[gmx-users] modify bondfree.c and recompile

[He, Yang]

Hi David,


Thank you for your reply. As for the new non-bond potential, if I want to use the gromacs to deal with them, what should i do in the gromacs? Do you have any suggestions about that? Change the source code?

Thank you for your help.

Regard,

Yang
________________________________________
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of David van der Spoel [spoel at xray.bmc.uu.se]
Sent: Tuesday, October 21, 2008 11:09 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] modify bondfree.c and recompile

He, Yang wrote:
> Hi Jian,
>
> Do you also need to change the source code to get a new potential function? I am also engaged in this job. DO you have any experience about this job?
>
>
You can use tables for bonded potentials as well, without changing any code.

> Regards,
>
> Yang
> ________________________________________
> From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Jian Zou [jianzou at gmail.com]
> Sent: Tuesday, October 21, 2008 7:24 AM
> To: gmx-developers at gromacs.org; gmx-users at gromacs.org
> Subject: [gmx-users] modify bondfree.c and recompile
>
> Hi,
>
> If I only change some functional form in bondfree.c (the number of
> parameters are kept the same), can I just do "make mdrun" and "make
> install-mdrun" to recompile from the source?
>
> I cannot find the dependency between the source files and the Gromacs
> utilities (grompp and mdrun).
>
> I compare the tpr file generated before and after the change and they
> are the same. Therefore it seems to me that grompp does not read the
> formulation of bonded interactions, am I right?
>
> Thank you very much for the reply.
>
>
> Regards,
>
> Jian
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
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