On 1/14/16 12:18 PM, valerio di giulio wrote:
Hi Justin,
I need the LJ potential just between the two DNAs, instead gmx energy
calculates the total LJ energy. Is it right?
gmx energy does what you tell it. You specified DNA1 and DNA2 as energygrps,
therefore all short-range nonbonded interaction energies are decomposed. This
is actually no different than what you were trying to do with gmx enemat, except
that enemat is a more roundabout way to obtain what you want. The information
you need is in the .edr file; gmx energy is the first port of call for
extracting anything related to energy.
-Justin
Valerio
Il giovedì 14 gennaio 2016, Justin Lemkul <jalem...@vt.edu
<javascript:_e(%7B%7D,'cvml','jalem...@vt.edu');>> ha scritto:
On 1/14/16 4:48 AM, Peter Stern wrote:
Hi Valerio,
Sorry, I don't know then.
Peter
-----Original Message-----
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of valerio
di giulio
Sent: Wednesday, January 13, 2016 11:17 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Help for gmx enemat
Hi Peter,
I have already created an index file with make_ndx in which I specify
what atoms are in DNA1 and DNA2 groups. Moreover the two groups are present
in the file topol.top. Indeed GROMACS doesn't produce any error about the
declaration of them in the file .mdp. I send you also my topol.top file for
clarity:
You don't need g_enemat to get the numbers you want. Just use g_energy;
there's no point in plotting them as a matrix when all you need are the
values.
-Justin
.................................
; GROMACS topology
;
; Include the force field
#include "/amber03.ff/forcefield.itp"
; Include chain topologies
#include "topol1.itp"
#include "topol2.itp"
; Include water topology
#include "amber03.ff/tip4p.itp"
; Include generic ion topology
#include "amber03.ff/ions.itp"
[ system ]
Two all-AT in water
[ molecules ]
DNA1 1
DNA2 1
SOL 39390
NA 190
CL 146
.............................
Thanks,
Valerio
2016-01-13 20:40 GMT+01:00 Peter Stern <peter.st...@weizmann.ac.il>:
I believe that you need to define which nucleotides are in each group
DNA1 and DNA2 using make_ndx, since those are not "default" groups. I
think that you can do this and then do an Metin -rerun just to define
the new groups.
Peter
Sent from my iPad
On 13 בינו׳ 2016, at 20:53, valerio di giulio
<digiuliovale...@gmail.com>
wrote:
Hi,
I have a problem with the use of "gmx enemat". I'm trying to
calculate the contribution of SH-LJ to the potential that exists
between two DNA strands with GROMACS 5.1.1. I've already got a
Potential of Mean Force doing an umbrella sampling.
For this reason I have already many files .edr each one linked to a
window,
from
which I would like to extract the SH-LJ contribution but every time
I use "enemat" this is the output:
......................
GROMACS: gmx enemat, VERSION 5.1.1
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Command line:
gmx enemat umbrella1e.edr -ljsr
Opened ener.edr as single precision energy file Will read groupnames
from inputfile Read 2 groups group 0WARNING! could not find group
Coul-SR:DNA1-DNA1 (0,0)in energy
file
WARNING! could not find group LJ-SR:DNA1-DNA1 (0,0)in energy file
WARNING! could not find group Coul-SR:DNA1-DNA2 (0,1)in energy file
WARNING! could not find group LJ-SR:DNA1-DNA2 (0,1)in energy file
group 1WARNING! could not find group Coul-SR:DNA2-DNA2 (1,1)in
energy
file
WARNING! could not find group LJ-SR:DNA2-DNA2 (1,1)in energy file
Will select half-matrix of energies with 0 elements Last energy
frame read 500 time 500.000 Will build energy half-matrix of 2
groups, 0 elements, over 501 frames Segmentation fault (core dumped)
...........................
Although I have written to the .mdp file:
energygrps = DNA1 DNA2
Thank you in advance,
Valerio Di Giulio
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==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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