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

David spoel at xray.bmc.uu.se
Sun Aug 17 11:40:01 CEST 2003

On Fri, 2003-08-15 at 17:32, Nuno R. L. Ferreira wrote:
> 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.
epsilon_r should be different from 1 only when using a reaction field.

> 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.
It corrects for the fact that you have a cut-off of LJ, since the LJ at
long range is always attractive. For SPC water with a cut-off of 0.9 nm
the pressure contribution is -200 bar. Energy is a constant term and not
so important.

> 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?
Doesn't g_velacc do that for you? Otherwise check some textbook like
Allen & Tildesley (that never hurts!)

> 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?
PME is preferred... Ions depends on system size etc., but if your system
is large enough (more than a few thousand waters) I'd recommend adding

> Thank you,
> Nuno
> #######
> 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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Groeten, David.
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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