[gmx-users] Vritual Sites and simulation time-step

[James Starlight]

Mark,

thanks for advise. As I understood for the usage of virtual sites in
typical protein-water system I should
(1) define all hydrogens as the virtual atoms  (2) increase  atom masses of
the hydrogens presented in the water, COOH NH2 OH and SH as well as polar
groups (3) make virtual sites for the angles and dihedrals of peptide bond
as well as sidechains.

Also I've noticed that (1) and (2) can be done with the pdb2gmx with
options  -vsite and -heavyh respectfully. From this point its not quite
clear for me
(1) should I make some corrections in topology for dihedrals? In the manual
6.7 I've found some suggestions for the dihedrals of the different
functional groups.
(2) should I define VSITES for solvent  molecules filled into the box by
the genbox ?
(3) As I understood the inclusion of the VSITES for hydrogens would allow
me to increase timestep up to 5-8fs. What possible  negative side-effects
of the inclusion of VSITES might occur in simulation ?

James

2013/5/30 Mark Abraham <mark.j.abraham at gmail.com>

> Manual 6.7?
>
>
> On Thu, May 30, 2013 at 7:05 AM, James Starlight <jmsstarlight at gmail.com
> >wrote:
>
> > Dear Gromacs users!
> >
> > In some discussions I've noticed that people told about usage of virtual
> > sites which allow to increase time step of the simulation of such
> systems.
> > >From manual and tutorial its not quite understand for me how with
> > inclusion
> > of such dummy atoms (which can be used to reduce number of atoms of the
> > some solvent-like molecule or to mimic  electron pairs in the water for
> > instance)  influence on time-step can be achieved ?
> >
> >
> > James
> > --
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