[gmx-users] Energy minimizations with gmx3.2

David spoel at xray.bmc.uu.se
Fri May 21 19:03:26 CEST 2004

On Fri, 2004-05-21 at 16:45, Alan Wilter Sousa da Silva wrote:
> So, would not better use
> nstlist             =  5 ;(for G96, instead of 10) ?
> Am I right dear Dr. van der Spoel?

that's correct for md sims, for energy min. it has no effect.
> BTW, I still cannot understand such change in -DFLEXIBLE, but fine, I 
> follow this beleiving it's just a sintaxe change.
this is just some lines in the different water topologies that make
somewhat more sense. For instance tip4p is not spc therefore flex_spc
seemed an unsuitable name. Please go ahead and check the files: spc.itp
flexspc.itp tip3p.itp and so on in the library, to convince yourself
that it is not a syntax change and not black magic either...

> And I cannot figure out why dt parameter could have any influence in EM.
> Sometimes I think I'll never finish my articles if I have to rerun my 
> all simulations again. :-)
No worries. I do it all the time...

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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