From: Anna James (annajamesmatrix_at_hotmail.com)
Date: Tue Aug 16 2011 - 08:38:14 CDT
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.
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
Leeds
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:57:35 CST