Thanks a lot!
________________________________ De: Justin Lemkul <jalem...@vt.edu> Para: Discussion list for GROMACS users <gmx-users@gromacs.org> Enviadas: Segunda-feira, 15 de Outubro de 2012 9:42 Assunto: Re: [gmx-users] bonds braking On 10/15/12 8:40 AM, Eduardo Oliveira wrote: > Thanks! > > So, if i understood correctly the correct workflow of trjconf? > I posted the link for two reasons: (1) so you would understand the nature of what was actually happening in the simulation and (2) so you would be aware of the solution. In your case, a protein in water, the remedy is very easy: trjconv -pbc mol -ur compact -center Center on the protein. You can apply various fitting operations afterwards if you like. -Justin > -------------------------------------------------------------------------------- > *De:* Justin Lemkul <jalem...@vt.edu> > *Para:* Eduardo Oliveira <eduardo...@yahoo.com.br>; Discussion list for > GROMACS > users <gmx-users@gromacs.org> > *Enviadas:* Segunda-feira, 15 de Outubro de 2012 9:14 > *Assunto:* Re: [gmx-users] bonds braking > > > > On 10/15/12 8:09 AM, Eduardo Oliveira wrote: > > Hi, > > > > I'm having trouble simulating a protein kinase on water. During the > simulation, the molecule moves towards the box limits and some residues apear > on > the other side. Almost like they are interacting with water molecules on > different sides of the box. I'm on my third simulation and the problem > persists. > I've already tried changing the periodic conditions but with no success. Waht > are your thoughts on that? > > > > For additional information: > > Before the dynamics step I performed 4 minimization steps then i did water > dynamics and the entire system dynamics. > > Here is all the ".mdp " files. > > > > Sorry in advance for the long email. > > > > This is a perfectly normal consequence of PBC. > > http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions > > -Justin > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- 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
