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

James Starlight jmsstarlight at gmail.com
Sun Jun 2 16:56:02 CEST 2013


could you also provide me with some examples when usage of VS could give
artifacts in simulations ?
In particular I'm interesting in usage of VS on hydrogens with membrane


2013/6/1 James Starlight <jmsstarlight at gmail.com>

> 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.
> James
> 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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