From: MIke S (vmd.namd_at_gmail.com)
Date: Fri Oct 24 2008 - 16:26:02 CDT
Thank you for your assistance. I've determined that the best approach for
my system is to use a large cutoff value. I'm using a cutoff value of 2000
which should suffice since my protein stretched out is shorter than 2000
angstroms. I've managed to successfully run simulations with this cutoff
and the protein undergoes unfolding as expected. So far, our calculations
correspond fairly well with our experimental results (which are based on ion
mobility experiments where the temperature of the ions is similar to the
buffer gas temperature and the electric field is considered to be low).
Thank you for pointing out the discrepancy in the force field parameters for
solvent- vs. vacuum-based simulations. It is something that I overlooked.
All the best,
On Thu, Oct 16, 2008 at 11:08 AM, Axel Kohlmeyer <
> On Thu, 16 Oct 2008, MIke S wrote:
> MS> Hello,
> MS> I'm simulating a protein in vacuo. The results from the MD simulation
> MS> be compared with my mass spectrometry data. I would like to compute
> MS> electrostatics for the protein so I can accurately simulate the
> unfolding of
> MS> the protein at different charge states. As I understand, full
> MS> electrostatics can be implemented using PME, however this requires a
> if you want the interactions in vacuo and _no_ interactions
> between periodic images, then you must _not_ use PME. a plain
> cutoff of half the box size with a sufficiently large box
> should do the trick. how accurate that would finally be,
> is to some degree a matter of opinion. an interesting question
> for examples is: what is the temperature of the molecules/fragments
> that you detect in your mass spectrometer? ...and they are passing
> through an electric field gradient at high speed, right?
> MS> periodic boundary condition. Since I'm working without a solvent and I
> MS> don't want to apply an external restraining force is it still possible
> MS> calculate full electrostatic interactions in some other way? If not,
> MS> thinking of using a large cutoff value, but I don't know how large I
> MS> make it and whether or not this is even accurate. Wouldn't a large
> MS> value affect the accuracy of the van der Waals calculations (since
> these are
> MS> short-range interactions)? Also, I've noticed that there is a certain
> van der Waals interactions decay much faster than coulomb (r^-6
> !!) so the error will be small. moreover, unless you are using
> a special force field parameterized for simulations in vacuo, you'll
> be having a much larger error from the fact that your force field
> will include a mean-field type polarization from water molecules
> that you don't have in your setup.
> MS> limit to the cutoff value that I can use. Beyond this value I get a
> MS> error message in my simulation.
> for efficiency reasons, NAMD makes certain assumptions about how it
> can partition the amount of work and what kind of simulations you
> want to do. whenever you try a very unusual setup, you may run into
> limitations due to these assumptions.
> MS> My plan for now is to use the following parameters to evaluate the
> MS> non-bonded interactions:
> MS> cutoff 12
> MS> switching on
> MS> switchdist 10
> MS> pairlist 13.5
> MS> nonbondedFreq 1
> MS> fullElectFrequency 1
> MS> With my current knowledge of NAMD this is the logic I'm using: To
> MS> van der Waals interactions accurately I will use a short cutoff value
> with a
> MS> switching function to smooth out the van der Waals potential energy.
> MS> the fullElectFrequency parameter full electrostatics will be calculated
> MS> atom pairs beyond the cutoff of 12 angstroms. The configuration file
> MS> not include anything related to PME. So, I'm assuming that by invoking
> MS> fullElectFrequency parameter NAMD will automatically evalute full
> MS> electrostatic interactions.
> MS> Do you think this would work?
> MS> Your suggestions will be more than helpful.
> MS> Mike
> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> Center for Molecular Modeling -- University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> If you make something idiot-proof, the universe creates a better idiot.
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