On 6/8/12 11:04 AM, Turgay Cakmak wrote:
Hi all,
I have 2 questions related to the electrostatic energy of the system..
1) Is *total electrostatic energy* equal to *Coulomb-(SR)* + *Coul.-recip*. OR
*Coulomb-14* + *Coulomb-(SR)* + *Coul.-recip*. I am so confused.
The total electrostatic energy is the sum of all Coulombic components. Whether
that is relevant is up to you.
I specified in my .mdp file;
coulombtype = PME
rvdw = 1.0
rlist = 1.0
rcoulomb = 1.0
fourierspacing = 0.16
pme_order = 4
ewald_rtol = 1e-5
2) I want to calculate electrostatic interaction energy between 2 residues in my
system which has 10 peptides in total. But I think, I should have specified the
energy groups composed of that 2 residues in my mdp file before starting the
simulation. So in this case, is there any way to get this interaction energy OR
can I just calculate the electrostatic energy of the whole system?
Yes, to get an energy decomposition between two residues you need to specify
appropriate energygrps. You can create a new .tpr file and back-calculate these
quantities using the mdrun -rerun feature. Be aware though, that the PME
reciprocal term cannot be (easily) decomposed and the best you can do is
calculate short-range nonbonded energies between your chosen groups. Whether or
not that is useful is something you must demonstrate.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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