[gmx-users] is there any special tutorial for the interaction of nanosheet and amino acids?

[Alex]

Hi Rose,

It sounds like a lot of things packed in a very short message, so let me
try to clarify a few points:

1. Gromacs is not DFT, it is particle-based. You simulated your nanosheet
in Gaussian and it is my understanding that you used CHELPG to obtain the
partial atomic charges.

2. Those charges in general are not compatible with most MD forcefields
implemented in Gromacs. If I remember correctly, AMBER is the closest to
using CHELPG charges. So, my point is that you need to choose the MD
forcefield properly and set the charges (all non-bonded parameters, really)
accordingly. The same goes for the bonded parameters to represent the
nanomechanical properties of the sheet. This is beyond the scope of this
discussion, as you definitely need to do a thorough literature search and
see what forcefield is appropriate.

3. You ask if your nanosheet is "suitable." Any structure is "suitable" in
principle, as long as the interactions are set properly.

It is hard to give any advice beyond that. Simulation of "custom"
structures is a lot of effort. If your system of interest is small, an
alternative to all of this could be DFTMD simulations using CP2K package.

Alex

On Wed, Oct 18, 2017 at 1:50 PM, rose rahmani <rose.rhmn93 at gmail.com> wrote:

> first thank you for your attntion, i made ZnS nanosheet with VNL
> software,it has 33 atoms,i choosed vaccum gap,then i optimized and charged
> it with gaussian03,the amino acid is threonin,for the first time i want to
> study the interaction of these two structures, i am not even sure that my
> nano sheet is suitable for this simulation or not,but for the as a
> beginning i prfeer to test it.
>
>
>
> On Wed, Oct 18, 2017 at 10:48 PM, Alex <nedomacho at gmail.com> wrote:
>
> > Hi,
> >
> > That would probably depend on the nanosheet material, the particular
> amino
> > acid, the solvent & ionic strength, temperature, etc, etc. But no, there
> is
> > no tutorial and yes, a "nanosheet" can be viewed as a ligand. :)
> >
> > I don't know if this helps, but could you please first give us an idea of
> > what you're trying to do?
> >
> > Alex
> >
> >
> > On 10/18/2017 1:09 PM, rose rahmani wrote:
> >
> >> Hi
> >>
> >> I am a beginner user of GROMACS, i want to simulate the interaction of
> >> nano
> >> sheet with amino acid ,but i dont know what should do, how should i
> behave
> >> with these structures ? is there any tutoroial for interaction of nano
> >> sheet and amino acids?
> >> is it like protein-ligand tutorial in GROMACS tutorial?
> >>
> >> with regards
> >>
> >> Rose
> >>
> >
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