[gmx-users] grommp warning

Mark Abraham Mark.Abraham at anu.edu.au
Wed Aug 15 07:29:06 CEST 2012

On 15/08/2012 2:43 PM, rama david wrote:
> Hi Justin ,
> Thank you for immediate reply and providing the link.
> But I am wonder for following things...
> For protein simulation in your lysozyme tutorial we use
> refcoord_scaling = com
> In lipid tutorial also same one..
> So Is there are any case when to use
> refcoord_scaling no or all .....??????

Depends whether rigidity or scaling make more sense in your model of 
real physics, which depends what's in your system.

> Is there any way to find out which option to use when????

Thinking about it :-)

> How all the things going to affect the result????
> I goes trough archive but not find satisfactory answer...
> I am looking for clear and simple explanation...

Using position restraints ensures you do not reach the NPT ensemble. 
Whatever option you choose, you will need to simulate further without 
your position restraints to reach equilibrium. You should focus on 
minimizing the need for them, by making your system have the right 
density to start with. Then the volume change will be negligible, and 
the difference between these options likewise.


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