[gmx-developers] More about the Ekin issue.

[Xavier Periole]

Berk Hess wrote:

>
>>
>> Ok, I sorted out the problems.
>>
>> 1) for the small system, the reaction-field was actually gone from 
>> the mdp file
>> I used to run gmx33b. Using the tpr from gmx3.1 gives a difference of 
>> Epot
>> but this time it is what one would expect from the difference of T.
>> 2) for the big system the RF for excluded atoms was responsible. 
>> Again using
>> the tpr from gmx3.1 give a difference but expected from the 
>> difference in T.
>>
>> I'd like to get more detail about this RF correction that is included 
>> (or excluded)
>> in gmx33. could you be more precise ?
>
>
> See the CVS manual and the CVS mdp_opt.html
>
where can I find the CVS Manual ?

> BTW the CVS code also includes nice REMD code (in which I will fix the 
> NPT part today).
>
I know about this version... and actually tried it. But I am used to 
another one where I can
manipulate everything very easily !! Next project probably ... where 
would I find the analysis
tools of REMD ??

Best
XAvier

> Berk.
>
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-- 
----------------------------------
 Xavier Periole - Ph.D.

 Dept. of Biophysical Chemistry / MD Group   
 Univ. of Groningen
 Nijenborgh 4
 9747 AG Groningen
 The Netherlands
 
 Tel: +31-503634329
 Fax: +31-503634800
 email: x.periole at rug.nl
 web-page: http://md.chem.rug.nl/~periole
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