On 7/15/13 8:56 AM, rajat desikan wrote:
I guess, the more important question is whether the checkpoint file stores
the previous checkpoints as well. If it stores only the last checkpoint at
20 ns, then I guess there is no way to rerun from 18 ns.
It does not. Checkpoints are recycled every -cpt minutes. You can keep all
checkpoints by using the mdrun -cpnum option, but I suspect that will use up a
lot of disk space.
I do not store a .trr because of space constraints and hence I do not have
the velocities. otherwise, I would have used the snapshot from 18ns and
extended the simulation. Now, it looks like I will have to re-generate the
velocities and re-equilibrate the system.
Or just re-run the simulation from the same .tpr file you used before.
-Justin
On Mon, Jul 15, 2013 at 6:22 PM, rajat desikan <rajatdesi...@gmail.com>wrote:
Hi Justin,
The checkpoint file has gone on to 20 ns. If I do a rerun, the simulation
will finish in one step.
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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