[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 
> statistics.
> 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.
> Cheers,
> Jeroen
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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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