[gmx-users] Energy minimization has stopped....

[Kalyanashis Jana]

Hi,
Whenever I am trying to do position retrained MD run, It has been stopped
at middle of the MD run. I have given the following error. Can you please
suggest me something to resolve this error?
Energy minimization has stopped, but the forces havenot converged to the
requested precision Fmax < 100 (whichmay not be possible for your system).
It
stoppedbecause the algorithm tried to make a new step whose sizewas too
small, or there was no change in the energy sincelast step. Either way, we
regard the minimization asconverged to within the available machine
precision,given your starting configuration and EM parameters.

Double precision normally gives you higher accuracy, butthis is often not
needed for preparing to run moleculardynamics.

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 20514 steps,
but did not reach the requested Fmax < 100.
Potential Energy = -9.9811250e+06
Maximum force = 6.1228135e+03 on atom 15461
Norm of force = 1.4393512e+01

gcq#322: "The Feeling of Power was Intoxicating, Magic" (Frida Hyvonen)

[jkrieger]

What does your curve look like? What parameters are you using in the mdp?
How big is your system and what kind of molecules are in there? Providing
this kind of information would help people work out what the problem is.

Then again it may be ok that the minimisation has converged without
reaching the Fmax cutoff. 20000 is a large number of steps.

Post by Kalyanashis Jana
Hi,
Whenever I am trying to do position retrained MD run, It has been stopped
at middle of the MD run. I have given the following error. Can you please
suggest me something to resolve this error?
Energy minimization has stopped, but the forces havenot converged to the
requested precision Fmax < 100 (whichmay not be possible for your system).
It
stoppedbecause the algorithm tried to make a new step whose sizewas too
small, or there was no change in the energy sincelast step. Either way, we
regard the minimization asconverged to within the available machine
precision,given your starting configuration and EM parameters.
Double precision normally gives you higher accuracy, butthis is often not
needed for preparing to run moleculardynamics.
writing lowest energy coordinates.
Steepest Descents converged to machine precision in 20514 steps,
but did not reach the requested Fmax < 100.
Potential Energy = -9.9811250e+06
Maximum force = 6.1228135e+03 on atom 15461
Norm of force = 1.4393512e+01
gcq#322: "The Feeling of Power was Intoxicating, Magic" (Frida Hyvonen)
--
Kalyanashis Jana
email: kalyan.chem.in at gmail.com
--
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[Kalyanashis]

I have given my .mdp file,
; title = trp_drg
warning = 10
cpp = /usr/bin/cpp
define = -DPOSRES
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps = 1000000 ; total 2000.0 ps.
nstcomm = 100
nstxout = 250 ; ouput coordinates every 0.5 ps
nstvout = 1000 ; output velocities every 2.0 ps
nstfout = 0
nstlog = 100
nstenergy = 100
nstlist = 100
ns_type = grid
rlist = 1.0
coulombtype = PME
rcoulomb = 1.0
vdwtype = cut-off
rvdw = 1.0
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 6
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temparature coupling is on
Tcoupl = berendsen
tau_t = 1.0 1.0 -0.1 1.0 1.0
tc_grps = SOL NA protein OMP CL
ref_t = 300 300 300 300 300
; Pressure coupling is on
pcoupl = berendsen ; Use Parrinello-Rahman for research work
pcoupltype = isotropic ; Use semiisotropic when working with
membranes
tau_p = 2.0
compressibility = 4.5e-5
ref_p = 1.0
refcoord-scaling = all
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529


And It is a large protein system containing drug molecule and the atoms of
whole system is near about 16000.
As I did not get any .gro file, thus the MD run was not properly finished.
Please suggest me the probable source this kind error.
Thank you so much..



On Tue, Nov 5, 2013 at 5:29 PM, jkrieger at mrc-lmb.cam.ac.uk [via GROMACS] <

Post by jkrieger
What does your curve look like? What parameters are you using in the mdp?
How big is your system and what kind of molecules are in there? Providing
this kind of information would help people work out what the problem is.
Then again it may be ok that the minimisation has converged without
reaching the Fmax cutoff. 20000 is a large number of steps.

Post by Kalyanashis Jana
Hi,
Whenever I am trying to do position retrained MD run, It has been stopped
at middle of the MD run. I have given the following error. Can you

please

Post by Kalyanashis Jana
suggest me something to resolve this error?
Energy minimization has stopped, but the forces havenot converged to the
requested precision Fmax < 100 (whichmay not be possible for your

system).

Post by Kalyanashis Jana
It
stoppedbecause the algorithm tried to make a new step whose sizewas too
small, or there was no change in the energy sincelast step. Either way,

we

Post by Kalyanashis Jana
regard the minimization asconverged to within the available machine
precision,given your starting configuration and EM parameters.
Double precision normally gives you higher accuracy, butthis is often

not

Post by Kalyanashis Jana
needed for preparing to run moleculardynamics.
writing lowest energy coordinates.
Steepest Descents converged to machine precision in 20514 steps,
but did not reach the requested Fmax < 100.
Potential Energy = -9.9811250e+06
Maximum force = 6.1228135e+03 on atom 15461
Norm of force = 1.4393512e+01
gcq#322: "The Feeling of Power was Intoxicating, Magic" (Frida Hyvonen)
--
Kalyanashis Jana
email: [hidden email]<http://user/SendEmail.jtp?type=node&node=5012256&i=0>
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[Justin Lemkul]

Post by Kalyanashis
I have given my .mdp file,
; title = trp_drg
warning = 10
cpp = /usr/bin/cpp
define = -DPOSRES
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps = 1000000 ; total 2000.0 ps.
nstcomm = 100
nstxout = 250 ; ouput coordinates every 0.5 ps
nstvout = 1000 ; output velocities every 2.0 ps
nstfout = 0
nstlog = 100
nstenergy = 100
nstlist = 100
ns_type = grid
rlist = 1.0
coulombtype = PME
rcoulomb = 1.0
vdwtype = cut-off
rvdw = 1.0
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 6
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temparature coupling is on
Tcoupl = berendsen
tau_t = 1.0 1.0 -0.1 1.0 1.0
tc_grps = SOL NA protein OMP CL
ref_t = 300 300 300 300 300

These settings make no sense. Please read
http://www.gromacs.org/Documentation/Terminology/Thermostats.

Post by Kalyanashis
; Pressure coupling is on
pcoupl = berendsen ; Use Parrinello-Rahman for research work
pcoupltype = isotropic ; Use semiisotropic when working with
membranes
tau_p = 2.0
compressibility = 4.5e-5
ref_p = 1.0
refcoord-scaling = all
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
And It is a large protein system containing drug molecule and the atoms of
whole system is near about 16000.
As I did not get any .gro file, thus the MD run was not properly finished.
Please suggest me the probable source this kind error.

The run crashes because your energy minimization effectively failed.

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

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | [phone]

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

[Justin Lemkul]

Post by Kalyanashis Jana
Hi,
Whenever I am trying to do position retrained MD run, It has been stopped
at middle of the MD run. I have given the following error. Can you please
suggest me something to resolve this error?
Energy minimization has stopped, but the forces havenot converged to the
requested precision Fmax < 100 (whichmay not be possible for your system).
It
stoppedbecause the algorithm tried to make a new step whose sizewas too
small, or there was no change in the energy sincelast step. Either way, we
regard the minimization asconverged to within the available machine
precision,given your starting configuration and EM parameters.
Double precision normally gives you higher accuracy, butthis is often not
needed for preparing to run moleculardynamics.
writing lowest energy coordinates.
Steepest Descents converged to machine precision in 20514 steps,
but did not reach the requested Fmax < 100.
Potential Energy = -9.9811250e+06
Maximum force = 6.1228135e+03 on atom 15461
Norm of force = 1.4393512e+01

Visualize the output, specifically near atom 15461. The forces there are too
high and cannot be resolved further. Any attempt to use these coordinates for
dynamics will probably lead to a crash.

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

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | [phone]

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

[Kalyanashis Jana]

Dear Justin,
Can you please tell me, how I can solve this problem?? If I will change
the coordinate of atom 15461, will it help me? But you know, I did this
step changing the position of drug molecule and I got same error.

Post by Justin Lemkul

Post by Kalyanashis Jana
Hi,
Whenever I am trying to do position retrained MD run, It has been stopped
at middle of the MD run. I have given the following error. Can you please
suggest me something to resolve this error?
Energy minimization has stopped, but the forces havenot converged to the
requested precision Fmax < 100 (whichmay not be possible for your system).
It
stoppedbecause the algorithm tried to make a new step whose sizewas too
small, or there was no change in the energy sincelast step. Either way, we
regard the minimization asconverged to within the available machine
precision,given your starting configuration and EM parameters.
Double precision normally gives you higher accuracy, butthis is often not
needed for preparing to run moleculardynamics.
writing lowest energy coordinates.
Steepest Descents converged to machine precision in 20514 steps,
but did not reach the requested Fmax < 100.
Potential Energy = -9.9811250e+06
Maximum force = 6.1228135e+03 on atom 15461
Norm of force = 1.4393512e+01

Visualize the output, specifically near atom 15461. The forces there are
too high and cannot be resolved further. Any attempt to use these
coordinates for dynamics will probably lead to a crash.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | [phone]
==================================================
--
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[Justin Lemkul]

Post by Kalyanashis Jana
Dear Justin,
Can you please tell me, how I can solve this problem?? If I will change
the coordinate of atom 15461, will it help me? But you know, I did this
step changing the position of drug molecule and I got same error.

You should first do what I suggested before. The reason for a large force is
either (1) bad atomic clashes that should be apparent upon visual inspection or
(2) bad topology for the drug.

-Justin

Post by Kalyanashis Jana

Post by Justin Lemkul

Post by Kalyanashis Jana
Hi,
Whenever I am trying to do position retrained MD run, It has been stopped
at middle of the MD run. I have given the following error. Can you please
suggest me something to resolve this error?
Energy minimization has stopped, but the forces havenot converged to the
requested precision Fmax < 100 (whichmay not be possible for your system).
It
stoppedbecause the algorithm tried to make a new step whose sizewas too
small, or there was no change in the energy sincelast step. Either way, we
regard the minimization asconverged to within the available machine
precision,given your starting configuration and EM parameters.
Double precision normally gives you higher accuracy, butthis is often not
needed for preparing to run moleculardynamics.
writing lowest energy coordinates.
Steepest Descents converged to machine precision in 20514 steps,
but did not reach the requested Fmax < 100.
Potential Energy = -9.9811250e+06
Maximum force = 6.1228135e+03 on atom 15461
Norm of force = 1.4393512e+01

Visualize the output, specifically near atom 15461. The forces there are
too high and cannot be resolved further. Any attempt to use these
coordinates for dynamics will probably lead to a crash.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | [phone]
==================================================
--
gmx-users mailing list gmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at http://www.gromacs.org/
Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-request at gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

--
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | [phone]

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