Re: [gmx-users] Why my protein always falls out of the water box?
Shanjie Huang wrote: Hi dear friends, I performed a molecular dynamics of a ligand-receptor complex for 5ns; but I found that my complex always fall out from the water box quickly in the first 1ns. What may be the problem? Can I constrain some residues which are far away from the active site to aviod this problem? But I am worry about the extra constrain would interfere my MD result, for in the normal situation there should be no constrains. Thanks. When using comm-grps= Protein in your mdp file the center of mass of you protein will stay at its starting position. good luck, Jochen -- Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
Re: [gmx-users] Why my protein always falls out of the water box?
Hi you!it may not be as bad as it looks like. Usually the one happening to your protein is only a visualization problem, if an atom of your protein crosses the periodic simulation box, it might appear as if the whole molecule jumps out of the box, because the coordinates of one of its periodic images are shown instead of those referring to the real box. You can simply assess if this is the case by running a single step dynamics, at a low temperature, if the protein jumps out all the same, it can't be because of the real protein movement! In this case, you can just convert you trajectory by trjconv -center -pbc wholethis way you should have a trajectory in which your protein quietly stays in its box.hope it helps!greetings,MGiòOn 3/13/06, Shanjie Huang <[EMAIL PROTECTED]> wrote: Hi dear friends,I performed a molecular dynamics of a ligand-receptor complex for 5ns;but I found that my complex always fall out from the water box quicklyin the first 1ns. What may be the problem?Can I constrain some residues which are far away from the active site to aviod this problem? But I am worry about the extra constrain wouldinterfere my MD result, for in the normal situation there should be noconstrains.Thanks.-- Shanjie Huang [EMAIL PROTECTED]--http://www.fastmail.fm - A no graphics, no pop-ups email service___gmx-users mailing list gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease 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 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
[gmx-users] Why my protein always falls out of the water box?
Hi dear friends, I performed a molecular dynamics of a ligand-receptor complex for 5ns; but I found that my complex always fall out from the water box quickly in the first 1ns. What may be the problem? Can I constrain some residues which are far away from the active site to aviod this problem? But I am worry about the extra constrain would interfere my MD result, for in the normal situation there should be no constrains. Thanks. -- Shanjie Huang [EMAIL PROTECTED] -- http://www.fastmail.fm - A no graphics, no pop-ups email service ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
