[gmx-users] Different temperature

[Andrea Carotti]

Dear Prof. van der Spoel,
I'm trying to use this parameters 
nstlist             =  10
ns_type             =  grid
rlist               =  0.8
coulombtype         =  cut-off
rcoulomb            =  1.2
rvdw                =  1.2
Do you think that I should change something?
Thnaks a lot
Andrea 
----- 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:
>> 
>>> Hi,
>>> 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 by
>>> 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.
> 
>> 
>> Mark
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> 
> 
> -- 
> David.
> ________________________________________________________________________
> 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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