[gmx-users] box of methanol

[David van der Spoel]

On Mon, 29 Jul 2002, Luca Monticelli wrote:

>Hi David,
>
>I followed your advices, and run a 5ns 
>MD on my methanol boxes with constraints 
>on all bonds and dispersion correction. 
>The good news is that the difference in 
>the density between the cut-offs 0.8/1.4 
>and 0.9/1.4 reduces dramatically, as you 
>predicted; the bad news is that both 
>results get worse: density is now 856 
>and 850, respectively (the error 
Could you elaborate on what cut-offs you use once more:
I would use:
0.9/1.4 for Vanderwaals (combined with dispersion correction)
and
0.9/1.4 for Coulomb, or (better!)
0.9/PME 
Furthermore you want to set nstlist to 5. (and ns_type to 5 for
performance).

>increased from ~1% to 7~8%). No 
>dependence on the box size, in any case, 
>as opposed to what reported by Yiannis 
>using OPLS (but he was using very 
>different cut-offs in his 2 boxes).
>Actually, I couldn't find in van 
>Gunsteren's papers if they used 
>dispersion correction or not, nor any 
>informations about the density they got. 
If they don't state it, they probably haven't used it. However I would be
amazed if they didn't mention the density at all...


Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++