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

[Mark Abraham]

On Thu, May 30, 2013 at 12:17 PM, James Starlight <jmsstarlight at gmail.com>wrote:

> 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,


Not applicable if you are using a rigid water model.


> 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.
>

Generally, use what pdb2gmx will generate and don't worry further. I have
heard the thought expressed that the aromatic constructions are not good in
practice, but I don't know any details.


> (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 ?
>

The vsites are generally fine. See paper referenced there for some details.

Mark


>
> 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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