[gmx-users] Some parameters in the mdp file

[qiwenpeng at sinap.ac.cn]

----- 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: Wednesday, February 08, 2006 8:49 PM
Subject: Re: [gmx-users] Some parameters in the mdp file


> qiwenpeng at sinap.ac.cn wrote:
>> Dear all,
>>  
>> I don't use constraints, so I set constraints : none.
>>  
>> Under this condition the parameter "unconstrained start" can work or not 
>> ? Does it apply constraints on the system in the beginning when it is 
>> set no.
>>  
> this is irrelevant unless you have settles.
You mean if  I use constraints = none, no mater yes or no I set for the "unconstrained start"

There will be no constraints added to the start conformation, right?
> 
>> The second question: what the parameter "domain-decomposition" mean? and 
>> what the function of it?
> this is obsolete but when you use it your simulation will crash.
> 
> 
>>  
>>  
>> Thanks
>>  
>> Best Regards
>>  
>>  
>> 
>> 
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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://folding.bmc.uu.se
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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