[gmx-users] Regarding polymer equillibration (pressure changes)

Jeroen van Bemmelen J.J.M.vanBemmelen at tnw.tudelft.nl
Mon Jul 16 16:39:29 CEST 2007

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.

> 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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