[gmx-users] big protein dynamics

[Tsjerk Wassenaar]

Hi Adriana,

Did you energy minimize your system before this?

A pretty robust regime to follow is:

1. energy minimize in vacuum
2. energy minimize after solvation
3. perform position restrained MD
4. run a short simulation with temperature coupling to equilibrate
5. turn on pressure coupling and let the system equilibrate
6. harvest

Cheers,

Tsjerk

On 11/30/05, Adriana Pietropaolo <adriana at ms.fci.unibo.it> wrote:
>
> Thanks a lot for your help!
> Now, I had been able to make a reasonable box with 26000 water molecules
> and my protein.
> I used grompp and I processed the topology file with 4 tasks.
> When I run MD simulation, constraining all bonds to equilibrate my water
> molecules there's this error:
> Constraint error in algorithm Lincs at step 0
>    Energies (kJ/mol)
>           Angle    Proper Dih. Ryckaert-Bell.          LJ-14
> Coulomb-14
>     6.38409e+03    2.55973e+02    4.45790e+03    5.51719e+03
> 2.38409e+04
>         LJ (SR)        LJ (LR)   Coulomb (SR)   Coulomb (LR) Position
> Rest.
>     3.85342e+05   -5.67173e+03   -1.17926e+06   -1.72551e+05
> 4.23618e+00
>       Potential    Kinetic En.   Total Energy    Temperature Pressure
> (bar)
>    -9.31678e+05    2.39317e+05   -6.92360e+05    3.43853e+02
> 1.93620e+04
>
> I put in my sistem a pressure of 1.013 bar, but I see a pressure of
> 1.93e+04. The mdrun goes in segmentation fault...
> I tried to run a NVT too, but nothing.
> How can I follow?
> Thanks in advance,
> Adriana
>
>
>
> --
> _____________________________________________
> Adriana Pietropaolo,
> PhD student,
> dipartimento di Chimica Fisica ed Inorganica,
> Facolta' di Chimica Industriale
> Universita' di Bologna
> Tel 051/6446992
> FAX 051/2093690
> _____________________________________________
>
>
>
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--

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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