Hi,
I am trying to do molecular dynamics on a cyclic lipodepsipeptide of 9
standard amino acids. I derived charges and parameters for the lipid
tail (a beta-hydroxy decanoic acid moiety) using Antechamber. I added
any missing paramaters to the leaprc.ff99SB force field. This works
very well in vacuum or implicit solvent. However, when I try to do the
exact same simultation in explicit solvent (TIP3PBOX), my molecule
explodes already during the first step. Lowering the time step and/or
temperature does not resolve this issue. Using charges derived via RED
does not help either.
I was just wondering what could be causing this problem since implicit
solvent works fine. Isn't this odd?
Does anyone have an idea to overcome this problem?
Kind regards
Niels
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Received on Fri Apr 19 2013 - 01:30:02 PDT
