[gmx-users] System broken after energy minimization
tsjerkw at gmail.com
Sat Jun 15 14:16:25 CEST 2013
When increasing the system size like that, make sure that all molecules in
the original box are whole (trjconv -pbc mol). Only then can you, e.g., use
genconf to double the system.
On Sat, Jun 15, 2013 at 1:49 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 6/15/13 6:21 AM, Kieu Thu Nguyen wrote:
>> Dear users,
>> I make a rectangle bilayer by doubling two equilibrated cubic boxes. But
>> after minimizing, the system have been crashed. I do not understand why. I
>> attach the em.mdp below
> The list does not allow attachments. Either copy and paste or provide a
> link to where the file can be downloaded. The .mdp file may or may not be
> useful. You should carefully inspect the starting configuration for atomic
> overlap, and then otherwise follow the instructions described here:
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> gmx-users mailing list gmx-users at gromacs.org
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Tsjerk A. Wassenaar, Ph.D.
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