[gmx-users] question on ffG43a1p force field

[Justin Lemkul]

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

-- 
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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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