[gmx-users] Help for gmx enemat
valerio di giulio
digiuliovalerio at gmail.com
Thu Jan 14 23:00:51 CET 2016
Hi Justin,
You are right!! Thanks a lot!! Your help was precious.
Again thanks.
Valerio
2016-01-14 18:26 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:
>
>
> 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
>
> ==================================================
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> Gromacs Users mailing list
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