[gmx-users] gromacs.org_gmx-users Digest, Vol 175, Issue 95

[Seketoulie Keretsu]

Dear Alex

Thank you for the "shameless self promotion". Have been looking for
some classic gromacs products lately. Have seen some interesting
methods in area of protein-ligand interactions. If you have some new
and interesting gromacs papers related to Protein-ligand studies
please suggest it here.

Also came across this paper out of Stanford university. 400 micro sec
simulations. Just blown my mind.
https://www.nature.com/articles/s41467-016-0015-8

Will really appreciate if you can suggest .

Appreciate you guys for all the help so far.

Best, Seke
On Tue, Nov 27, 2018 at 1:05 PM

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than "Re: Contents of gromacs.org_gmx-users digest..."
1. Parameterizing N-terminal capping (Raji)
2. Re: Distance calculation (rose rahmani)
3. Re: Interaction energy (Mark Abraham)
4. shameless self-promotion (Alex)
5. Gromacs 2018.3 Exceeding Memory Issue (Peiyin Lee)
6. Re: Charge system simulation problem (Karpurmanjari Kakati)
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Message: 1
Date: Mon, 26 Nov 2018 12:50:05 -0600
Subject: [gmx-users] Parameterizing N-terminal capping
Content-Type: text/plain; charset="utf-8"
Hi
I am trying to parameterize the N-terminal ?carboxybenzyl? capping for
peptide within CHARMM force field. Charges and bonded terms are transferred
by analogy from available amino acid and lipid parameters. Grompp throwing
errors for missing dihedral and bond terms of the linkage between ester
group and peptide backbone. I appreciate any ideas.
[image: image.png]
Thanks
Raji
------------------------------
Message: 2
Date: Mon, 26 Nov 2018 22:29:07 +0330
Subject: Re: [gmx-users] Distance calculation
Content-Type: text/plain; charset="UTF-8"
Can i use -dist option?
Would you please help me?

Hi,
My system contains 20 amino acids around nanotube. I want to know the
adsorption amount of AA during simulation time; the adsorption occurs
when the distance between one of non-hydrogen atoms of AA and the tube
surface was less than 0.5 nm. So how can i calculate this property?
Would you please help me?
Best

------------------------------
Message: 3
Date: Mon, 26 Nov 2018 21:51:50 +0100
Subject: Re: [gmx-users] Interaction energy
Content-Type: text/plain; charset="UTF-8"
Hi,

Hi
I am beginner in MD. Maybe it is not a wise question but i want to
calculate the interaction energy between protein and ligand and also

PMF

in

different distances. But i don't know what is the didference between

PMF, i

mean free energy in particular(by umbrella sampling) and the

interaction

energy (by g_energy tool) in my case?

Interaction energy is a pairwise decomposition of short-range

nonbonded

interaction energy in the system. This energy is usually not

physically

meaningful, but if the force field has been parametrized in such a way
that it is, the interaction energy is a contribution to the enthalpy

of

the system.

What forcefields embedded in GROMACS do, yes?

AFAIK only CHARMM.

Interesting! You mean interaction energy calculated by for example AMBER
may not be true? Why?? What makes CHARMM unique??

As Justin said, the difference is in the way it is parametrized.
Forcefields are generally built to be additive, but it does not follow that
they are decomposable.

If coulomb energy is also existed between pairs, so the interaction
energy

will be LJ+Coulomb yes?

Pairs are 1-4 (intramolecular) interactions, so if you define
interaction energy between two nonbonded species, you'll get zeroes for
all the pair energies, by definition.

It's exactly the SR(short range) selection in g_energy, yes?

You seem to be using a looser definition of pairs than is usual in
discussion of GROMACS topologies.

all long range
are zero.

If there's a long-range model, then such interactions are not uniformly of
zero magnitude...

But coulomb and LJ are non-zero. So, in this case the interaction
energy would be
Short range LJ+ Short range Coulomb , true?

As far as I'm concerned, you can invent whatever quantity you want, but the
burden is on you to demonstrate that there's a reason to connect it to
something physical.
Mark

So what about PMF. It seems like an interaction energy too, but more
accurate one???

That's not what a PMF is. A PMF is the change in free energy of a system
as a function of progress along a reaction coordinate.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
http://www.thelemkullab.com
==================================================
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------------------------------
Message: 4
Date: Mon, 26 Nov 2018 14:20:21 -0700
Subject: [gmx-users] shameless self-promotion
Content-Type: text/plain; charset="UTF-8"
Hi all,
This isn't a Gromacs question, but a bit of self-promotion with a
not-so-hidden agenda.
1. Here's our paper that I think might be of interest to you beautiful
biophysics folks: https://www.nature.com/articles/s41563-018-0220-4
2. All of this was done with Gromacs. I cannot imagine any other package
capable of providing simulated timescales like this without an actual
supercomputer (we had three GPU-accelerated nodes). We use other MD
packages (which will not be named) and nothing comes close speed-wise. Our
endless love and gratitude go to the developers.
3. GMX developers: We will _NOT_ stop using Gromacs for non-biomolecules!
It can be done and it should be done, and Gromacs works for these systems.
Sometimes with a little bit of system design pain, but it does. Maybe one
day you will find it in your hearts to listen to the solid-state folks and
start extending software capabilities to meet our needs more directly. One
can only hope. ;)
I invite your "wow that's interesting stuff" and other comments here.
Again, thanks!
Alex
------------------------------
Message: 5
Date: Mon, 26 Nov 2018 22:30:18 -0500
Subject: [gmx-users] Gromacs 2018.3 Exceeding Memory Issue
Content-Type: text/plain; charset="UTF-8"
Hi, all GROMACS users,
I am trying to run jobs with Gromacs 2018.3 version and constantly got a
memory exceeding error. The system I ran is an all-atom system with 21073
atoms. The largest file that is estimated to be generated is around 5.8 GB.
My jobs got constantly killed after running for only around 15 minutes and
got an error message like this: "slurmstepd: error: Job 12381762 exceeded
memory limit (123122052 > 122880000), being killed". I have tried using a
larger memory specification (12GB/core) but it would take too long to wait
and I don't think my job really uses that many memories. I have attached my
"title = NVT Production Run for Trpzip4 in pure H2O
define = ; position restrain the protein
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 50000000 ; 0.002 * 50000 = 100000 ps (100 ns)
dt = 0.002 ; 2 fs
; Output control
nstenergy = 10000 ; save energies every 20 ps
nstlog = 10000 ; update log file every 20 ps
nstxout-compressed = 10000 ; 20ps
compressed-x-precision = 200 ; 0.05
compressed-x-grps = System
; Bond parameters
continuation = yes ; Restarting after NVT
constraint_algorithm = lincs ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid ; search neighboring grid cels
nstlist = 5 ; 10 fs
rlist = 1.2 ; short-range neighborlist cutoff (in nm)
rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)
rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = V-rescale ; More accurate thermostat
tc-grps = Protein SOL NA ; 2 coupling groups - more accurate
tau_t = 0.5 0.5 0.5 ; time constant, in ps
ref_t = 400 400 400 ; reference temperature, one for each group, in K
; Pressure coupling is on
pcoupl = No ; Pressure coupling on in NPT
pcoupltype = isotropic ; uniform scaling of x-y box vectors,
independent z
tau_p = 5.0 ; time constant, in ps
ref_p = 1.0 ; reference pressure, x-y, z (in bar)
compressibility = 4.5e-5 ; isothermal compressibility, bar^-1
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no ; Velocity generation is off"
and the command I used to run was "mpirun -np 80 gmx_mpi mdrun -npme 16
-noappend -s md.tpr -c md.gro -e md.edr -x md.xtc -cpi md.cpt -cpo md.cpt
-g md.log". This is my first time posting so please excuse anything that's
unclear. I will try to clarify if needed. Any help is greatly appreciated!
Regards,
Peiyin Lee
------------------------------
Message: 6
Date: Tue, 27 Nov 2018 09:32:59 +0530
Subject: Re: [gmx-users] Charge system simulation problem
Content-Type: text/plain; charset="UTF-8"
Hi Justin,
Because I have self generated the itp file, and that's the only place where
charge in terms of partial charge is added. Is the problem lying there?
Also can't we denote the partial charges in decimal because in real some
atoms will have net charges that can be decimal values due to presence or
absence of electronegative atoms adjacent to it?
And are all the other notes and warnings generated are all because of that?
karpurmanjari
On Mon, Nov 26, 2018 at 10:31 AM Karpurmanjari Kakati <

Dear All,
My System contains, while doing NVT of the same, I got the following Note
12.936997 Total charge should normally be an integer. See
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
<http://www.gromacs.org/Documentation/Floating_Point_Arithmetic> for
discussion on how close it should be to an integer.*
This is possibly because of the partial charges in the molecules in the
ITP fie.
My doubt is can't I have a system with non zero and a decimal charge value.
*WARNING 1 [file sa.top, line 80]: You are using Ewald electrostatics in
a system with net charge. This can lead to severe artifacts, such as ions
moving into regions with low dielectric, due to the uniform background
charge. We suggest to neutralize your system with counter ions, possibly
in combination with a physiological salt concentration.*
Can Someone help me with this?
*Velocities were taken from a Maxwell distribution at 300 KRemoving all
charge groups because cutoff-scheme=VerletAnalysing residue names:There
are: 1 Other residuesThere are: 100000 Water residues*
Removing all charge group because the cut off scheme is verlet.
If That happens then will it show the behavior I want to see. Or shall I
put any other scheme on that ?
Please help

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