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

[Justin A. Lemkul]

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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