[gmx-users] md continuation
jalemkul at vt.edu
Thu May 18 15:17:26 CEST 2017
On 5/18/17 6:04 AM, Kashif wrote:
> It means I should conver my md.mdp file for 40 ns from 20 ns in the same
> folder and then run this command ...
> grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr -extend
> after that this command...
> mdrun -deffnm md_0_1
> Please suggest the correct command if it is not correct.
No, because grompp does not have an -extend option and your mdrun command makes
no reference to starting from an existing checkpoint file (with -cpi). Read
> On Wed, May 17, 2017 at 3:22 PM, Kashif <kashifzamir180.mk at gmail.com> wrote:
>> I have already run my 20 ns md simulation of my protein. The log file is
>> showing completion of my 20 ns data. I have also done analysis by using
>> trjconv command and g_rms.
>> Now I want to increase my simulation at least for 20 ns more and make my
>> data of protein simulation for 40 ns. Kindly help for continuation of my
>> simulation. I have used this command but it did not help and shows error.
>> command: mdrun -deffnm md_0_1 -cpi md_0_1.cpt -append
>> NOTE: 23 % of the run time was spent communicating energies,
>> you might want to use the -gcom option of mdrun
>> Core t (s) Wall t (s) (%)
>> Time: 25.000 2.843 879.2
>> (ns/day) (hour/ns)
>> Performance: 0.061 394.912
>> Finished mdrun on node 0 Sat Apr 29 11:46:36 2017
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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