... and, in the case that you have several not-covalently-bound chains, use a 'topol.tpr' corresponding to a simulation beginning with all the chains within the same box. (I think Tsjerk suggested that to me several months ago)
Mauricio Sica > > Hi Tangj Jioawei, Erik. > > This is due to periodic boundary conditions. Make sure your molecules > stay together (clustered/nojump) before determining the rmsd. Use > trjconv... > > Tsjerk > > On 9/27/07, Erik Marklund <[EMAIL PROTECTED]> wrote: > > My first guess, without knowing how you used g_rms, is that the larde > rmsd > > for certain subunits is due to inadequate roto-translational fit > prior to > > rmsd-calculation. Does that help? If not, please be more explicit > about what > > you aim to do and what you have done. > > > > /Erik > > > > > > 27 sep 2007 kl. 11.29 skrev TANG JIAOWEI: > > Dear all, > > I am studying on a big protein with 16 subunits and when i used > g_rmsd to > > one subunit of the protein, the result seems strange that the > structure of > > the subunit changes much but it should not.. I searched the mailing > list and > > it may be caused by the periodic thing. Could you tell me how to > remove the > > periodic thing in detail before i use g_rmsd. > > > > Thank you > > > > Tang jiaowei _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
