[gmx-users] mdrun cpt
pavan.gromacs at gmail.com
Mon Oct 28 16:27:27 CET 2013
I have need to collect 100ns but I can collect only ~1ns (1000steps) per
run. Since I dont have .trr files, I rely on .cpt files for restarts. For
grompp -f md.mdp -c md_14.gro -t md_14.cpt -p system.top -o md_15
This runs into a problem when the run gets killed due to walltime limits. I
now have a .xtc file which has run (say) 700 steps and a .cpt file which
was last written at 600th step.
- To set up the next run I use the .cpt file from 600th step.
- Now during analysis if I want to center the protein and such, /trjconv/
needs an .xtc and .tpr file but not a .cpt file. So how does /trjconv/ know
to stop at 600th step? If this has to be put in manually, it becomes
On Sun, Oct 27, 2013 at 11:38 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 10/27/13 9:37 AM, Pavan Ghatty wrote:
>> Hello All,
>> Is there a way to make mdrun put out .cpt file with the same frequency as
>> .xtc or .trr file. From here
>> http://www.gromacs.org/**Documentation/How-tos/Doing_**Restarts<http://www.gromacs.org/Documentation/How-tos/Doing_Restarts>I see that we
>> can choose how often (time in mins) the .cpt file is written. But clearly
>> if the frequency of output of .cpt (frequency in mins) and .xtc (frequency
>> in simulation steps) do not match, it can create problems during analysis;
>> especially in the event of frequent crashes. Also, I am not storing .trr
>> file since I dont need that precision.
>> I am using Gromacs 4.6.1.
> What problems are you experiencing? There is no need for .cpt frequency
> to be the same as .xtc frequency, because any duplicate frames should be
> handled elegantly when appending.
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> jalemkul at outerbanks.umaryland.**edu <jalemkul at outerbanks.umaryland.edu> | (410)
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