[gmx-users] question on ffG43a1p force field

[Lei Qian]

Hi Dr. Lemkul,

Thank you for your reply.
I have sent the links to you. Hope they could reach to you.
The links include three log files.
1. WT protein running for 1ns production step.(wall time: 1h40min).
2. WT protein running for 10ns production step (wall time: 6d09h17).
3. Mutant protein running for 1ns production step. (wall time: 17h30min).

>From the log, I can find each of them was run on one node with 24 cores.
It seems the wall times for all these three files do not have linearly
proportional relationship.
Thanks for your time and help!
Lei















On Fri, Aug 23, 2019 at 3:42 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 8/23/19 2:27 AM, Lei Qian wrote:
> > Thank you Dr. Lemkul,
> > I continued to use the GROMOS 43a1p for my simulation.
> >
> > I did simulation for 2 proteins separately: one is WT, the other one is
> its
> > one-residue mutant.
> > And I finished em, NVT, NPT and 1 ns Production (4 steps) for both
> proteins.
> >
> > However, I found for each of these 4 above steps, the wall time was a lot
> > more longer for mutant than WT protein.
> > Actually I used the same set of parameters for both proteins: e.g. same
> mdp
> > files for both protein in each step.
> > Both proteins get acceptable results after 100-step NVT, 100-step NPT
> etc.,
> > but the wall-time for mutant was much more longer than WT.
> > Could I ask the reason for this?
> > Sorry for this inconvenience. Thank you for your time and all your help!
>
> There is no way to know what is going on without seeing the .log files
> from the runs and knowing the commands you gave. If you want to share
> files, upload them to a file-sharing server and provide a link. The
> mailing list does not accept attachments.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
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