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

[James Starlight]

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

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

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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>