Few suggestions:
1. If I understood it correctly, you raised the system temperature
to 300K during a constant pressure MD. I have had problem doing
this. In my case the system expanded too much, which ultimately
lead to SHAKE problems later. I fixed this my raising the system
temperature during a constant volume run and then did a constant
pressure run.
2. What is the step size are you using for MD? In my system there are
close interactions between the protein and DNA and the atoms kept
coming too close with a step size of 2 fs. I found a step size of 1 fs
appropriate.
3. If nothing else works, you could also try more steps in the initial
minimizations.
4. Regarding the solvent moving out of the box, is this after "imaging"
the system?
Good luck.
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Received on Tue Apr 29 2003 - 15:53:01 PDT
