Good morning (evening, afternoon, night) to everybody!
I want to make GB calculations as precise as possible without seriously affecting computational time (no more than 70-100% increase).
Probably this doesn't influence the protein structure too much, but anyway I want to test the difference
between the default parameters and parameters more close to the experiment. Let's take some intracellular protein as drug biotarget.
The goal is to get a model for high throughput molecular dynamics with implicit solvent and small molecules bound to the biotarget.
So here is the list of some parameters for which I am not sure what is best to use.
PBTEM=310 K
EPSOUT = 75 // At 37 degrees dielectric constant is used according some table which I've found
http://www.tpub.com/content/ArmyCRREL/SR98_02/SR98_020009.htm
probably near the surface it s different.
EPSIN = 3.0
http://peds.oxfordjournals.org/cgi/reprint/2/3/177
I wonder how important can be the continuous change of dielectic constant from border to the core of the protein.Anyway I think
such constant is more reliable like 3 or 4.
Related to the previous question I think it's reasonable to setup:
SMOOTHOPT = 1
ISTRING = 20 // I can't find anything reasonable on ionic strength there are values of 20mM if concentration of salt is used or I=0,16 for charges calculations
http://pubs.acs.org/doi/pdf/10.1021/ac50031a026
it s 20 mM/L, right?
igb = 7 // it is described as newest model, that eliminates the interstitial regions of high dielectric smaller than a solvent molecule
gbsa = 1 // surface area will be computed using the LCPO model.
NSNBA = 5 // Sets how often atom-based pairlist is generated; As far as 5 is recommended for molecular dynamics in the manual I setup it to 5, but don't understand why default is 1 then.
ntx = 5 // for second run only when rst is used for the coordinates.
gamma_ln = 5.0 // I use the biggest gamma_ln recommended in the manual as far as natural water gamma_ln is about 50 .
tautp=5.0 // In manual it is written: "Generally, values for TAUTP should be in the range of 0.5-5.0 ps, with
a smaller value providing tighter coupling to the heat bath and, thus, faster
heating and a less natural trajectory. Smaller values of TAUTP result in
smaller fluctuations in kinetic energy, but larger fluctuations in the total
energy."
So what does it mean? That I should setup tautp as much as possible within recommended margins, like tautp=5.0?
IG=-1 // as far as I plan want to restart trajectoreis, for the initial trajectory this shouldn't be a problem as well, right?
Should albp=1 PB calculations improve simulation of solvent? As I understand it is required more for non polar solvents, but wha tis about water?
saltcon = 0.15 // is used according this
http://wiki.answers.com/Q/What_concentration_of_salt_is_used_in_an_isotonic_solution
Best regards,
Andrew
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Received on Fri Jan 15 2010 - 07:30:04 PST
