[gmx-users] minimization problem (Martini simulation)

[Justin A. Lemkul]

politr at fh.huji.ac.il wrote:
> Dear Justin,
> Thank you very much for your answer.
> Can you please explain me what do you mean by saying "EM wasn't 
> sufficient". What information do you need in order be able to help?
> I run EM with emtol=60 and I got the following energies:
> Steepest Descents converged to Fmax < 60 in 2256 steps
> Potential Energy = -1.2244622e+07
> Maximum force = 4.7755444e+01 on atom 1659
> Norm of force = 6.3245118e-01

This was the information I wanted to see.  Without it, no one had any idea if 
your EM converged reasonably.

> Everything seems ok.

Indeed it does.

> After that I run MD using mdp file attached and I got the following error:
> Started mdrun on node 0 Tue Jun 28 00:10:12 2011
> 
> Step Time Lambda
> 0 0.00000 0.00000
> 
> Energies (kJ/mol)
> Bond G96Angle Improper Dih. LJ (SR) Coulomb (SR)
> 6.39093e+03 9.79589e+03 3.77765e+02 -1.22386e+07 -1.82773e+03
> Potential Kinetic En. Total Energy Temperature Pressure (bar)
> -1.22239e+07 1.25745e+00 -1.22239e+07 2.55766e-04 -1.14611e+03

Here's your problem.  The initial temperature is ridiculously small, indicating 
something has gone wrong.

> Cons. rmsd ()
> 4.25390e-06
> 
> DD step 9 load imb.: force 3.0%
> 
> -------------------------------------------------------
> Program mdrun_mpi, VERSION 4.0.3

Any reason you're using a really old version of Gromacs?

<snip>

Here's your problem.  The combination of:

> tcoupl                   = Berendsen

and

> gen_vel                  = no

is generally not stable.  You should set "gen_vel = yes" to start a reasonable 
equilibration period.

-Justin

-- 
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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

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