[gmx-users] Re: Am I wrong ?

[Nicolas Michel]

>>......

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?
 
----------------------------------------------------
Nicolas Michel
Laboratoire de Chimie BioOrganique et des Systemes Moleculaires Vectoriels
Avignon
France


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