[gmx-users] how to include multiple energy groups for interaction energy calculation?

[Александр Лашков]

*3 valence bond/.

вт, 21 янв. 2020 г. в 10:19, Александр Лашков <alashkov83 at gmail.com>:

> This ok. This term show non-bonded interaction for atoms
> located through two valence bonds.
> Alex
>
> вт, 21 янв. 2020 г. в 10:06, sunyeping <sunyeping at aliyun.com>:
>
>> Hi Justin,
>>
>> Thank you for reply. "energygrps = Protein LIG1 LIG2 LIG3 LIG4" can do
>> the work. I still have a couple of questions:
>>
>> (1) When using the "gmx energy -f ie.edr -o ie.xvg" to extract the
>> interaction energy, the interested energy terms should be input. Because
>> there are four ligands in my structure, there are accordingly 16 terms, for
>> example, 22 Coul-SR:Protein-LIG1, 23 LJ-SR:Protein-LIG1, 24
>> Coul-14:Protein-LIG1 and 25 LJ-14-LIG1 etc.. I can input the no. of these
>> 16 terms one by one as "22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37",
>> but is there a simple syntax for this selection? I tried "22 to 37" and
>> "22-37", but they doesn't work.
>>
>> (2) I find that the values of  all  Coul-14 and LJ-14 terms are zero.
>> Does this make any sense?
>>
>> Best,
>>
>> Yeping Sun
>> ------------------------------------------------------------------
>> From:Justin Lemkul <jalemkul at vt.edu>
>> Sent At:2020 Jan. 20 (Mon.) 22:17
>> To:gromacs <gmx-users at gromacs.org>; 孙业平 <sunyeping at aliyun.com>
>> Subject:Re: [gmx-users] how to include multiple energy groups for
>> interaction energy calculation?
>>
>>
>>
>> On 1/20/20 7:58 AM, sunyeping wrote:
>> > Dear all,
>> >
>> > I am doing MD simulations on a protein-ligand complex. This complex has
>> 4  protein subunits, with each subunits binding one ligand, so there are 4
>> ligands (named LIG1, LIG2, LIG3 and LIG4, respectively) in it. I have
>> finished the production run and get a trajectory, and now I want to
>> calculate the interaction energy between each ligand and their binding
>> protein subunit, respectively. I include the  "energygrps" parameter in the
>> mdp file for generating a tpr file for rerun the trajectory as following:
>> >      energygrps      =  Protein LIG1
>> >
>> > This seems to work fine. However, could it be possible to include all
>> four ligands in the "energygrps" parameter and rerun the trajectory once to
>> get the interaction energy between all the four ligands and their
>> respective binding protein subunit? I tried to write the "energygrps"
>> parameter as following:
>> >    energygrps      =  Protein LIG1, Protein LIG2, Protein LIG3, Protein
>> LIG4
>> > and run the "grompp" command:
>> >       gmx grompp -f ie.mdp -c npt.gro -t npt.cpt -p topol.top -n
>> index.ndx -o ie.tpr
>> > I received the following error:
>> >      Fatal error:
>> > Group LIG1, referenced in the .mdp file was not found in the index file.
>> > Group names must match either [moleculetype] names or custom index group
>> > names, in which case you must supply an index file to the '-n' option
>> > of grompp.
>> >
>> > I am sure that LIG1 is included in the index file. This error is most
>> probably caused by the incorrect input of the "energygrps" parameter in the
>> mdp file.
>> >
>> > So I wonder whether it is possible to include multiple energy groups in
>> the mdp file or I have to rerun the trajectory four times to get the
>> interaction energy for the four ligands?
>>
>> The list of energygrps should not be comma-delimited. You should specify:
>>
>> energygrps = Protein LIG1 LIG2 LIG3 LIG4
>>
>> and this will generate a full matrix of interactions among all four
>> species. The LIG1-LIG2, LIG1-LIG3, etc. may not be interesting to you
>> but this is how you get all of the interaction energies with the protein
>> in one shot.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Office: 301 Fralin Hall
>> Lab: 303 Engel Hall
>>
>> Virginia Tech Department of Biochemistry
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================
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>
>