<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><span>Thank you Tsjerk, this is encouraging for me!</span></div>
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<div><span>Gloria<br>
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<div><br></div> <div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"> <div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"> <font face="Arial" size="2"> <hr size="1"> <b><span style="font-weight: bold;">Da:</span></b> Tsjerk Wassenaar <tsjerkw@gmail.com><br> <b><span style="font-weight: bold;">A:</span></b> Gloria Saracino <glosara@yahoo.it>; Discussion list for GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight: bold;">Inviato:</span></b> Venerdì 25 Novembre 2011 10:10<br> <b><span style="font-weight: bold;">Oggetto:</span></b> Re: [gmx-users] multiple molecules simulations<br> </font> <br>Hi Gloria,<br><br>It think it's pretty obvious that loose pieces will see one another<br>across periodic boundaries diffusing around the place. Whether it's a<br>good model of reality is something for you to verify. A priori, the<br>approach seems
fine.<br><br>Cheers,<br><br>Tsjerk<br><br>On Fri, Nov 25, 2011 at 8:46 AM, Gloria Saracino <<a ymailto="mailto:glosara@yahoo.it" href="mailto:glosara@yahoo.it">glosara@yahoo.it</a>> wrote:<br>> Dear all,<br>> I did not get an answer yet.<br>> I really want know your opinion.<br>> If you need other details about the simulation I'm willing to give it to<br>> you.<br>> Thank you in advance,<br>> Gloria<br>><br>><br>> ________________________________<br>> Da: Gloria Saracino <<a ymailto="mailto:glosara@yahoo.it" href="mailto:glosara@yahoo.it">glosara@yahoo.it</a>><br>> A: "<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>" <<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> Inviato: Giovedì 24 Novembre 2011 17:06<br>> Oggetto: [gmx-users] multiple molecules simulations<br>><br>>
Dear all,<br>> I have performed a simulation on eight identical peptides (composed by 11<br>> residues) embedded in explicit water. Box dimensions (cube of 7.92nm) have<br>> been chosen to get a high concentration to accelerate the aggregation<br>> process. PME has been used and rvdw=rcoulomb=0.9.<br>> The trajectory has been centered on a residue of a chain with<br>> trjconv -f *.xtc -center -pbc mol -s *.tpr -n *.ndx<br>> During the first 16ns even if each peptide cannot see its periodic image,<br>> the whole set of peptides (Protein in the index file) see itself in some<br>> frames at distances below 2nm, and in a very few of them below 0.9nm.<br>> Looking at the trajectory in vmd after less then 2ns I see the formation of<br>> an oligomer composed by six peptides, the other two peptides move around<br>> leaving the oligomer on a side and approaching on an other side. The<br>> oligomer never sees its periodic
image as well as the two peptides never see<br>> their periodic image. The pi violations observed for the whole system<br>> correspond to the two peptides that, together or one at time, are placed<br>> between the oligomer and its pi. Considering 0.9nm as the distance below of<br>> which there is a direct interaction I found that when the minimum distance<br>> of the two peptides from one side of the oligomer is close to 0.9, the<br>> minimum distance from the other side is always above 1.4nm.<br>> Moreover the LJ and coulomb trends don't show abnormalities.<br>> Even if in simulations of a single molecule the effect of periodic image<br>> violation is a clear signal of a too small box to approximate a condition of<br>> infinite diluition, how I have to interpret such a violation for a system<br>> composed by multiple molecules and in which I want to reproduce a condition<br>> of high concentration?<br>> Can I use
this simulation to study the behavior of the system at the chosen<br>> concentration?<br>> There are particular simulation settings or checks that I have to take into<br>> account to handle a high concentrated solution a<br>> nd that I overlooked?<br>><br>> Any help will be appreciated (I apologize if some questions may seem<br>> trivial),<br>><br>> Gloria<br>><br>><br>> --<br>> gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>> Please search the archive at<br>> <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>> Please don't post (un)subscribe requests to the list. Use
the<br>> www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>><br>><br>> --<br>> gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>> Please search the archive at<br>> <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>> Please don't post (un)subscribe requests to the list. Use the<br>> www interface or send it to <a
ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>><br><br><br><br>-- <br>Tsjerk A. Wassenaar, Ph.D.<br><br>post-doctoral researcher<br>Molecular Dynamics Group<br>* Groningen Institute for Biomolecular Research and Biotechnology<br>* Zernike Institute for Advanced Materials<br>University of Groningen<br>The Netherlands<br><br><br> </div> </div> </div></body></html>