Hi,
Does the structure look correct in VMD? If not then make sure you're
using a topology file that corresponds to your trajectory file and
that you are choosing "AMBER Coordinates with Periodic Box" as your
trajectory type.
-Dan
On Thu, May 12, 2016 at 2:18 AM, Sneha Rai <rai.sneha51.gmail.com> wrote:
> Dear Amber users,
>
> I have used the following input file for 20 ns production run. The output
> file indicates that run is complete without any errors. However, when I
> load mdcrd file of production run in VMD, only 1367 frames were loaded and
> I was expecting 4000 frames. Following is my input file for production run,
> kindly suggest possible solution for this problem.
>
> Production
> &cntrl
> imin=0,
> ntx=5,
> irest=1,
> nstlim=10000000,
> dt=0.001,
> ntf=2,
> ntc=2,
> temp0=300.0,
> ntpr=2500,
> ntwx=2500,
> ntwr=2500,
> cut=8.0,
> ntb=2,
> ntp=1,
> ntt=3,
> gamma_ln=2.0,
> /
>
>
> Thanks & Regards
>
> Sneha Rai
> Ph.D. Research Scholar
> Computational and Structural Biology Lab
> Division of Biotechnology
> NSIT
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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 Thu May 12 2016 - 09:00:04 PDT
