[gmx-users] Test particle insertion method

[Rafael I. Silverman y de la Vega]

At the end of the .top file, add an entry for the test particle (make sure
its a separate entity from the SOL, even though it will probably be named
SOL also), at the end of the .gro structure file add the molecule to be
inserted. Update all relevant particle numbers in the files you altered.
grompp with the appropriate .mdp file and then mdrun, with the -rerun
option and the trajectory file as the input there.

tpic is a little more involved, but its still do-able.
When I alter the trajectory file for tpic, I turn it first into a .gro,
then add all the empty coordinate to every frame (this coordinate counts as
a particle for the particle number at the top of every frame.) Then use
trjconv to turn this multiframe .gro back into a .xtc or .trr file.

Hope that helps
~Rafael
On Sun, Nov 24, 2013 at 11:47 AM, jinhong zhou <jinhongzhou87 at gmail.com>wrote:

> Hi,Rafael,
>
> Yes. I want to know how to prepare the input files for TPI method in
> gromacs. I can't find any test set for it. Could you please kindly send me
> an example?
> Thanks a lot.
>
> jinhong zhou
>
> >Date: Sat, 23 Nov 2013 18:14:54 -0800
> >From: "Rafael I. Silverman y de la Vega" <rsilverm at ucsc.edu>
> >To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >Subject: Re: [gmx-users] Test particle insertion method
> >Message-ID:
>         <
> >CAOrpqKpsUz9kDerCekiUASZJ2Ozv9pHAukEEuTob7tCxjte=_w at mail.>gmail.com<
> w at mail.gmail.com>
> >
> >Content-Type: text/plain; charset=ISO-8859-1
>
> >What do you mean test files? Do you want to see how to alter the .top .gro
> >and trajectory files?
>
>
> >On Sat, Nov 23, 2013 at 4:28 PM, jinhong zhou <jinhongzhou87 at gmail.com
> >>wrote:
>
> > Hello,
> >
> > I am a new user of gromacs.
> > I want to calculate the chemical potentials of some molecules, such as
> > water. But I can't find any test files for "test particle insertion
> > method".
> > Is there anyone kind to send me some examples?
> >
> > Thanks a lot.
> > --
> > jinhong zhou
>
>
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