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 molecule.
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 | | H 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. moeed
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