[gmx-users] calculating energy between certain groups

[Justin Lemkul]

On 5/21/18 10:51 AM, Irem Altan wrote:
> Thanks. My .mdp file does not contain energy groups, so that was the problem. Given your comments about enemat giving qualitative results, is it possible to get interaction energy between certain groups with gmx energy? I would like to calculate the energy between two protein chains, between solvent and protein, etc. What is the correct way of doing this?

Exactly as I said, with gmx energy.

-Justin

> Best,
> Irem
>
> On May 21, 2018, at 8:13 AM, Justin Lemkul <jalemkul at vt.edu<mailto:jalemkul at vt.edu>> wrote:
>
>
>
> On 5/20/18 9:49 PM, Irem Altan wrote:
> I tried the following:
>
> mdrun -rerun umbrella0.xtc -np cpu -deffnm umbrella0
>
> and also I can verify from the output file that it didn’t use GPUs. However, I still get the same error with gmx enemat:
>
> GROMACS:      gmx enemat, version 2016.3
> Executable:   /opt/gromacs/bin/gmx_mpi
> Data prefix:  /opt/gromacs
> Working dir:  /oasis/scratch/comet/nano3/temp_project/c4_m_4C/rerun
> Command line:
>    gmx_mpi enemat -f umbrella0.edr
>
> Opened umbrella0.edr as single precision energy file
> Will read groupnames from inputfile
> Read 2 groups
> group 0WARNING! could not find group Coul-SR:Protein-Protein (0,0)in energy file
> WARNING! could not find group LJ-SR:Protein-Protein (0,0)in energy file
> WARNING! could not find group Coul-SR:Protein-SOL (0,1)in energy file
> WARNING! could not find group LJ-SR:Protein-SOL (0,1)in energy file
> group 1WARNING! could not find group Coul-SR:SOL-SOL (1,1)in energy file
> WARNING! could not find group LJ-SR:SOL-SOL (1,1)in energy file
>
> Will select half-matrix of energies with 0 elements
> Last energy frame read 2000 time 20000.000
> Will build energy half-matrix of 2 groups, 0 elements, over 2001 frames
> Segmentation fault
>
> What could be the problem?
>
> A seg fault almost always indicates buggy behavior, but you need to make sure you specified appropriate energygrps in the .mdp file that created the .tpr and that they are present in the .edr file. Note that you should probably just be using gmx energy to get the time series and statistics. enemat produces a graphical representation (qualitative) whereas energy gives a quantitative description.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu<mailto:jalemkul at vt.edu> | (540) 231-3129
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.thelemkullab.com&d=DwIGaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4&m=kqCQXzDaAlIbcm-qnrJwU1nxQJsc80ubIUgfrK3dXGg&s=WQbAcZl9zG7WZqWA0VeI3oTiv5NXK7avLQISb6C8FN0&e=
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at https://urldefense.proofpoint.com/v2/url?u=http-3A__www.gromacs.org_Support_Mailing-5FLists_GMX-2DUsers-5FList&d=DwIGaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4&m=kqCQXzDaAlIbcm-qnrJwU1nxQJsc80ubIUgfrK3dXGg&s=xHvNWS5tpCB8uGPFxraXl6mfMeN99tD1f9pA194XNnQ&e= before posting!
>
> * Can't post? Read https://urldefense.proofpoint.com/v2/url?u=http-3A__www.gromacs.org_Support_Mailing-5FLists&d=DwIGaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4&m=kqCQXzDaAlIbcm-qnrJwU1nxQJsc80ubIUgfrK3dXGg&s=bIUt7jjjzxOMl9dxnPaNNpU12qTWmyudq97uGWbcs_Y&e=
>
> * For (un)subscribe requests visit
> https://urldefense.proofpoint.com/v2/url?u=https-3A__maillist.sys.kth.se_mailman_listinfo_gromacs.org-5Fgmx-2Dusers&d=DwIGaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4&m=kqCQXzDaAlIbcm-qnrJwU1nxQJsc80ubIUgfrK3dXGg&s=knQRWH77KL0dXN4B_dItSwuDCqfP_cypubYLaf8ApKg&e= or send a mail to gmx-users-request at gromacs.org<mailto:gmx-users-request at gromacs.org>.
>

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

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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