I will give this a shot! I know it is not a difficult issue to overcome,
but it is just my lack of knowledge and practice with ptraj.
Thanks a tonne, Daniel.
Best regards
Rohit
On 18 October 2013 15:59, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Fri, Oct 18, 2013 at 2:34 AM, rohitarora10.gmail.com
> <rohitarora10.gmail.com> wrote:
> > Now, if I restart my MD using this rst file, it will again write the
> frames
> > which are already in the previous trajectory (till the point where it
> > crashed i.e. Y) and then proceed to write the rest.
>
> Be aware this is not necessarily true depending on what kind of
> simulation you are doing. In particular if you are using the Langevin
> thermostat the random number stream will be different, so the
> trajectory of your restarted run from X to Y will probably not match
> the previous run from X to Y.
>
> >
> > My question is, while using ptraj to combine these two trajectories, how
> > can I make sure that the duplicate frames are written only once? Is
> there a
> > flag I can use, maybe something similar to -overwrite flag in
> > gromacs?
>
> You can do this in cpptraj/ptraj by specifying appropriate frame
> ranges to your trajin argument. For example, say your first trajectory
> crashed at frame 105 and you are restarting from frame 100 (assuming
> the second traj didnt crash as well):
>
> trajin traj1 1 100
> trajin traj2
> trajout combined
>
> Hope this helps,
>
> -Dan
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
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Received on Fri Oct 18 2013 - 07:30:05 PDT
