[gmx-users] POPC number
Hi gmx-users, whats the number of POPC molecules should be there after inserting protein into popc? In my case 90 popc molecules are there around the protein from 128 molecues which I downloaded from Dr.Tielman's website. Any suggestion will be appreciated Thanks in advance. ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] POPC number
I guess that depends on the size of your protein. You should have enough lipds such that the protein doesn't interact with its preriodic image. 90 POPC seem to be a bit to few for that. In my aquaporin simulations, I usually had something like 270 POPE molecules, but if you simulate a smaller protein, less lipids may be sufficient. You may also want to use a hexagonal box which will allow you have less lipids and water. cheers, jochen sudheer babu wrote: Hi gmx-users, whats the number of POPC molecules should be there after inserting protein into popc? In my case 90 popc molecules are there around the protein from 128 molecues which I downloaded from Dr.Tielman's website. Any suggestion will be appreciated Thanks in advance. ___ 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 [EMAIL PROTECTED] 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] POPC number
I guess that depends on the size of your protein. You should have enough lipds such that the protein doesn't interact with its preriodic image. 90 POPC seem to be a bit to few for that. In my aquaporin simulations, I usually had something like 270 POPE molecules, but if you simulate a smaller protein, less lipids may be sufficient. You may also want to use a hexagonal box which will allow you have less lipids and water. A hexagonal box? Great. How does one go about constructing that? Is this a cylinder-like box with hexagonal shape or just a triclinic one? In the triclinic case, does the PBC membrane turn out as it should? Thanks, Chris. ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] POPC number
[EMAIL PROTECTED] wrote: I guess that depends on the size of your protein. You should have enough lipds such that the protein doesn't interact with its preriodic image. 90 POPC seem to be a bit to few for that. In my aquaporin simulations, I usually had something like 270 POPE molecules, but if you simulate a smaller protein, less lipids may be sufficient. You may also want to use a hexagonal box which will allow you have less lipids and water. A hexagonal box? Great. How does one go about constructing that? Is this a cylinder-like box with hexagonal shape or just a triclinic one? In the triclinic case, does the PBC membrane turn out as it should? Hey Chris, a hexagonal box is a special case of a triclinic one: Here we go: echo CRYST1 90.0 90.0 40.00 90.00 90.00 60.0 P 1 1 x.pdb genbox -cp x.pdb -cs tip4p -o filled.pdb echo 0|trjconv -f filled.pdb -o compact.pdb -ur compact -s filled.pdb pymol compact.pdb Have fun, Jochen Thanks, Chris. ___ 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 thewww interface or send it to [EMAIL PROTECTED] 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] POPC number
[EMAIL PROTECTED] wrote: I guess that depends on the size of your protein. You should have enough lipds such that the protein doesn't interact with its preriodic image. 90 POPC seem to be a bit to few for that. In my aquaporin simulations, I usually had something like 270 POPE molecules, but if you simulate a smaller protein, less lipids may be sufficient. You may also want to use a hexagonal box which will allow you have less lipids and water. A hexagonal box? Great. How does one go about constructing that? Is this a cylinder-like box with hexagonal shape or just a triclinic one? In the triclinic case, does the PBC membrane turn out as it should? And yes, the PBCs work just fine, as expected from any triclinic box. cheer, jochen Thanks, Chris. ___ 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 thewww interface or send it to [EMAIL PROTECTED] 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
