[gmx-users] essential dynamics

Isabella Daidone i.daidone at caspur.it
Fri Sep 24 14:56:12 CEST 2004


Sorry if I'm not right,
but using g_covar with the option -ref should provide what smith is 
asking for.
Is it correct?

Ciao
Isabella

On Fri, 24 Sep 2004, David van der Spoel wrote:

> On Fri, 2004-09-24 at 14:12, smith wrote:
>>   dear users,
>>
>>
>>
>>
>>
>>
>>
>> Can essential dynamcis be perfomed in gromacs chosing the reference as starting structure rather than average one.
>>
> Not really, since the covariance analysis actually analyzes the variance
> around the average. What you may want to do is to look at the 2d
> projection plots and project the starting structure on it as well, such
> that you can see whether or not you are sampling close to the starting
> structure.
>> thanks for any help
>>
>> smith
>>
>> ______________________________________________________________________
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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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