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?
Mark
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