Hi,
genconf -nbox 2 2 1
will help you.
Best,
rainer
himanshu khandelia wrote:
Hi,
My message did not go through properly to the mailing list (only the
attachment went through). Here is a repeat attempt:
##########
Hi Folks,
I was trying to make a large POPC system from Tieleman's 128 lipid assembly.
Everything went well until I tried to run dynamics. While trying to run
dynamics, I got a large velocity for the center of mass (Large VCM) error.
The log file, mdp file, and the top file are attached as a suse .zip
Here is what I did:
- replicated the system thrice to make is 512 lipids (this was done in VMD),
and translated replicas along the bilayer plane accordingly
- to remove bad contacts, minimized it in GROMACS (steep minimization)
- to remove bad contacts farther, minimized using CG
(The system looks fairly reasonable after minimization on visual
inspection)
- tried to assign velocities at 50 K and run NPT dynamics, with water
molecules constrained along the bilayer normal (z)
In the last step, the system crashes after a few hundred steps, reporting a
large VCM. A look at the pdb files reveals that the system is exploding with
large vacuum regions appearing.
THE BOX CENTER WAS VERY FAR FROM THE GEOMETRIC ORIGIN. The box is ~ 13 x 13
x 6.7, and the center is at 6.3, 6.3, 3.5. So I also tried the following
before running dynamics:
- used editconf -c to center the box, before running dynamics. But this only
moved the center by less than 5 angstroms. Why ?
- used editconf -c -center 0 0 0 as a variant of the above.
The above did not solve the problem.
Please let me know if you want me to send you more details ?
Thanks for the help,
-Himanshu
MEMPHYS,
SDU, Denmark
##########
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--
__________________________________________________________
Dr. Rainer Böckmann
Theoretical & Computational Membrane Biology
Center for Bioinformatics Saar
Universität des Saarlandes
Gebäude C7.1 (17.1), EG
D-66041 Saarbrücken, Germany
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