From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Aug 16 2011 - 08:43:00 CDT
On Tue, Aug 16, 2011 at 9:38 AM, Anna James <annajamesmatrix_at_hotmail.com> wrote:
> Hello NAMD Experts
> I have a query about setting up a PBC unit.Unfortunately I am working with a
> large Globular Protein,the extent of which is around 90A in all the three
> X,Y Z axes that would mean My PBC Unit has to be larger than it to encompass
> the whole protein. I Created a Methanol Box of 100*100*100 A and filled it
> up with Methanol molecules as the per the density of Methanol .The number of
> Molecules exceeded 35000 and VMD/PSFGEN cannot process PDBs that have
> residues more than 9999.
just use multiple segments (and multiple files). the numbers
can start fresh for each segment.
> I am sure lot of people would have worked with PBC units as large as 90A
> ,What is the way to go about solvating them ?Do we have to compromise on the
> number of Methanol Molecules while setting up the system?
> I am using the following parameters :
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 12.0
> switching on
> switchdist 10.0
> pairlistdist 14.0
> timestep 2.0
> rigidBonds all
> nonbondedFreq 1 .
> Looking at the above parameters, What would be the safe distance between the
> images while setting up PBC units?
> Are the above parameters good enough ?
> In anticipation of an encouraging reply
> Anna James Vaughan
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 Institute for Computational Molecular Science Temple University, Philadelphia PA, USA.
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