[gmx-users] md continuation

[Justin Lemkul]

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 
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations carefully.

-Justin

> regards
>
> kashif
>
>
> 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
>>
>> error:
>> 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
>>
>> regards
>> kashif
>>

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

==================================================