[gmx-users] rerun problem

[Maira d'Alessandro]

yes, the parameters in the mdp are exactly the same except for the changes I 
reported in my first mail.
other suggestions?

-- 
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 David van der Spoel <spoel at xray.bmc.uu.se>:

> 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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