[gmx-users] water box with prescribed volume and density

grivet grivet at cnrs-orleans.fr
Tue Mar 30 16:54:08 CEST 2010

Thank you for your quick and detailed answer.

> First, begin by using the right genbox flags :)  The -nmol flag is for insertion 
> of extra molecules (specified in -ci).  This operation is not what you want.  If 
> you wish to cap the number of solvent molecules, you want the -maxsol option.
> > By the way, I notice that the number of molecules in topol.top is not
> > updated; is that normal ?
> Given your commands, yes.  You are not passing your topology to genbox using -p. 
>   If you do, it will happily update it for you.
I followed your prescriptions with succes. 

> Also understand that the number of water molecules present in the box is 
> dependent upon other species (i.e., solute).  If you are trying to compare 
> results with some other system (with a different solute), the space available 
> for solvent may be different, and really is an irrelevant consideration. 
> Provided you have a reasonable unit cell that does not violate the minimum image 
> convention, and you use the same run parameters, then the comparison should be 
> legitimate.  If you simply wish to run a new simulation from a previous 
> configuration, there is no need to re-build the system; just start a new 
> simulation with different starting velocities.

No, I simply want to simulate a box of water and compare results with
those obained with GROMOS and spc water.

Having cleared the first hurdle, I ran mdrun for steepest descent (5832
molecules). The program stopped after 2067 steps, with maximum force =
1.58E02 on atom 4870. How important is that warning?

Anyway, I started mdrun again for a dynamics run (0.5 fs step, 25 ps
long, temperature and pressure cooupling with Berendsen thermostats).
How can I judge the quality of results ?

The temperature quickly evolved from 300K to the prescribed 270 K and
then fluctuated by 2-3 K. (One would think that velocities are generated
according to the reference temperature, 270K?)

The pressure fluctuated a lot and is -179 at the end of the run; what is
the significance of this result?

The volume and density evolved rather smoothly to reasonable values. I
have two values for the density; according to the .log file, it is
0.9937E03 and according to g_energy, it is 1.015E03; which should I

Can I consider my system to be fully equilibrated? Since the run lasted
50 mn on a signle node, I cans easily extend the equilibration. A last
point is not clear; which file should I start from to extend the
computation: .cpt, .trr, or .xtc?

Thank you again for taking pains with an ignorant user
JP Grivet

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