[gmx-users] box of methanol

David van der Spoel spoel at xray.bmc.uu.se
Mon Jul 29 16:23:01 CEST 2002

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)
0.9/1.4 for Coulomb, or (better!)
Furthermore you want to set nstlist to 5. (and ns_type to 5 for

>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

More information about the gromacs.org_gmx-users mailing list