[gmx-users] Vritual Sites and simulation time-step
jmsstarlight at gmail.com
Fri May 31 17:19:52 CEST 2013
3) Also I've already performed small simulation with the time step 5 fs
(defining virtual sites by means of pdb2gmx -vsites and introducing heavy
hydrogens. I've not observed any errors during my simulation. When I've
tried to increase dt up to 7 fs I've obtained warnings according to that I
should increase tau_p (from 2 ps with Parinello coupling). How tau_p is
relevant to the timestep and when I could obtain more information about
such constants ? E.g if i increase tau_p doest it means that I provide
weaker coupling to the system with pressure bath ? (higher constant- higher
relaxation times )
2013/5/30 James Starlight <jmsstarlight at gmail.com>
> 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
>>> > 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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