[gmx-users] energy minimization in vacuum
zhoumadison at gmail.com
Fri May 5 21:43:01 CEST 2006
Thanks for the try. I did searched the literature, however, so far I haven't
found anything talking about the difference between G43a1 and G43b1. My
impression is that most people just use G43a1 as default.
BTW, cutoff distance set as infinite means that all atom are calcualted
explicitly with the rcoulomb set as 0. This is recommended for the NM
analysis by several experts on this email list. What I am trying to figure
out is whether there is a better way to describe the coulomb interactions,
such as taking the solvent effect into consideration, since the potential
function for the system is the foundation for the NM analysis.
On 5/5/06, David Mobley <dmobley at gmail.com> wrote:
> 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.
> On 5/5/06, Lei Zhou <zhoumadison at gmail.com> wrote:
> > Dear Gmx-users,
> > I have questions about energy minimization in vacuum. Since there are
> > 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
> > added to the surface of protein to get a closer to nature description of
> > protein for NM analysis. In this case (protein with a layer of water),
> > force field should I use for energy minimization, G43a1 or G43b1?
> > For the electrostatic interaction, I choose cut-off and infinite
> > 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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