Thankyou - a few hundred ps was quite doable. Temperature is (fortunately!) consistent between groups to well within a couple of degrees, which is probably fine, but I just want to check that the temperatures from groups in g_traj are directly comparable with each other? They're not the same as the ref_t which is consistent with g_energy, which is fine as I gather temperatures with g_traj are inherently out due to ignoring constraints; I'm assuming, though, that the different constraints from the molecules being different don't make the errors different... if you see what I mean? i.e. that the error due to not accounting for constraints is constant.
Alan. ----- Original Message ---- From: David van der Spoel <[EMAIL PROTECTED]> To: Discussion list for GROMACS users <[email protected]> Sent: Tuesday, January 29, 2008 9:45:01 PM Subject: Re: [gmx-users] Temperature without trr Alan Dodd wrote: > Gromacs users, > I want to look at the temperature difference between groups, to check whether > temperature coupling is working ok (specifically if the lipid is at the same > temperature as the water). > Unfortunately, I've rather foolishly deleted all my trrs due to a lack of > space, thinking xtc/edr would be all I needed. While I can get the *system* > temperature from g_energy, it doesn't take an index file, and g_traj needs > velocities (which I don't have any more). Anyone know of a way around this, > short of continuing the simulations and taking the .trr from that? > > Alan. If g_energy does only give you the system T it means you have not used T-coupling groups and hence your Temperatures will differ between lipid and water. Best way to know is to continue the simulation for few hundred ps and don't delete the trr :(. > > > > ____________________________________________________________________________________ > Looking for last minute shopping deals? > Find them fast with Yahoo! Search. > http://tools.search.yahoo.com/newsearch/category.php?category=shopping > _______________________________________________ > gmx-users mailing list [email protected] > 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 list [email protected] 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 ____________________________________________________________________________________ Looking for last minute shopping deals? Find them fast with Yahoo! Search. http://tools.search.yahoo.com/newsearch/category.php?category=shopping _______________________________________________ gmx-users mailing list [email protected] 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
