Re: [gmx-users] Getting out of the box!!!
Marcelo, Have you considered reading the FAQ, searching the mailing list, reading the manual or just paying attention? Just yesterday there was mention of a ligand jumping out of the box, to which several replies were given and your exact question is asked on this list at least every month! I'll keep my temper. It's just due to the periodic boundary conditions, nothing wrong, you can use trjconv with option -pbc nojump afterwards or you can set comm_mode to linear with the protein as comm_group. Now please read the manual on periodic boundary conditions and for further reference search the mail list (e.g. periodic boundary conditions, PBC, jumping, etc...) TsjerkOn 5/10/06, Marcelo Fabricio Masman [EMAIL PROTECTED] wrote: Hello gmx users: I am running a very common MD simulation andthe protein system is getting OUT of the box after approximately 200 ps. I have tried several things. Does it happen very frequently? (common mistake) Is there any way to keep, during the whole calculation, the protein system into the center of the box? What could I do for avoiding this phenomenon? Thanks in advance. Marcelo ___gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, M.Sc.Groningen Biomolecular Sciences and Biotechnology Institute (GBB)Dept. of Biophysical ChemistryUniversity of Groningen Nijenborgh 49747AG Groningen, The Netherlands+31 50 363 4336 ___ 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] Getting out of the box!!!
Thank you very much foryour recommendations, Tsjerk. Marcelo On 5/10/06, Tsjerk Wassenaar [EMAIL PROTECTED] wrote: Marcelo,Have you considered reading the FAQ, searching the mailing list, reading the manual or just paying attention? Just yesterday there was mention of a ligand jumping out of the box, to which several replies were given and your exact question is asked on this list at least every month! I'll keep my temper. It's just due to the periodic boundary conditions, nothing wrong, you can use trjconv with option -pbc nojump afterwards or you can set comm_mode to linear with the protein as comm_group. Now please read the manual on periodic boundary conditions and for further reference search the mail list ( e.g. periodic boundary conditions, PBC, jumping, etc...)Tsjerk On 5/10/06, Marcelo Fabricio Masman [EMAIL PROTECTED] wrote: Hello gmx users: I am running a very common MD simulation andthe protein system is getting OUT of the box after approximately 200 ps. I have tried several things. Does it happen very frequently? (common mistake) Is there any way to keep, during the whole calculation, the protein system into the center of the box? What could I do for avoiding this phenomenon? Thanks in advance. Marcelo___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 -- Tsjerk A. Wassenaar, M.Sc.Groningen Biomolecular Sciences and Biotechnology Institute (GBB)Dept. of Biophysical ChemistryUniversity of Groningen Nijenborgh 49747AG Groningen, The Netherlands+31 50 363 4336___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
Re: [gmx-users] Getting out of the box!!!
Tsjerk Wassenaar wrote: Marcelo, Have you considered reading the FAQ, searching the mailing list, reading the manual or just paying attention? Just yesterday there was mention of a ligand jumping out of the box, to which several replies were given and your exact question is asked on this list at least every month! Well, it is just possible Marcelo is new, Tsjerk... :-) I do echo your frustration from time to time that people don't display much initiative in solving their own problems, even to the point of not reading readily-available material in the manual. In general I'm happy to help someone, but I'm much happier to do so if I get the impression they're working actively to solve the problem, rather than doing an imitation of a sponge... after all, I'm giving up *my* time to help with someone else's problem that is of no consequence to me... Mark ___ 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
