Hi Daniel,
I have one more question that popped into my head while thinking about
doing this.
How do I determine the number of frame where the simulation crashed? The
mdcrd (traj1) will have information till frame Y. So in that case, how do I
determine X?
Once I determine X, I can do as you suggested and read 1 to X frames of
traj1 and then read in traj2 (starting from X) and combine the both.
Appreciate your help.
Thanks
Regards
Rohit
On 18 Oct 2013 16:20, "rohitarora10.gmail.com" <rohitarora10.gmail.com>
wrote:
> 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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>
>
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Received on Fri Oct 18 2013 - 16:30:02 PDT
