[gmx-users] Question regarding coarse-graining martini

Peter Kroon p.c.kroon at rug.nl
Wed Mar 1 10:59:54 CET 2017

Hey Ali,

1) You usually can't use PR for equilibration - it'll oscillate out of
control and blow up. What I usually do is use Berendsen for
equilibration, and PR for the production run.

2) What do you mean exactly? The numbers mean the same, but I'm not sure
of any physical effect as a result of the coarse-graining. I think the
approximation you make by CGing is larger anyway. What you *do* see is
an effect in effective timescales, CG beads experience less "drag", and
diffuse and equilibrate faster than they should. So comparing dynamics
directly is extremely tricky.


On 28-02-17 21:10, ali.khourshaei71 at student.sharif.edu wrote:
> Dear Gromacs users, 
> 1. Through a stage of my thesis ( through which I'm using coarse-grained
> martini), I'm monitoring the change of the pressure of the system and
> this quantity experience a noticeable amount of changes. So, due to the
> fact that system experiences a large amount of pressure change, to the
> best of my knowledge I think using parrinello-rahman through the
> simulation is out of question and I have to use berendsen barostat
> coupling. Is this conclusion wrong? 
> 2. In case I want to compare the result of All-atom and coarse grain, is
> there any general relation between the parameters of the simulation (
> such as tau-p, tau-t and So on) ? 
> Eagerly looking forward to hear back from you. 
> yours sincerely, 
> Ali

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