Re: setting solvent density during solvation

From: Cesar Luis Avila (cavila_at_fbqf.unt.edu.ar)
Date: Mon Aug 20 2007 - 15:29:17 CDT

In the simulations I have performed so far, instant pressure always
presents large fluctuations. What you should monitor is the box size
fluctuations. You should get to a constant volume. I don't know how to
properly describe the margin keyword, but I will give it a try. I has
something to do with the partitioning of the total simulation space into
patches. If you expect the volume to change you should give a rather
large margin, for example 5. When your box reaches a constant volume
you can change it to 1 or even 0 if you switch to NVT.
I don't know what might be the relationship between margin and PME that
you mention.
Regards
Cesar

Adam Fraser escribió:
> Thanks Cesar,
> We've been trying to equilibrate in NPT actually by using Nosé-Hoover
> Langevin piston pressure control, but are having trouble. The
> pressure reports throughout the equil vary +/-1000 bar. The average
> pressure is 1bar, but the fluctuations are extremely large and I don't
> know why.
>
> I submitted this question to the group before and received a few
> different suggestions... amongst them was one suggesting to use margin
> 1.0-3.0 because the fluctuations were an artifact of faulty ewald
> summation due to coarse grid size in ewald. I haven't tried this as I
> don't yet understand it completely, but it does make sense because the
> system's energy is also fluctuating strangely.
>
> Any input you might have on this would be great.
>
> Thanks very much,
> Adam
>
> On 8/20/07, *Cesar Luis Avila* < cavila_at_fbqf.unt.edu.ar
> <mailto:cavila_at_fbqf.unt.edu.ar>> wrote:
>
> Dear Adam,
> I think that the solvation box was built with a rather low density to
> avoid getting high VdW forces when building the system. You are
> expected
> to run a few equilibration steps using NPT until you get to the
> desired
> density. Then you can switch to the ensemble you want to use.
> Hope this helps
> Cesar
>
>
> Adam Fraser escribió:
> > I was wondering if there is a way to specify a solvation density of
> > 1.0 (rather than 0.93) using vmd.
> >
> > This is the script I'm currently using in vmd:
> >
> > resetpsf
> > readpsf 2HEX.psf
> > coordpdb 2HEX.pdb
> > resetpsf
> > package require solvate 1.2
> > solvate 2HEX.psf 2HEX.pdb -o 2HEX_solv2 -s WT -b 2.4 -minmax { {-7.5
> > -12.5 -12.5} {47.5 12.5 12.5} }
> >
> > Any help or suggestions would be great. Thanks,
> > Adam
>
>

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