[gmx-users] Help for gmx enemat

[valerio di giulio]

Hi Justin,

I need the LJ potential just between the two DNAs, instead gmx energy
calculates the total LJ energy. Is it right?

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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