RE: [gmx-users] position restraints with npt ensemble
It will be problematic, so I think it would be better to do NVT simulations. Gromacs 4.0 will support scaling of position restraints coodinates in two different ways: all coordinates or only the center of mass. If you really need it you can try to use the current CVS version, but there all still things being changed and there might be bugs. Berk. From: "Zhou Bo" <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: Subject: [gmx-users] position restraints with npt ensemble Date: Thu, 20 Dec 2007 21:21:49 +0800 Hi gmx-users, I want to restrain some atoms of a certain protein in water for production, but I am not sure whether it makes sense to make NPT simulations with position restraints. I mean if the coordinates of the restrained atoms are not scaled, it would be problematic in pressure coupling. 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 _ Talk with your online friends with Messenger http://www.join.msn.com/messenger/overview ___ 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] position restraints with npt ensemble
Hi gmx-users, I want to restrain some atoms of a certain protein in water for production, but I am not sure whether it makes sense to make NPT simulations with position restraints. I mean if the coordinates of the restrained atoms are not scaled, it would be problematic in pressure coupling. 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] g_hbond (Version 3.3 vs Version 3.14)
Anil Kumar wrote: Dear David, Thanks for your concern. i am using g_hbond (After vacuum md, just for one step) Command with options is g_hbond -f *.pdb -s *.tpr -num *_num.xvg -hx *_hbhelix.xvg and when i compare the result of v 3.3.1 and v 3.14, i found there is difference in *_hbhelix.xvg. Even for standard helix PDB of octa-alanine capped with ACE and NAC, v 3.3.1 is giving hydrogen bonds under n-n (Value is 3), n-n+1 (Value is 3) and rest is showing zero value. While on contrary v 3.1.4 is giving the correct answer with the value of 6 under the n-n+4. So, am i doing something wrong or is it bug in v 3.3.1! Probably a bug. Please submit a bugzilla. thanks in advance, With Regards anil ANIL KUMAR(Research Scholar), Bio-Organic Lab No-336(2nd Floor), Dept. of Chemistry,I.I.T.Bombay,Powai, Mumbai-400076, Ph. No.-022-25764780(Lab) - Residence:- Hostel#1,Room#297,IIT Bombay,Powai, Mumbai-400076,Ph.No.:-+91-9819638547 (Mobile) - Web:http://chemanil.googlepages.com/ -- "Education is a progressive discovery of our ignorance" - Will Durant ___ 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 -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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] g_hbond (Version 3.3 vs Version 3.14)
Dear David, Thanks for your concern. i am using g_hbond (After vacuum md, just for one step) Command with options is g_hbond -f *.pdb -s *.tpr -num *_num.xvg -hx *_hbhelix.xvg and when i compare the result of v 3.3.1 and v 3.14, i found there is difference in *_hbhelix.xvg. Even for standard helix PDB of octa-alanine capped with ACE and NAC, v 3.3.1 is giving hydrogen bonds under n-n (Value is 3), n-n+1 (Value is 3) and rest is showing zero value. While on contrary v 3.1.4 is giving the correct answer with the value of 6 under the n-n+4. So, am i doing something wrong or is it bug in v 3.3.1! thanks in advance, With Regards anil ANIL KUMAR(Research Scholar), Bio-Organic Lab No-336(2nd Floor), Dept. of Chemistry,I.I.T.Bombay,Powai, Mumbai-400076, Ph. No.-022-25764780(Lab) - Residence:- Hostel#1,Room#297,IIT Bombay,Powai, Mumbai-400076,Ph.No.:-+91-9819638547 (Mobile) - Web:http://chemanil.googlepages.com/ -- "Education is a progressive discovery of our ignorance" - Will Durant ___ 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
