Re: [gmx-users] intermolecular distance restraint
warren deng wrote: Hi Gromacs users, In my simulation, I need to restrain distances between atoms on two protein molecules. But the Gromacs manual on NOE seems to imply that the atom indices belong to the same molecule type. So I am wondering whether it is possible to create distance restraint between two molecule types in Gromacs? Indeed. You will need to create a moleculetype that contains both/all the molecules of interest. Note that atom numbers within a moleculetype must be unique. Mark ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] intermolecular distance restraint
Thank you Mark. The problem is, in order to use the couple-moltype option for decoupling, I want to keep the two proteins in separate moleculetype(s). Now I noted that Gromacs has a pull option for doing umbrella sampling, but I don't know how it might be used to apply distance restraint between two atoms belonging to two molecules. Any susggestions on how the pull code can be utilized is very much appreciated! Warren On Tue, Apr 14, 2009 at 2:14 PM, Mark Abraham mark.abra...@anu.edu.auwrote: warren deng wrote: Hi Gromacs users, In my simulation, I need to restrain distances between atoms on two protein molecules. But the Gromacs manual on NOE seems to imply that the atom indices belong to the same molecule type. So I am wondering whether it is possible to create distance restraint between two molecule types in Gromacs? Indeed. You will need to create a moleculetype that contains both/all the molecules of interest. Note that atom numbers within a moleculetype must be unique. Mark ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. 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 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] intermolecular distance restraint
Hi Warren, if you want to use distance restraints, the two proteins must be in the same gromacs molecule. AFAIK, it is impossible to use distance restraints between atoms of different molecules. Altermatively, you may want to consider bonds of type 6 (not subject to lincs). pdb2gmx -merge is useful to create the topology of a molecule that actually contains 2 proteins. If the two proteins must be in different gromacs molecules, you would have to use the pull code. Best, Jochen warren deng wrote: Hi Gromacs users, In my simulation, I need to restrain distances between atoms on two protein molecules. But the Gromacs manual on NOE seems to imply that the atom indices belong to the same molecule type. So I am wondering whether it is possible to create distance restraint between two molecule types in Gromacs? Many thanks, Warren ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312 ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] intermolecular distance restraint
Hi Jochen, Thanks a lot for the information, I appreciate. I will merge the two proteins into a single moleculetype and apply the distance restraint, as you suggested. Although I could try use the pull code, I am not sure if they interfere with free energ (lambda) code which I am also using. With best wishes, Warren On Tue, Apr 14, 2009 at 6:59 PM, Jochen Hub j...@gwdg.de wrote: Hi Warren, if you want to use distance restraints, the two proteins must be in the same gromacs molecule. AFAIK, it is impossible to use distance restraints between atoms of different molecules. Altermatively, you may want to consider bonds of type 6 (not subject to lincs). pdb2gmx -merge is useful to create the topology of a molecule that actually contains 2 proteins. If the two proteins must be in different gromacs molecules, you would have to use the pull code. Best, Jochen warren deng wrote: Hi Gromacs users, In my simulation, I need to restrain distances between atoms on two protein molecules. But the Gromacs manual on NOE seems to imply that the atom indices belong to the same molecule type. So I am wondering whether it is possible to create distance restraint between two molecule types in Gromacs? Many thanks, Warren ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312 ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. 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 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] intermolecular distance restraint
Hi Gromacs users, In my simulation, I need to restrain distances between atoms on two protein molecules. But the Gromacs manual on NOE seems to imply that the atom indices belong to the same molecule type. So I am wondering whether it is possible to create distance restraint between two molecule types in Gromacs? Many thanks, Warren ___ gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
