[gmx-users] Temperature without trr

David van der Spoel spoel at xray.bmc.uu.se
Wed Jan 30 19:38:17 CET 2008

Alan Dodd wrote:
> 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.

Not sure. Water has six degrees of freedom per molecule, your lipids may 
have more or less (relative) so you will have to add the numbers up 
until you reproduce the system T in your energy file.

> ----- Original Message ----
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> 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    gmx-users at 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-request at gromacs.org.
>> 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.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

More information about the gromacs.org_gmx-users mailing list