[gmx-users] Different temperature
and.carotti at farmchim.uniba.it
Fri Dec 23 14:14:56 CET 2005
I have changed some parameters and now I'm having better results, but
the temperature is still larger (3-6 degrees). Now my question is: Is this
value acceptable? Could someone share opinions and experiences?
Thanks to all
----- 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: Thursday, December 22, 2005 8:22 PM
Subject: Re: [gmx-users] Different temperature
> Mark Abraham wrote:
>> Andrea Carotti wrote:
>>> I've followed the procedure of a paper that used gromacs for the MD
>>> simulation on the same target I have (same xray starting structure). I
>>> have followed the lines you mentioned:
>>> 1) energy minimization to relieve bad contacts after solvation, followed
>>> 2) position-restrained NPT simulations
>>> Do you have some suggestions? do I have to change something or this
>>> temperature can be considered acceptable?
>>> In other simulations I have found a good reproducibility of some
>>> published results
>> OK, that might be reasonable. I'd still encourage an NVT stage if nothing
>> else works for you. I would check all of the output of grompp and
>> editconf, etc. very carefully for warnings that you haven't paid
>> attention to. I would not consider this temperature behaviour acceptable,
>> and think it likely that there is something wrong with the way you've set
>> up the system. Perhaps it's too obvious, but have a look at the structure
>> at each stage of the preparation process :-)
> Reduce tau_T to 0.1 and increase tau_p to 1.0. How about cut-offs etc.?
> Heating is mainly a cut-off artifact.
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> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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