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

James Starlight jmsstarlight at gmail.com
Sat Jun 1 13:11:10 CEST 2013

Thanks for so detailed explanation!

I've also forced with the problem of barostat during simulation of my
membrane protein with N-H chains  ( see adjacent topic). I'll be also very
thankful for you suggestion in that case too.


2013/6/1 Mark Abraham <mark.j.abraham at gmail.com>

> On Fri, May 31, 2013 at 5:19 PM, James Starlight <jmsstarlight at gmail.com
> >wrote:
> > 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 )
> >
> You're integrating forces calculated at one instant and assuming they are
> applicable over a finite time period. Obviously this is an approximation,
> and it gets worse with longer time step. The worse approximation means the
> sampling is from a shadow Hamiltonian that is even further from the real
> one. P-R is not very stable if the sampling is not from equilibrium, so
> probably the change suggested in the warning helps keep P-R working.
> The absence of the simulation crashing is not a suitable proxy for assuming
> there are no problems. You should compare observables with those from
> conservative parameter sets and see whether differences exist.
> Mark
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