[gmx-users] multiple molecules simulations

[Tsjerk Wassenaar]

Hi Gloria,

It think it's pretty obvious that loose pieces will see one another
across periodic boundaries diffusing around the place. Whether it's a
good model of reality is something for you to verify. A priori, the
approach seems fine.

Cheers,

Tsjerk

On Fri, Nov 25, 2011 at 8:46 AM, Gloria Saracino <glosara at yahoo.it> wrote:
> Dear all,
> I did not get an answer yet.
> I really want know your opinion.
> If you need other details about the simulation I'm willing to give it to
> you.
> Thank you in advance,
> Gloria
>
>
> ________________________________
> Da: Gloria Saracino <glosara at yahoo.it>
> A: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Inviato: Giovedì 24 Novembre 2011 17:06
> Oggetto: [gmx-users] multiple molecules simulations
>
> Dear all,
> I have performed a simulation on eight identical peptides (composed by 11
> residues) embedded in explicit water. Box dimensions (cube of 7.92nm) have
> been chosen to get a high concentration to accelerate the aggregation
> process. PME has been used and rvdw=rcoulomb=0.9.
> The trajectory has been centered on a residue of a chain with
> trjconv -f *.xtc -center -pbc mol -s *.tpr -n *.ndx
> During the first 16ns even if each peptide cannot see its periodic image,
> the whole set of peptides (Protein in the index file) see itself in some
> frames at distances below 2nm, and in a very few of them below 0.9nm.
> Looking at the trajectory in vmd after less then 2ns I see the formation of
> an oligomer composed by six peptides, the other two peptides move around
> leaving the oligomer on a side and approaching on an other side. The
> oligomer never sees its periodic image as well as the two peptides never see
> their periodic image. The pi violations observed for the whole system
> correspond to the two peptides that, together or one at time, are placed
> between the oligomer and its pi. Considering 0.9nm as the distance below of
> which there is a direct interaction I found that when the minimum distance
> of the two peptides from one side of the oligomer is close to 0.9, the
> minimum distance from the other side is always above 1.4nm.
> Moreover the LJ and coulomb trends don't show abnormalities.
> Even if in simulations of a single molecule the effect of periodic image
> violation is a clear signal of a too small box to approximate a condition of
> infinite diluition, how I have to interpret such a violation for a system
> composed by multiple molecules and in which I want to reproduce a condition
> of high concentration?
> Can I use this simulation to study the behavior of the system at the chosen
> concentration?
> There are particular simulation settings or checks that I have to take into
> account to handle a high concentrated solution a
> nd that I overlooked?
>
> Any help will be appreciated (I apologize if some questions may seem
> trivial),
>
> Gloria
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands