Full Electrostatic Calculations on Protein in Vacuo

From: MIke S (vmd.namd_at_gmail.com)
Date: Thu Oct 16 2008 - 02:07:29 CDT


I'm simulating a protein in vacuo. The results from the MD simulation will
be compared with my mass spectrometry data. I would like to compute full
electrostatics for the protein so I can accurately simulate the unfolding of
the protein at different charge states. As I understand, full
electrostatics can be implemented using PME, however this requires a
periodic boundary condition. Since I'm working without a solvent and I
don't want to apply an external restraining force is it still possible to
calculate full electrostatic interactions in some other way? If not, I'm
thinking of using a large cutoff value, but I don't know how large I should
make it and whether or not this is even accurate. Wouldn't a large cutoff
value affect the accuracy of the van der Waals calculations (since these are
short-range interactions)? Also, I've noticed that there is a certain
limit to the cutoff value that I can use. Beyond this value I get a fatal
error message in my simulation.

My plan for now is to use the following parameters to evaluate the
non-bonded interactions:

cutoff 12
switching on
switchdist 10
pairlist 13.5
nonbondedFreq 1
fullElectFrequency 1

With my current knowledge of NAMD this is the logic I'm using: To calculate
van der Waals interactions accurately I will use a short cutoff value with a
switching function to smooth out the van der Waals potential energy. With
the fullElectFrequency parameter full electrostatics will be calculated for
atom pairs beyond the cutoff of 12 angstroms. The configuration file will
not include anything related to PME. So, I'm assuming that by invoking the
fullElectFrequency parameter NAMD will automatically evalute full
electrostatic interactions.

Do you think this would work?

Your suggestions will be more than helpful.


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