Hi,
I have run a 50 ns MD on DNA divided into 1 ns intervals. I looked at
the RMSD using two methods: First, in my ptraj input file I trajin
each individual .trj file, i.e.:
trajin X3_md.1.trj 1 500 10
trajin X3_md.2.trj 1 500 10
trajin X3_md.3.trj 1 500 10
trajin X3_md.4.trj 1 500 10
[.....etc]
center :1-12 origin mass
image origin center familiar
center :13-24 origin mass
image origin center familiar
center :1-24 origin mass
image origin center familiar
# Strip the water and chloride ions
strip :WAT
strip :Na+
strip :Cl-
rms first out X1_50ns_rms.dat .N,CA,C mass
Using this method, the RMSD appears normal (~2-5 A).
However, the analysis program I wish to use requires me to combine all
my trajectories into one file. For this I created a combination .trj
file. However, when I look at the RMSD vs. time of the combi file, it
comes out around 8 Angstroms and there are several spikes at around
25ns. When I look at the trajectory in VMD, the two strands split
apart spontaneously at these spikes. So, there must be a problem with
the way I am combining the trajectory files. Here is my ptraj.in file:
trajin X3_md.1.trj 1 500 10
trajin X3_md.2.trj 1 500 10
trajin X3_md.3.trj 1 500 10
trajin X3_md.4.trj 1 500 10
[....etc]
strip :WAT
trajout combi_nowat.trj nobox
What am I doing wrong?
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Received on Sat Feb 12 2011 - 01:00:02 PST
