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
As per
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
Dear shima and Justin,
These error is come on Gromacs 4.5.5 at the time of NPT if
refcoord_scaling option not used..
But it is not come on Gromacs 4.5.4 when you not use refcoord_scaling
option at npt
Is any one else has same experience?
I really surprised by my observation
With
On 8/14/12 11:15 AM, rama david wrote:
Dear shima and Justin,
These error is come on Gromacs 4.5.5 at the time of NPT if
refcoord_scaling option not used..
But it is not come on Gromacs 4.5.4 when you not use refcoord_scaling
option at npt
Is any one else has same experience?
I really
Justin,
Thank you for your reply,
I check the manual but it is giving only small information..
I would be greatly thankfull to you if you shed some light on
these option ...
With best wishes and regards
Rama David
--
gmx-users mailing listgmx-users@gromacs.org
On 8/14/12 11:28 AM, rama david wrote:
Justin,
Thank you for your reply,
I check the manual but it is giving only small information..
I would be greatly thankfull to you if you shed some light on
these option ...
A simple search of the list archive turns up lots of discussions like
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 .??
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
Dear gmx users,
I'm simulating a system of protein and water. In NPT equilibration step, I get
the error of too many warnings.
Anybody knows about this warning?
The warning is :
WARNING 1 [file NPT.mdp]:
You are using pressure coupling with absolute position restraints, this
will give
Dear gmx users,
I'm simulating a system of protein and water. In NPT equilibration step, I get
the error of too many warnings.
Anybody knows about this warning?
The warning is :
WARNING 1 [file NPT.mdp]:
You are using pressure coupling with absolute position restraints, this
will give
On 8/13/12 12:36 PM, Shima Arasteh wrote:
Dear gmx users,
I'm simulating a system of protein and water. In NPT equilibration step, I get
the error of too many warnings.
Anybody knows about this warning?
Yes, and there are several posts in the list archive explaining its origin,
:-)
Sincerely,
Shima
From: Justin Lemkul jalem...@vt.edu
To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS
users gmx-users@gromacs.org
Sent: Tuesday, August 14, 2012 12:08 AM
Subject: Re: [gmx-users] grommp warning
On 8/13/12 12:36 PM
On 8/13/12 3:47 PM, Shima Arasteh wrote:
OK, thanks.
But please let me know something:
Is the pressure coupling with absolute position restraints is an option to
fix a volume significantly? If yes, then It's me to think about keeping fix the volume
of my system or not.
You can't have
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