebrh
2)What about the dielectric constant (the dielectric constant for
toluene is 2-2.4), but the default value is 80 ( I assume this is for
water- am I right).

Yes, the default again assumes water as the solvent.

Post by teklebrh
3)Is always rvdw = 1.4 nm for GROMOS96. As a result I have to increase
my box size of the solute at the beginning to a min of 2*1.4 =2.8 ( min
image convection). Is this the right way to do!

At an absolute minimum. Keep in mind that the box vectors will fluctuate under
NPT, so if the box decreases even a little bit below 2.8, you will be violating
the minimum image convention.

Post by teklebrh
4)I run an NVT simulation to equilibrate my system for 100 ps. When I
checked my simulation at the end (successfully completed) I noticed that
the shape of my simulation box looks CIRCULAR! some how the rectangular
shape looks distorted. What does this tell! Do you guys think something
is wrong in my simulation.

This could be some visualization artifact, or the components of your system have
condensed within the box. Without actually seeing it, it's hard to tell. If
you post an image online (Photobucket, etc) then we might get a better sense of
what's going on.

Post by teklebrh
5)I included the polar and aromatic hydrogens in my simulation (
ffG43a1.itp ? GROMOS96.1 in PRODRG). Does these hydrogen influence my
result as the force field is a united atom force field. Or How can I get
rid of them if I want. With or without the aromatic hydrogen gave good
results ( besides lower computational cost). Does Gromos96 model
correctly aromatic-Aromatic interaction.

Well, "correct" is a relative term for all force fields, but you need to follow
the prescribed setup of the force field itself, otherwise you can throw it all
away. If you lump the hydrogens into the ring carbons and have an uncharged
ring, the result will be different than if you have the hydrogens there with a
small charge on each C and H. Again, refer to the force field .rtp file for
examples. You can also create a better toluene topology by renaming the residue
in your coordinate file PHE and trick pdb2gmx:

pdb2gmx -f toluene.pdb -missing

Then change the mass of the CH2 group (which pdb2gmx thinks is a CB for PHE) to
reflect a CH3 group. Make an .itp file out of the resulting .top by removing
the unnecessary #includes, [system], and [molecule] directives. Then you don't
have to worry about messing with PRODRG. I should note, as well, that this is
about the only appropriate use of -missing I can think of at the moment (just
for clarity in the archives; I usually warn against using -missing).

-Justin
--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================

Justin A. Lemkul

2010-03-03 22:10:37 UTC

Permalink

Dear Justin,
I really appreciate your help and feedback. once again thank you for
your time.
--------This could be some visualization artifact, or the components of
your
system have condensed within the box. Without actually seeing it,
it's hard to tell. If you post an image online (Photobucket, etc)
then we might get a better sense of what's going on.
Here is my .gro file taht looks like condensed.------------
Attached please find the NVT.gro file
or the images in .jpeg file format

Please note that this is not what I suggested you do. Posting images online
(not to the list) is a far better method. Users who subscribe to the list in
digest format will not get these attachments, and thus you alienate others who
might be able to help you. Also, for the security-conscious, download
attachments is not always preferable.

It seems pretty clear from what's going on that your system is simply
condensing, so your initial configuration placed all the molecules too far apart
(at too low of a density). Display the box vectors in VMD and you will see
exactly what's going on:

(Tk console)
package require pbctools
pbc box

-Justin

Best,
Rob