[gmx-users] Vritual Sites and simulation time-step
jmsstarlight at gmail.com
Thu May 30 12:31:49 CEST 2013
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)
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>
> 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 ?
> 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
>> > 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
>> > >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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