it may not be as bad as it looks like. Usually the one happening to your protein is only a visualization problem, if an atom of your protein crosses the periodic simulation box, it might appear as if the whole molecule jumps out of the box, because the coordinates of one of its periodic images are shown instead of those referring to the real box. You can simply assess if this is the case by running a single step dynamics, at a low temperature, if the protein jumps out all the same, it can't be because of the real protein movement! In this case, you can just convert you trajectory by
trjconv -center -pbc whole
this way you should have a trajectory in which your protein quietly stays in its box.
hope it helps!
greetings,
MGiò
On 3/13/06,
Shanjie Huang <[EMAIL PROTECTED]> 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.
--
Shanjie Huang
[EMAIL PROTECTED]
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