Shanjie Huang wrote:
Hi dear friends,
I performed a molecular dynamics of a ligand-receptor complex for 5ns;
but I found that my complex always fall out from the water box quickly
in the first 1ns. What may be the problem?
Can I constrain some residues which are far away from the active site to
aviod this problem? But I am worry about the extra constrain would
interfere my MD result, for in the normal situation there should be no
constrains.
Thanks.
When using
comm-grps = Protein
in your mdp file the center of mass of you protein will stay at its
starting position.
good luck,
Jochen
--
************************************************
Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
************************************************
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