[gmx-users] Regarding polymer equillibration (pressure changes)
David van der Spoel
spoel at xray.bmc.uu.se
Mon Jul 16 17:24:12 CEST 2007
Jeroen van Bemmelen wrote:
> Hi Ann,
>> So my first question is
>> wether this can be possible or not? or am I doing something wrong?
>> if so, then how can i rectify the same error?
> I think you should definitely use 'editconf -density' to rescale your
> simulation box to the right density. editconf automatically rescales
> the box vectors AND the coordinates, so you won't have the problem of
> atom coordinates suddenly being larger than the box vectors.
> But anyhow it seems a bit weird to me that you're coordinates are so
> much larger than your box vectors (4.3 versus 3.4 nm). Perhaps this
> is related to the long molecule chains in combination with pbc? I'm
> not sure, maybe one of the developers can comment on this.
How long are your chains? If more than 0.9 nm then this can happen.
>> I think the fluctuations are okay and admittable.but the change in pressure
>> averages make me confused.
>> If I am right, at equillibrium all the observables (temp, pressure, density)
>> should average around a steady value with some fluctuations. but the change
>> in averages (pressure) makes me confused. I have read from literature that
>> the equillibriation of polymers is comparitively diffcult.
> Fluctuations in the average pressure do not necessarily mean there's
> a equilibration problem, depending on the time it takes for the
> average pressure to converge for your system. Simply a matter of
> Since the pressure is always fluctuating enormously and converging
> slowly compared to other observables, I don't think that (only)
> checking the average pressure is a good way of determining whether a
> system is equilibrated or not. Of course, a drift in the average
> pressure could mean that your system is not equilibrated. But in that
> case you'd probably also see a significantly large drift in other
> observables, especially the potential energy and partial potential
> energy terms in your case.
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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://folding.bmc.uu.se
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