[gmx-users] minimization problem (Martini simulation)

[politr at fh.huji.ac.il]

Thank you very much. It worked.
Regina
Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:

>
>
> 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
>
> -- 
> ========================================
>
> 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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