[gmx-users] grommp warning

Mark Abraham Mark.Abraham at anu.edu.au
Wed Aug 15 10:44:00 CEST 2012

On 15/08/2012 4:52 PM, rama david wrote:
> Thank you Mark for reply.
> as you said ...
> Depends whether rigidity or scaling make more sense in your model of
> real physics, which depends what's in your system.
> My system is generally consist of proteins or peptides ( single ,
> double or many)..
> I am using option com Is it right????

Probably. That's up to you. Only you know your overall objective about 
why you want to use PR and NPT.

> As per your answer in these archieve...
> http://lists.gromacs.org/pipermail/gmx-users/2011-November/065815.html
> Under NPT the box size changes each step. You are using position
> restraints to a pre-defined set of reference coordinates. This option
> allows you to choose how those *reference coordinates* should change
> when the box size changes (respectively do not scale them at all, scale
> them all, or scale their COM but leave their internal geometry fixed).
> Position restraints are then applied using the updated reference
> coordinates.
> In some archives I found if any one used freeze group
> suggested to use refcoord_scaling = no
> When we applied position restrain, the position of backbone atom is restrained..
> I make my assumption as like follow..
> No = no scalling in position of atoms.(system maintain rigidity).
> all  = the system bcome flexible
> com= ????? ( scalling com means changing com co-ordinates or something else????)

There's a definition in manual 7.3... what else are you asking for?


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