[gmx-users] building up a polymer chain

Moeed lecielll at googlemail.com
Wed Jun 23 18:27:27 CEST 2010

Hello Justin,

Thanks for your help. Actually, I meant if I use -d option rather than -box
I would have better control on bond distance between monomer units. By try
and error I found out if I used -d 0.0017 the distance between two adjacent
C (2 monomer ends) is 1.54A. which is the bond length for C-C in the

editconf -f prodrg.pdb -o prodrgD.gro -d 0.017 -bt cubic

1- To get CH2CH2CH2CH2 repeating unit I removed the H s from both ends by
deleting one of the H at each end of CH3CH2CH2CH3. My chemistry background
is not good, so I wanted to know if the difference in C-H angle and CH2 as a
result of removing the third H in CH3 is negligible. Also the angle between
C atoms at chain ends are not the same as those within the chain. I have
just manupulated the -d option so       |
that bond distance is similar to that of C-C on backbone.

I am guessing the answer is by using pdb2gmx the structure file will be
modified so that the mentioned angles are set properly. Please let me know
if I am right and this issue is remediable... How can I make sure this is
not going to affect the simulation given that I am going to build up a very
long chain..

Thanks for your attention.
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