[gmx-users] mdrun -rerun to obtain the non-bond interaction energy among energy groups

[Dai Ling (IHPC)]

Ya, it is the reason of using GPU. I have just tried with "-nb cpu" & it works well. 

Thanks so much, Justin.



-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Justin Lemkul
Sent: Wednesday, 6 April, 2016 5:59 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] mdrun -rerun to obtain the non-bond interaction energy among energy groups



On 4/6/16 2:38 AM, Dai Ling (IHPC) wrote:
> I defined energy groups in .mdp file at the very beginning. Then after 1st mdrun, I did create a new .tpr file with everything the same & rerun. But it didn't output correctly, any suggestions?
>

You don't needed to use mdrun -rerun if you had the desired groups originally.

If all those values are zero, that suggests you did the run on a GPU, since energygrps are not compatible with GPU.  In this case, you do need to use mdrun -rerun and use only CPU to do so.  If you didn't run on GPU and you're still getting zeroes, then you need to check your group definitions (index groups), exclusions, etc.  If you need to diagnose further, please post the actual gmx energy output for the problematic groups.  Note that some will be zero, like
LJ(1-4) between groups because 1-4 are purely intramolecular; they show up in the output just by quirk of the way the code works.

-Justin

> -----Original Message-----
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se 
> [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf 
> Of Nikhil Maroli
> Sent: Wednesday, 6 April, 2016 2:17 PM
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] mdrun -rerun to obtain the non-bond 
> interaction energy among energy groups
>
> I think you have to create a new tpr file with desired energy groups 
> and run md rerun
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
>

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

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

==================================================
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.