[gmx-users] Some questions: epsilon_r , DispCorr , g_velacc and PME

[Nuno R. L. Ferreira]

Dear * gmx's

My system is composed of protein + solvent.
Some questions are puzzling me, and for a mind seeking rest, nothing better
than to solve the problems, or ask for help.

1) If I use a solvent different from water, do I have to change the
*epsilon_r* value and why?
    Read something about it in this mail list, saying to not change the
value .
http://www.gromacs.org/pipermail/gmx-users/2002-September/029287.html
    By the way, I'm using PME.

2) Don't understand the dispersion correction concept.  I just know that to
get the correct density at normal pressure I have to enable this feature.

3) I'm starting to work with autocorrelation functions, namely VACF. Can
anibody give me some hints on how to calculate diffusion coefficients from
this?

4) My protein has zero charge, so I didn't added ions to the system.  If I
add ions maintaining the neutrality of the system, will the results be
different? Of course, trying and compare the results is the best way.
Should I use PME when I don't add ions to the system, or there's no problem
with that?


Thank you,
Nuno

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Nuno Ricardo Santos Loureiro da Silva Ferreira
Grupo de Química Biológica
Departamento de Química
Faculdade de Ciências e Tecnologia
Universidade de Coimbra
3004-535 Coimbra
Portugal
www.biolchem.qui.uc.pt
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