On 12/12/12 6:10 AM, Bahar Mehrpuyan wrote:
thanks for the reply.
How i can check the stability of integration?
If the integration is unstable, the system will crash.
If i consider 2 first ns for equlibration, can I trust the rest results?
Without significantly more information, no one on this list will be able to say
if some arbitrary time is sufficient.
-Justin
________________________________
From: Justin Lemkul <jalem...@vt.edu>
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Sent: Tuesday, December 11, 2012 5:01 PM
Subject: Re: [gmx-users] gen-vel=no
On 12/11/12 1:19 AM, Venkat Reddy wrote:
The check point file you submit will have the velocity information.
A checkpoint file is indeed a better set of information to pass to -t, but it is
not clear if the OP even used -t in the invocation of grompp. If not, there
will be a discontinuity in the ensemble and the initial forces are simply
calculated from the potential of the initial configuration. This may or may not
produce stable integration, but at the very least certainly will require some
time to be discarded as new equilibration.
-Justin
On Tue, Dec 11, 2012 at 10:55 AM, Bahar Mehrpuyan
<baharmehrpu...@yahoo.com>wrote:
hi gmx user
I've done a production simulation with gen_vel= no, but in grompp I forgot
that use .trr file of equlibration simulation for initial velocities,
my question is how gromacs treats with initial velocities in this case?
thanks in advance.
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
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http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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