Hi,
You also need to provide your script for ptraj. I see your tgtfitmask and
tgtrmsmask are different. So, I suppose your ptraj script has multiple rms
commands.
On Thu, May 13, 2010 at 3:19 PM, <map110.pitt.edu> wrote:
> Hi everyone,
>
> I'm trying to run a 2 ns targeted md simulation in which the rmsd of the
> protein structure from the reference structure is gradually reduced over
> time. In order to test my input files, I ran a 1 ps test simulation and
> found that there was a discrepancy between the "current RMSD from
> reference" given in the .out file and the actual rmsd between the
> reference structure and the outputted frame0.rst file (found using ptraj).
> Specifically, in frame0.out the rmsd is 5.124, compared to the actual rmsd
> of 3.28614.
>
> This is the command I used:
>
> mpiexec -n 8 nice -19 sander.MPI -0 -i md.in -o frame0.out -p complex.top
> -c eq3.rst -r frame0.rst -x frame0.crd -ref origmin.rst
>
> I'm also attaching all my input and output files. If anyone has an input
> on this problem it would be greatly appreciated.
>
> Thanks in advance for your help!!
>
> Maria
>
>
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>
--
Best,
InSuk Joung
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Received on Thu May 13 2010 - 13:00:04 PDT
