baharmehrpuyan at yahoo.com
Wed Dec 12 12:10:13 CET 2012
thanks for the reply.
How i can check the stability of integration?
If i consider 2 first ns for equlibration, can I trust the rest results?
From: Justin Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at 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.
> On Tue, Dec 11, 2012 at 10:55 AM, Bahar Mehrpuyan
> <baharmehrpuyan at 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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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