The G43b1 force field is for running _simulations_ in vacuum. If you just want to perform energy minimization prior to a simulation in solvent, than you can just use the G43a1 (or a2). The point is that you want to get rid of them bad contactsin the structure, so your simulation won't blow...
Cheers,
Tsjerk
On 5/5/06, David Mobley <[EMAIL PROTECTED]> wrote:
Lei,
I think I saw this question on the list before, which means you
probably didn't get a response. It is in general probably a bad idea
to send exactly the same e-mail twice, as the fact that it didn't get
a response the first time usually means you've phrased it in such a
way that people find it difficult/uninteresting to answer. However,
I'll give it a shot.
I haven't the foggiest idea as to the right answer to your question,
but my suggestion would be that you read the literature on G43a1 and
G43b1. Presumably each of them has certain differences and might be
expected to perform well in different situations. From that
literature, you can find out what the major differences are, and then
you can get an idea of which would be most appropriate for what you
are trying to do.
I'm not sure what you mean by choosing "infinite distances" for the
electrostatic interactions.
David
On 5/5/06, Lei Zhou <[EMAIL PROTECTED]> wrote:
>
> Dear Gmx-users,
>
> I have questions about energy minimization in vacuum. Since there are two
> force fields available, G43a1 and G43b1, should I use G43b1 for energy
> minimization in vacuum? What are the major difference between these two
> force fields?
>
> In one previous paper (Amadei et al, 1999), a layer of water molecules were
> added to the surface of protein to get a closer to nature description of the
> protein for NM analysis. In this case (protein with a layer of water), which
> force field should I use for energy minimization, G43a1 or G43b1?
>
> For the electrostatic interaction, I choose cut-off and infinite distances.
> Is this acceptable, comparing to the treatment with a distance-dependent
> dielectric constant?
>
> Thank you for the help.
>
> Lei Zhou
> Columbia University
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--
Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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