Tsjerk,
Thanks for your reply.
I am doing a simple test case with 500 SPC/E water molecules. First I did
minimization with steepest decent, using a command like
mdrun -pd -s water.gro.tpr -c final.gro
The generated md.log looks like the following:
----------------
Step Time Lambda
0 0.00000 0.00000
Energies (kJ/mol)
LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
4.70442e+03 -7.34875e+02 -2.65916e+04 -1.28439e+03 -2.39065e+04
Pressure (bar)
2.27899e+04
.
.
.
Step Time Lambda
1000 1000.00000 0.00000
Energies (kJ/mol)
LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
5.53526e+03 -7.34875e+02 -3.22651e+04 -1.33018e+03 -2.87949e+04
Pressure (bar)
2.42765e+04
Steepest Descents did not converge to Fmax < 1 in 1001 steps.
Potential Energy = -2.87949018657418e+04
Maximum force = 6.95206177080918e+01 on atom 1033
Norm of force = 3.71165837023948e+00
--------
Just for testing I tried to do further optimization. I created a new tpr with
the generated final.gro file and the old top and mdp files, then run mdrun
again.
This time the generated md.log looks like the following:
===
Step Time Lambda
0 0.00000 0.00000
Energies (kJ/mol)
LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
4.70442e+03 -7.34875e+02 -2.65916e+04 -1.28439e+03 -2.39065e+04
Pressure (bar)
2.27899e+04
.
.
.
====
So it seems like final.gro has a potential energy that is very close to that of
the original, un-optimized structure.
While I repeat the same procedure with Gromacs 3.3, everything works as
expected. For the first optimization I got
---
Step Time Lambda
0 0.00000 0.00000
Energies (kJ/mol)
LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
4.70486e+03 -7.34875e+02 -2.65916e+04 -1.28441e+03 -2.39060e+04
Kinetic En. Total Energy Temperature Pressure (bar)
0.00000e+00 0.00000e+00 0.00000e+00 -1.63608e+03
.
.
.
Step Time Lambda
999 999.00000 0.00000
Energies (kJ/mol)
LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
5.48610e+03 -7.34875e+02 -3.21894e+04 -1.29343e+03 -2.87316e+04
Kinetic En. Total Energy Temperature Pressure (bar)
0.00000e+00 0.00000e+00 0.00000e+00 -1.63608e+06
Step Time Lambda
1000 1000.00000 0.00000
Steepest Descents did not converge to Fmax < 1 in 1001 steps.
Potential Energy = -2.87316123776041e+04
Maximum force = 2.72102300902620e+01 on atom 136
Norm of force = 2.08471187918543e+02
---
and for the further optimization I got
===
Step Time Lambda
0 0.00000 0.00000
Energies (kJ/mol)
LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
5.48626e+03 -7.34875e+02 -3.21871e+04 -1.29320e+03 -2.87289e+04
Kinetic En. Total Energy Temperature Pressure (bar)
0.00000e+00 0.00000e+00 0.00000e+00 -1.63608e+03
.
.
.
===
I don't know what causes the difference.
Hao Jiang
----- Original Message -----
From: "Tsjerk Wassenaar" <tsje...@gmail.com>
To: "Discussion list for GROMACS users" <gmx-users@gromacs.org>
Sent: 2009年11月30日 12:37 PM
Subject: Re: [gmx-users] Problem with output structures generated by energy
minimization with GROMACS 4
Ni Hao,
You don't give too much information here. What exactly are you doing?
What are the commands? What's the difference between the first and the
second pass of EM? One thing to check is whether the output/input file
has a correct box definition.
Cheers,
Tsjerk
2009/11/30 HAO JIANG <hj.pub...@gmail.com>:
> Hi,
>
> I got a problem with the output structure files (gro/trr/xtc) generated by
> the energy minimization with GROMACS 4. That is, when I used the generated
> structure as the input for further minimizations or MD simulations, I got
> very large potential energy and forces at step 0, as if the structure had
> not been optimized at all. On the other hand, there is no problem when
> the input structure is taken from a previous MD run, and I got the expected
> potential at step 0. There is no problem, too, if I use GROMACS 3 to do the
> minimization.
>
> Any help is greatly appreciated!
>
> Hao Jiang
>
> --
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--
Tsjerk A. Wassenaar, Ph.D.
Computational Chemist
Medicinal Chemist
Neuropharmacologist
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