[gmx-users] Polyethylene (PE) simulations in Gromacs - please!

Justin A. Lemkul jalemkul at vt.edu
Tue Mar 3 14:35:01 CET 2009

Chansoo Kim wrote:
> Dear Dr. Benkova and others:
> I am C. Kim and trying to simulation polymer system.
> Since I guessed that polyethylene (PE) is a simple system, it could be 
> not that hard to simulate it in Gromacs.
> Trying to do, I have read Dr. Benkova's articles in gmx-users mailing 
> list to tackle my problems.
> Sorry to say, I could not solve problems, so I am asking your help!
> Actually I have used your files written in followings,
> http://www.mail-archive.com/gmx-users@gromacs.org/msg12204.html
> [Q1]
> After getting the result from the pdb2gmx, I could not see any H-atoms 
> in my system.
> All the H-atoms have 0, 0, 0 positions!
> Therefore, my question is
>    how I should define hdb?

The .hdb file format is explained in the manual.

> [Q2]
> When I use -C2, and +C1 in hdb file, I always meet error.

What is the error?


> Is there any other things to add to the ffopls*.* files...?
> Thank you for your care!
> Sincerely 
> C. Kim
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Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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