[gmx-users] Different temperature

[David van der Spoel]

Andrea Carotti wrote:
> 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?

Depends on force field. The GROMOS force field is optimized with 0.8/1.4 
cut-offs and nstlist = 5.
We always use PME for Coulomb and 0.9/1.4 for VDW, with nstlis =5 and 
dispcorr = enerpres.

> 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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> 
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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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++