[gmx-users] Problem with output structures generated by energy minimization with GROMACS 4

Mon Nov 30 21:50:48 CET 2009

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" <tsjerkw at gmail.com>
To: "Discussion list for GROMACS users" <gmx-users at 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.public at 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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