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 <glos...@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 <glos...@yahoo.it> > A: "gmx-users@gromacs.org" <gmx-users@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 > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- 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 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
