[gmx-users] how to output intramolecular pair interaction parameters

[Srinivasa Ramisetti]

This is continuation to my previous question. I used gmx dump to output the 1-4 intramolecular interaction parameters. I could get the c6 and c12 values for all the list of 1-4 pair nteractions within my top file. However, I could not understand the following lines in the output information under the ffparams starting from functype[0] to functype[63]. I do not understand how these 64 of c6,c12 values are related to 36 atoms (8 atom types) that belong to my System. Could anyone explain me how can I know which functype belongs to a particular atom/atom type?


ffparams:

 atnr=8
      ntypes=108
         functype[0]=LJ_SR, c6= 1.54830217e-02, c12= 3.37031743e-05
         functype[1]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
         functype[2]=LJ_SR, c6= 5.60698984e-03, c12= 1.12160897e-05
         .
         .

         functype[63]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
         functype[64]=ANGLES, thA= 1.13000e+02, ctA= 2.92880e+02, thB= 1.13000e+02, ctB= 2.92880e+02
         functype[65]=ANGLES, thA= 1.21000e+02, ctA= 6.69440e+02, thB= 1.21000e+02, ctB= 6.69440e+02
         functype[66]=ANGLES, thA= 1.08000e+02, ctA= 5.85760e+02, thB= 1.08000e+02, ctB= 5.85760e+02

         .
         .

         functype[75]=PDIHS, phiA= 1.80000000e+02, cpA= 4.39319992e+01, phiB= 1.80000000e+02, cpB= 4.39319992e+01, mult=2
         functype[76]=RBDIHS, rbcA[0]= 2.30119991e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.30119991e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
rbcB[0]= 2.30119991e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.30119991e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
         functype[77]=RBDIHS, rbcA[0]= 2.61499996e+01, rbcA[1]=-3.13800001e+00, rbcA[2]=-2.30119991e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00

         .
         .

         functype[88]=LJ14, c6A= 1.02609140e-03, c12A= 1.18782930e-06, c6B= 1.02609140e-03, c12B= 1.18782930e-06
         functype[89]=LJ14, c6A= 2.52110331e-04, c12A= 1.06359074e-07, c6B= 2.52110331e-04, c12B= 1.06359074e-07
         functype[90]=LJ14, c6A= 1.57502061e-03, c12A= 3.56110013e-06, c6B= 1.57502061e-03, c12B= 3.56110013e-06
         functype[91]=LJ14, c6A= 3.86982108e-04, c12A= 3.18863499e-07, c6B= 3.86982108e-04, c12B= 3.18863499e-07

         .
         .

         functype[105]=CONSTR, dA= 1.08999997e-01, dB= 1.08999997e-01
         functype[106]=CONSTR, dA= 1.80999994e-01, dB= 1.80999994e-01
         functype[107]=CONSTR, dA= 1.33599997e-01, dB= 1.33599997e-01



Thank you,

Srinivasa

________________________________
From: Srinivasa Ramisetti
Sent: 16 November 2017 19:04:12
To: gmx-users at gromacs.org
Cc: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: Re: [gmx-users] how to output intramolecular pair interaction parameters


Thank you Wes. I think this should help me.


Srinivasa

________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Wes Barnett <w.barnett at columbia.edu>
Sent: 16 November 2017 18:51:52
To: gmx-users at gromacs.org
Cc: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: Re: [gmx-users] how to output intramolecular pair interaction parameters

On Thu, Nov 16, 2017 at 1:42 PM, Srinivasa Ramisetti <
S.B.Ramisetti at leeds.ac.uk> wrote:

> Hi Micholas,
>
>
> Thanks for your reply. I tried as you suggested and could not find the
> information on pair interaction parameters.
>
>
> I will try to rephrase my question so that it is clear to everyone. I have
> a list of intramolecular interactions between atoms in a molecule within
> the [ pairs ] section for which I believe gromacs generates the LJ C6 and
> C12 values when the gen-pairs is set to yes. So I want to know if there is
> any way to output/write the C6 and C12 values generated by gromacs to
> screen/file.
>

gmx dump -s topol.tpr

That will give you the processed topology, which includes c6 and c12.

--
James "Wes" Barnett
Postdoctoral Research Scientist
Department of Chemical Engineering
Kumar Research Group <http://www.columbia.edu/cu/kumargroup/>
Columbia University
w.barnett at columbia.edu
http://wbarnett.us
--
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