XAvier Periole skrev:
On Jun 30, 2010, at 10:34 AM, Carla Jamous wrote:
Dear all,
I'm running my first simulation of a dimer.
When I run g_rms on Calpha (lsq fit and RMSD calculation on Calpha)
to get the RMSD of the whole dimer, the graph is ascending, till
reaching a value of 8 A.
in this case, I take a .tpr file, a .xtc file and a .ndx file of the
whole dimer.
However, when I run g_rmsd on Calpha, but this time, to get the RMSD
of one chain (one monomer), the graph is constant with value around 1
A. and this for both chains, when taken alone.
In this case, I take a .tpr file, a .xtc file and a .ndx file of the
monomer.
So is this an error of using g_rms?
Well this is not an error. Evidently your monomers are stable
(rmsd~0.1nm)
and you dimer is not.
This might be result of either an actual deformation of the dimer or
one of your monomer is crossing the periodic boundaries and thereby
the rmsd is not representative.
try to trjconv your trajectory using the -pbc nojump and run g_rms again.
I suspect the former. If pbc crossing is the explanation, then it would
show up in the analysis of one of the monomers.
Erik
Thank you.
Carla
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Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
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[email protected] http://folding.bmc.uu.se/
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