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 <[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 :(.
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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.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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