[gmx-users] Re: compressing the system
vvchaban at gmail.com
Sun Aug 1 20:52:23 CEST 2010
> Moeed wrote:
>> My efforts for compressing a polymer chain all failed. Even when I am
>> compresing very slowly with tau-p=10 and ref_p of 1 bar simulation
>> crashes when box size is close to chain size.. I tried different
>> pressures of 1 10 30 and tau_p of 1 2 5 10 and cobination of these...Has
>> anyone idea on suitable parameters ?
>> ; Pressure coupling
>> Pcoupl = Parrinello-Rahman
>> Pcoupltype = semiisotropic
>> tau_p = 1 1
>> compressibility = 4.5e-5 4.5e-5 ;
>> ref_p = 1.0 1.0
> I have no real experience with polymers, but these settings bring several
> questions to my mind:
> 1. Why are you using Parrinello-Rahman for a system that is not yet
> equilibrated? The fluctuations in pressure for such a system could be huge.
> 2. Why are you using semi-isotropic pressure coupling? This setting is more
> suited to interfacial or membrane systems. For a box of PE, which should end up
> likely as an entangled systems eventually, what purpose does it serve? I would
> think isotropic coupling would be more appropriate.
> Please also remind me (and everyone on the list) what's in your system? You've
> been asking essentially the same question for what seems like weeks and I can't
> exactly remember the details. Was it 8 linear PE molecules in a rectangular
> configuration? If so, what makes you think that such an arbitrary configuration
> will even result in a reasonable system? The problem is the linearity, I would
> assume. The box is collapsing in before the chains can re-orient themselves in
> any way. I would think you could generate a far better starting structure by:
> 1. Simulating a single PE chain under NVT conditions (in a large box) such that
> the chain can re-orient and collapse on itself somewhat.
> 2. Constructing a new system from this collapsed molecule, and then worry about
> how to get a reasonable density.
Actually, the only problem is that Moeed does not want to do what is
suggested to him. More than a week ago I compressed his system
personally and sent him input and output configurations along with all
run parameters and topologies. Everything works.
The starting configuration is OK and it is well compressed during 1
ns. The pressure coupling can also be anisotropic in order to account
for the anisotropic shape of the polymer chains. The pressure
fluctuations will be certainly huge but the task is just to compress
I suspect that Moeed tries to make the system as small as possible and
it often leads to the situation when CUTOFF is less than LBOX/2. The
barostat is not guilty.
Dr. Vitaly Chaban
More information about the gromacs.org_gmx-users