[gmx-users] intermolecular contributions/building up a long polymer chain

[Moeed]

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?

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?

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.


thank you,
moeed
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