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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Received on Thu May 13 2010 - 12:30:03 PDT
