abdullah ahmed wrote:
Hello everyone,
I have just started using GROMACS, and apolise if my question is naive.
Basically, I'd like to ask if anyone has some suggestions regarding the
settings I should use for electrostatic interactions?
Well, you haven't shown us what settings you're using or what force field you're
using, so it's impossible to make any specific recommendation. Your cutoffs and
type of long-range electrostatics method will be largely dictated by the force
field you've chosen. The primary literature will tell you a lot.
I have two protein molecules similar in everyway except, one has a
single negative charge inside the molecule, and another has two opposite
charges facing each other. The opposite charges are close enough to form
electrostatic interactions, so would expect the coloumb energy for this
molecule to be less than the other after minimization/molecular
dynamics. However, the results show that they are almost the same.
It's hard to comment on the accuracy of these results without a lot more
information (see above). Other factors include the local geometry of other
surrounding residues; if the structures are different (even subtly) you
certainly can't make any generalizations.
-Justin
Thank you in advance for your help,
Abdullah Ahmed
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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