Hi, All molecules diffuse. As such, proteins are expected to move about. Preventing them form doing so is essentially non physical, so you'd need a good and thought-through reason for doing so.
Erik 15 jun 2012 kl. 10.27 skrev Shima Arasteh: > Thanks. > I read that it doesn't matter if the protein moves and even protrudes the > box. It's OK, but there is a question here; why doesn't the box move rather > than the protein? > Is it possible for box to be defined every step?, then the protein would stay > in the center of the box. > > Sincerely, > Shima > From: Mark Abraham <[email protected]> > To: Discussion list for GROMACS users <[email protected]> > Sent: Thursday, June 14, 2012 12:22 PM > Subject: Re: [gmx-users] protein near the edges of simulation box > > On 14/06/2012 5:47 PM, Shima Arasteh wrote: >> >> Dear gmx friends, >> >> I put a protein in a simulation box filled of water molecules and entered >> the mdrun command. After the simulation, I found the protein near one of the >> edges of the box and not in center. What is the problem? Anyone may suggest >> me? >> Does it mean that the simulation is meaningless? >> I expect the protein to stay in the center of box and goes unfold by passing >> the time. >> > See > http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions > > Mark > > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists ----------------------------------------------- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 6688 fax: +46 18 511 755 [email protected] http://www2.icm.uu.se/molbio/elflab/index.html
-- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
