Hi,
Did each MD run use the restart of the previous run as initial
coordinates (and use irest=1)?
-Dan
On Wed, Apr 27, 2016 at 9:32 AM, Saheb Dutta <sabdut.yahoo.com> wrote:
> Dear amber user
> We attempt to calculatethe time correlation function using amber11 (auto time-correlation function (tcf)of the N-H vector) for a protein molecule. We have the total trajectory dividedinto 44 mdcrd files of various time spans (such as 100 ps, 150 ps and 200 ps)for a total 6 ns trajectory length. Time step is 0.1 ps for each frame withinall mdcrd files. The problem is the calculated tcf exhibits a sudden riseat the time step corresponding to the beginning of the next mdcrd file. Forexample, the tcf decays from 1 in the first trajectory which ends at a value of0.8614 at 149.9 ps. However, the tcf value at 150 ps is 0.8734 at the start ofthe next mdcrd file and decays subsequently. Again, the value suddenly rises atthe time step corresponding to the beginning of the next mdcrd file.Consequently, the tcf plot exhibits spike like features through out its decay. The ptraj script used is appended below.
>
>
>
>
>
> Script used:
>
> trajin md1.mdcrd
>
> trajin md2.mdcrd
>
> … ….. …… …..
>
> … ….. …… …..
>
> … ….. …… …..
>
> trajin md44.mdcrd
>
> rms first out test.rms :1-527.CA,C,N time 0.1
>
> vector v349 :349.N corr :349.H order 2
>
> analyze timecorr vec1 v349 vec2 v349 tstep 0.1 tcorr1000 out tcorr349.out
>
> Thanks in advanceWith regards Saheb
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>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
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 Wed Apr 27 2016 - 09:30:03 PDT
