[gmx-users] Help for gmx enemat

Thu Jan 14 18:26:25 CET 2016

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 <jalemkul at vt.edu
> <javascript:_e(%7B%7D,'cvml','jalemkul at 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-bounces at maillist.sys.kth.se [mailto:
>>> gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of valerio
>>> di giulio
>>> Sent: Wednesday, January 13, 2016 11:17 PM
>>> To: gmx-users at 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.stern at 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
>>>>> <digiuliovalerio at 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
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
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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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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