Re: Full Electrostatic Calculations on Protein in Vacuo

From: Brian Bennion (bennion1_at_llnl.gov)
Date: Thu Oct 16 2008 - 10:19:32 CDT

Hello Mike

if you leave the cutoff at 12 then only those
interactions are going to be counted. The
fullElectFreq 1 just turns off multiple time
stepping algorithms. The VDW will not be
affected by a larger than 12A cutoff. Those
interactions are nearly zero at 10A. However,
without water the electrostatics are going to be
very different and at least one paper has shown
that you need different partial charges that
reflect the lack of water screening in your simulation.

check out

Biochemistry, 46 (4), 933 -945, 2007. 10.1021/bi061182y S0006-2960(06)01182-2
Web Release Date: January 5, 2007
Copyright 2007 American Chemical Society

Protein Structures under Electrospray Conditions

Alexandra Patriksson, Erik Marklund, and David van der Spoel*

Brian

At 12:07 AM 10/16/2008, MIke S wrote:
>Hello,
>
>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.
>
>Mike

Biosciences and Biotechnology Division
CMELS
Lawrence Livermore National Laboratory
Phone: 925-422-5722
Fax: 925-424-4334

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