[gmx-users] rerun problem

[David van der Spoel]

On Thu, 2003-11-06 at 14:52, Maira d'Alessandro wrote:
> thank you for your suggestion. 
> effectively in my first rerun I had nslist =5, but also with nslist=1 the 
> LJ(SR) still have problems even if the other quantities are now in very good 
> agreement.  
> I report below the all results for the same step 
>  
>                                                 *******   
>                 LJ(14)      Coulomb             LJ(SR)       Coulomb(SR)      
> original       1270.223417  18564.769168      59726.646291  -479536.291776   
>                Coulomb(LR)      Potential 
>                -100714.158182  -488448.307707 
> rerun nslit=5  1269.997266  18562.972545      72114.672713  -479429.595416  
>               -100698.935290  -475957.803363 
> rerun nslit=1  1270.230418  18564.756291      72109.127365  -479536.522266  
>               -100714.149281  -476102.205264 
>  
> do you have some other suggestion? 
yes do a gmxcheck -s1 old.tpr -s2 new.tpr | less

and see if the parameters are the same
> My best regards 
> maira 
>  
> --  
> Maira D'Alessandro    
> e-mail : m.dalessandro at caspur.it   
>    
> Post-Doc researcher    
> University of Rome "Tor Vergata"     
> Dep. of Chemical Science and Technology   
> Viale della Ricerca Scientifica, 00133 Roma    
> tel 0039(0)672594905 
>  
> 
> Scrive Anton Feenstra <feenstra at chem.vu.nl>: 
>  
> > Maira d'Alessandro wrote: 
> > > As you can see the big problem is in the LJ(SR) rerun which is 
> > overestimated. 
> > > Do you think that the other quantities are in sufficient agreement or 
> there 
> > is 
> > > some problem also in them? 
> >  
> > Could the source of these differences be in the neigborlist search? 
> > For rerun, this needs to be done every step and IIRC, there was a specific 
> > check for that in the code of mdrun (when I wrote it initially). You could 
> > check it easily by setting nstlist=1 in the .mdp for the rerun. 
> >  
> >  
> > --  
> > Groetjes, 
> >  
> > Anton 
> >   _____________ _______________________________________________________ 
> > |             |                                                       | 
> > |  _   _  ___,| K. Anton Feenstra                                     | 
> > | / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam | 
> > |(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   | 
> > | \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           | 
> > |             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       | 
> > |             | "If You See Me Getting High, Knock Me Down"           | 
> > |             | (Red Hot Chili Peppers)                               | 
> > |_____________|_______________________________________________________| 
> >  
> >  
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. 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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