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/[email protected]/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?
-Justin
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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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