[gmx-users] basic question for a MD run

David spoel at xray.bmc.uu.se
Fri Aug 8 23:17:00 CEST 2003

On Fri, 2003-08-08 at 09:36, jean-marc vuissoz wrote:
> hello,
> here are some basic question :
> a) when I put periodic conditions, does I have to have a neutral charge 
> for my system (ie probably putting some ion in the system) ? is there a 
> easy way to check the charge of your system once you have it ?
grompp will tell you when it's not neutral

> b) I try to equilibrate a system ( a protein with a ligan (also 
> protein) in a water box), what type of pressure condition should I put, 
> I try with berendsen but after 1.4ns I get an rmsd of the Calpha which 
> is between 0.5-0.6 nm (not very good for an equilibration )
Unless you have a multidomain protein that is too much. If you do have a
multidomain protein you may want to check the RMSD for the individual

Pressure coupling at ambient pressure (1 bar) with tau_p = 1-5 ps and
compressibility on the order of 5e-5 should work. You may also start
with position restraints, see tutorial

> best thanks
> vuissoz jean-marc
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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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