Hu Zhongqiao wrote:
Dear all,
I finish a 10-ns MD simulations for a system including 16 lysozyme
molecule chains, some solvents H2O molecules and 128 Cl- counter ions
under PBC. When I use the command to calculate the RMSF of residues as
follows:
g_rmsf -f ***.xtc -s ***.tpr -o rmsf_res.xvg (I selected 3 for groups)
The results showed that 3rd and 14the chain had RMSF 1.2-2nm, which is
obviously unreasonable. But compared with other chains, these 2 chains
have the basically same peak places. The difference is that RMSFs of
residues in these 2 chains are systematically much higher. Is there a
bug resulting in a systematic error or any other reasons? Any
suggestions are welcome. Thanks,
Zhongqiao Hu
Dept of Chemical and Biomolecular Engineering
National University of Singapore
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are all the lysozymes treated as one protein? in that case it might be a
PBC artifact. try doing the rmsf per molecule (by running the program 16
times) and then overlaying the result.
are you trying to crystallize it?
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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