[gmx-users] f(x) g(x) h(x)in the user defined potential functions

He, Yang yang.he at mavs.uta.edu
Fri Oct 24 22:02:51 CEST 2008

Hi Mark,

Thank you for your reply. From your point of view,   I wonder whether you mean I need to write a table based on different interaction types and then change the source code  for recognition when running my case in the gromacs .I just have no idea about that .Can you give me further suggestion about that? I am stuck by this point

Thank you very much.

From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Mark Abraham [Mark.Abraham at anu.edu.au]
Sent: Thursday, October 23, 2008 6:11 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] f(x) g(x) h(x)in the user defined potential functions

He, Yang wrote:
> Hi all users,
> When I am defining the user potential functions using the table, I encountered a problem that there are several unstable parameters  in the separate f(x),g(x),h(x) .For example, in the g(x), there is a parameter "epsilon" whose value will depend on different pairs.In this situation, I can not get a specific value in the table file . I don't know how to solve this problem.
> Can anyone of you give me some suggestions about that?

So your nonbonded interaction depends on your atom types. You could
write a table for each interaction type, modify GROMACS to read them all
in, and then modify the routine that calls the kernels to use the
correct one. This additional memory usage would grow as the square of
the number of atom types. You would also see some performance loss which
you could minimize by arranging to evaluate all of one type of nonbonded
interaction close together in the nonbonded routines, to minimize cache

Better would be if some of these functions (conveniently) differed only
by a multiplicative or additive constant so that you could re-use the
same table and then apply a correction function, but you'll have to look
at your own maths for that.

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