[gmx-users] Question about x2top

[Justin A. Lemkul]

Quoting Jussi Lehtola <jussi.lehtola at helsinki.fi>:

> Hi,
>
>
>
> first of all, thanks to Mark and David for helping me with building
> potentials.
>
> Is there any way to speed up x2top? When I have generated a system of
> thousands of molecules using genconf and make a topology for it using
> x2top, the process can take hours. Is it OK just to copy the
> single-molecule topology made by x2top N times for a system of N
> molecules?

You don't need to make explicit copies of the same parameters for a system of N
molecules.  If, for example, you have a "molecule.itp" file, in your topol.top,
you would #include "molecule.itp" and in your [molecules] section, add the line:

molecule     N

Think of water as an analogy.  You wouldn't include an "spc.itp" for each and
every water molecule, would you?  The parameters are applied to each molecule
of the same type.

-Justin

> --
> ------------------------------------------------------
> Jussi Lehtola, FM, Tohtorikoulutettava
> Fysiikan laitos, Helsingin Yliopisto
> jussi.lehtola at helsinki.fi, p. 191 50673
> ------------------------------------------------------
> Mr. Jussi Lehtola, M. Sc., Doctoral Student
> Department of Physics, University of Helsinki, Finland
> jussi.lehtola at helsinki.fi
> ------------------------------------------------------
>
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========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

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