jalemkul at vt.edu
Wed Dec 12 13:14:53 CET 2012
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.
> 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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