[gmx-users] big protein dynamics

David van der Spoel spoel at xray.bmc.uu.se
Wed Nov 30 21:01:40 CET 2005

Adriana Pietropaolo 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...
Minimize better,
use position restraints with NVT
use posres with NPT
then release protein

> I tried to run a NVT too, but nothing.
> How can I follow?
> Thanks in advance,
> Adriana

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

More information about the gromacs.org_gmx-users mailing list