[gmx-users] calculate average and maximum non-bonded energy between energy groups

[Justin Lemkul]

On 8/26/15 4:39 PM, Tushar Ranjan Moharana wrote:
> Hi Justin,
> Thanks for your precious advice. You replied that "I would agree with
> Vitaly that this is really not a useful quantity. It is force
> field-specific and not necessarily anything to do with thermodynamics or
> free energy." did you refer to maximum energy or average energy or both.
>

Both, but the maximum value of the interaction energy is probably even less 
useful.  Unless the force field was parametrized to produce something meaningful 
in this interaction energy term, anything you find from it is likely to be 
incidental.

-Justin

> You also adviced to use a terminal that allows scrolling. Now I am able to
> scroll in my terminal. However I read in many places about gmx enemat which
> can extract energy matrix. How ever in my case it gives following error.
>
> Read 40 groups
> group 0WARNING! could not find group Coul-SR:VAL171    -VAL171     (0,0)in
> energy file
> WARNING! could not find group LJ-SR:VAL171    -VAL171     (0,0)in energy
> file
> WARNING! could not find group Coul-SR:VAL171    -MET173     (0,1)in energy
> file
> WARNING! could not find group LJ-SR:VAL171    -MET173     (0,1)in energy
> file
> WARNING! could not find group Coul-SR:VAL171    -VAL174     (0,2)in energy
> file
> WARNING! could not find group LJ-SR:VAL171    -VAL174     (0,2)in energy
> file
> WARNING! could not find group Coul-SR:VAL171    -VAL187     (0,3)in energy
> file
> WARNING! could not find group LJ-SR:VAL171    -VAL187     (0,3)in energy
> file
> WARNING! could not find group Coul-SR:VAL171    -ILE203     (0,4)in energy
> file
> WARNING! could not find group LJ-SR:VAL171    -ILE203     (0,4)in energy
> file
> WARNING! could not find group Coul-SR:VAL171    -TYR204     (0,5)in energy
> file
>
> ...........
>
> group 38WARNING! could not find group Coul-SR:ODE    -ODE     (38,38)in
> energy file
> WARNING! could not find group LJ-SR:ODE    -ODE     (38,38)in energy file
> WARNING! could not find group Coul-SR:ODE    -ODA (38,39)in energy file
> WARNING! could not find group LJ-SR:ODE    -ODA (38,39)in energy file
> group 39
> Will select half-matrix of energies with 2 elements
> Last energy frame read 2000 time 2000.000
> Will build energy half-matrix of 40 groups, 2 elements, over 2001 frames
> Segmentation fault (core dumped)
>
>
> I read from GROMACS user mailing list where you have suggested someone to
> install GROMACS in debug mode or use GROMACS-4.6.5. I have tried both but
> nothing worked for me. am I doing any mistake? My energygrp-excl is empty
> as it is not supported by Verlet. In the above case what ever group was not
> found by gmx enemat was read by gmx energy and gives output in the same
> .edr file.
>
>
> Thank you in advance.
>
> "A society with free knowledge is better than a society with free food"
>
> Tushar Ranjan Moharana
> B. Tech, NIT Warangal
> Ph D Student, CCMB
>

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

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

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