[gmx-users] Re: Am I wrong ?

David spoel at xray.bmc.uu.se
Sun Dec 1 15:28:09 CET 2002

On Sun, 2002-12-01 at 13:31, Nicolas Michel wrote:
> >>......
> Hello, thank for your rapid answer.
> >Most of it sounds OK, only you will have to verify somehow (e.g. testing
> energy and density) that the charges can be used with the standard
> Lennar Jones parameters.
> Do you mean using g_density and g_energy? I tried to monitor the density (mass density - because I don't have any electrons.dat... by the way, do you think I can use Gamess output to edit one?) of my lipid with an ndx file but that's all...
> What should I verify with g_energy (potential, total or other)? With a simple md run (standard em.mdp), steepest descent converged to 100 in 2426 steps and Pot.En. was -1.35871E+05 (Max.Force was 9.94135E+02). Is this correct?
> Thank you.
> N.
> PS: is there somewhere on the web, or in the litterature, a tutorial or paper describing such work in details?
check e.g. 
 D.P. Tieleman, H.J.C. Berendsen. 1996. Molecular dynamics simulations
of fully hydrated DPPC with different macroscopic boundary conditions
and parameters, J. Chem. Phys. 105, pp. 4871-4880
> ----------------------------------------------------
> Nicolas Michel
> Laboratoire de Chimie BioOrganique et des Systemes Moleculaires Vectoriels
> Avignon
> France
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

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