[gmx-users] user defined potential function for 1-4 interaction

[Berk Hess]

Hi,

Unfortunately this is not possible.
If you do not have to many pairs, you can change all (or all minus one type)
from pairs to tabulated bonds (bonds type 9) in your topology.
Then you can supply as many different bond tables as you like.
Note that this will supply a single potential though,
not separate Coulomb, dispersion and repulsion tables.

Berk

From: mhrahman at Dal.Ca
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] user defined potential function for 1-4 interaction
Date: Fri, 9 Oct 2009 09:48:19 -0300










I think there must be a way in gromacs to pass tabulated 
potenttial for 1-4 interaction for two groups as interaction between 
different pairs can be significantly different and can change the structure of 
an indiviual molecule. 
I would request:  Please let me know if it is 
possible to pass tabulated potential for pair inteaction for two groups. if 
my method, which you will see below, is wrong please let me know the 
correct way. I searched previous communications regarding tabulated potential 
but could not get my answer. I hope I am not wasing your time.
 
Thanks.
 
 
----- Original Message ----- 

  From: 
  LuLanyuan 

  To: gmx-users at gromacs.org 
  Sent: Thursday, October 08, 2009 8:04 
  PM
  Subject: RE: [gmx-users] user defined 
  potential function for 1-4 interaction
  
Hi,
As I remember, you can only use one table for 1-4 
  interactions. Don't know if it's changed
in the latest 
  version.
Lanyuan

> From: mhrahman at dal.ca
> To: gmx-users at gromacs.org
> Subject: 
  Re: [gmx-users] user defined potential function for 1-4 interaction
> 
  Date: Thu, 8 Oct 2009 19:10:39 -0300
> 
> Hi all:
> I posted 
  this earlier but did not get any help I really need to slove this 
> 
  issue.
> 
> What should be the way to pass a formatted table for 
  the 1-4 interaction
> for two or more different groups? Reading page 150 
  and 180 of manual 4.0, 
> I
> understand user defined potential 
  functions can be passed for many groups
> using energygrp_table in .mdp 
  file but nothing is clearly mentioned
> regarding pair 
  interaction
> 
> I have two grps for 1-4 interactions MTN and 
  SFT.
> mdrun command includes:
> -table table.xvg -tablep 
  pair.xvg
> ; .mdp file contains,
> energygrps = MTN SFT
> 
  energygrp_table: MTN MTN MTN SFT
> 
> I passed three tables for 
  pair interaction in the
> name pair.xvg, pair_MTN_MTN.xvg and 
  pair_MTN_SFT.xvg.
> I see the later two tabels are not recognized. If 
  pair_MTN_MTN.xvg and 
> pair_MTN_SFT.xvg are not supplied GROMACS donot 
  issue any warning.
> I am afraid that I failed to submit separate table 
  for pair interaction 
> properly in this way.
> 
> 
  Thanks,
> M.H.Rahman 
> 
> 
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