[gmx-users] gen-vel=no

[Bahar Mehrpuyan]

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.

-Justin

>
> 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.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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