[gmx-developers] More about the Ekin issue.

[Xavier Periole]

David wrote:

>On Mon, 2005-08-15 at 18:17 +0200, Xavier Periole wrote:
>  
>
>>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 ?
>>    
>>
>
>cvs co manual
>
>  
>
got the error :
make: *** No rule to make target `programs.txt', needed by 
`proglist.tex'.  Stop.

>>>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 ??
>>    
>>
>
>What in particular are you thinking of? There is a new energy landscape
>tool (g_sham) and we are working on a trajectory demultiplexing tool.
>  
>
I think that the demultiplexing tool that I'd like ... I guess that 
would give you the
trajectory through the temperatures !!

>  
>
>>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
----------------------------------