[gmx-users] generating conf.gro

Vitaly Chaban chaban at univer.kharkov.ua
Mon Aug 18 10:29:16 CEST 2008


I want to create a system (conf.gro) consisting of a solvent and
polyatomic (brachiated enough) ions.

Using genconf and genbox I increase the number of molecules and then
ions (or contrariwise). But genbox refuses to add all the requested
particles at once (because of intersections, I guess). What I do? - I
add the number of ions it allows and make short md run. Then a few
other particles can be added. Repeating the procedure several times,
the system is ready.

The question is how to avoid these tricks? How to initialize the
system at once (even with intersections). Further, the energy
minimization will be done before MD itself. Of course, by means of
standard gromacs tools.


Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq., 4, Kharkiv 61077, Ukraine
email: chaban at univer.kharkov.ua
skype: vvchaban

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