On 7/15/13 8:52 AM, rajat desikan wrote:
Hi Justin,
The checkpoint file has gone on to 20 ns. If I do a rerun, the simulation
will finish in one step.
You need a checkpoint file that corresponds to a good frame before the
corruption. If you don't have that, you can't fix the broken trajectory. Your
first message implied that you had a good frame. Since that's not the case,
you'll have to either re-run the simulation or skip the bad frame and settle for
fewer data points.
-Justin
On Mon, Jul 15, 2013 at 6:11 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 7/15/13 8:38 AM, Rajat Desikan wrote:
Hi,
I have a 20 ns long trajectory which has become corrupted beyond 18ns. I
have the full checkpoint file. Is there any way I can use mdrun and the
.cpt
to rerun the simulation from 18ns and append it to the current .xtc
(After I
have clipped the part beyond 18ns by trjconv)? I did not find the
appropriate flag in the mdrun online manual pages.
It's no different than doing any restart.
mdrun -s topol.tpr -cpi good_state.cpt -noappend
Then concatenate trajectory and energy files with trjcat and eneconv.
-Justin
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Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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