On Fri, Apr 19, 2013 at 4:09 AM, Niels Geudens <Niels.Geudens.ugent.be>wrote:
>
> 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?
>
This does seem unusual. You can use the checkoverlaps command in ptraj or
cpptraj to see if any of your solvent atoms are overlapping atoms from your
solute (those kinds of things typically cause 'blowups' that are more
common in explicit solvent than implicit solvent.
> Does anyone have an idea to overcome this problem?
>
There are many ways that people overcome this kind of problem (because
there are many reasons this problem may exist in the first place). First,
make sure you follow one of the 'standard' protocols for preparing a system
(such as those outlined in the first basic tutorial on
http://ambermd.org):
1) Generate your prmtop/inpcrd using tleap and possibly
antechamber/parmchk/R.E.D.
2) Relax your structure with 500-1000 steps of minimization or so
3) Heat your structure slowly up to your target temperature
4) Run NPT dynamics to equilibrate the pressure and density
5) Begin your production run using whatever ensemble you need (NVT, NPT,
NVE, ...)
If you are still having problems, the key may lie in how exactly you carry
out the first couple steps. Some starting structures require more care,
and you may have to use a variety of restraints in order to relax the
solvent (and ion) distribution around your solute before you allow your
solute to move freely.
If you continue to have problems with pathological cases, you may benefit
from the experience of others on this list, but you will have to provide
specific details about exactly what you've tried (providing the exact input
files is typically a good idea, since that's the only way of
differentiating between what you meant/tried/wanted to do and what you
actually did), and the error messages, if any, that you got.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Apr 19 2013 - 04:00:02 PDT
