[gmx-users] Temperature without trr

[Alan Dodd]

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 <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 :(.
> 
> 
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-- 
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
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