Moeed wrote:
Dear gmx users,
Please kindly help me with the following issues:
I am trying to extract interaction energies (non bonded) between hexane
molecules (vdw and electrostatics). I have used rerun program to exclude
intramolecular non bonded terms and here is the breakdown of energy from
g_energy. However, in the manual I read about dispersion correction and
long range interactions.
Actually, I do not know for a hydrocarbon (hexane) system I should look
at which contributions to get intermolecular interaction energies (long
range, short range, dispersion correction) mainly because I can not
distinguish them even after reding the maual
1- Can you please explain the difference between longe range and short
range interactions. What this breakdown shows for intermolecular
contributions is just short range LJ and coulomb (SR). Is there any
other program (other than g_energy) to list other energy terms?
Long range interactions fall outside the short-range cutoff. You will not have
an explicit "LR" term unless you are using a twin-range cutoff, which presumably
you are not.
Energy Average RMSD Fluct. Drift
Tot-Drift
-------------------------------------------------------------------------------
Angle 4400.09 284.259 237.268 54.2184
542.293
Ryckaert-Bell. 1009.62 124.468 94.0379 28.2417
282.474
LJ-14 648.411 40.6844 39.926 2.70793
27.0848
Coulomb-14 -278.654 34.4227 11.8071 11.1987
112.01
LJ (SR) -3010.16 47.968 42.5388 7.67736
76.789
Coulomb (SR) 74.7846 2.5186 2.47007 0.170417
1.70451
Coul. recip. -78.0436 2.58606 1.54725 -0.717662
-7.17805
Potential 2766.05 454.268 342.141 103.497
1035.18
2- In the manual I see the unit for energy is :KJ/mol but the unit for
heat capacity obtained form g energy is in J/mol K. For this reason, I
doubt the unit of energy in this list. Is it KJ/mol or J/mol?
Energies are kJ/mol. Believe the manual.
3- I am trying to generate the top file for polyethylene chain using the
information from the archive:
http://lists.gromacs.org/pipermail/gmx-users/2009-March/040125.html
What I intend to do is investigating the conformations of a much longer
chain. Could you please tell me how to generate a longer chain with the
given residue types proposed in the above post.
The length of the chain is dependent solely upon what you have in your
coordinate file. The use of pdb2gmx with .rtp entries implies only that you
have some sort of repeating building blocks. Do confirm that the parameters in
the post you quote are appropriate; I created those entries as an example only,
and have had no reason to confirm their usefulness or validity.
-Justin
thank you,
moeed
--
========================================
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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