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

[Mark Abraham]

On Thu, May 30, 2013 at 12:31 PM, James Starlight <jmsstarlight at gmail.com>wrote:

> Also some questions about corrections in the mdp besides the time-step file
> which should be included with the VS.
>
> 1) What constrains algorithm should I use ?
> typically I use
> ; Bond parameters
> constraint_algorithm = lincs    ; holonomic constraints
> constraints     = all-bonds     ; all bonds (even heavy atom-H bonds)
> constrained
> lincs_iter      = 1             ; accuracy of LINCS
> lincs_order     = 4             ; also related to accuracy
>

At high parallelization, all-bonds becomes limiting, which can be mitigated
with changed lincs parameters. See manual.

2) Should I vary tau_t constant assuming that I use SD integrator as the
> thermostat ( I'm using 2 ps ) ?
>

Don't know.

Mark


>
> 2013/5/30 James Starlight <jmsstarlight at gmail.com>
>
> > 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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> >
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