Dear Justin
Thanks for your reply.
After energy minimization, all carbon atoms are in true position,
inside box but again, both ends of cnt were deformed, same problem I
had before I add bond length to the length of CNT in z dimension of box.
You mentioned possibly poor input geometry . Please
On Wed, Dec 11, 2013 at 3:39 AM, Atila Petrosian
atila.petros...@gmail.comwrote:
Dear Justin
Thanks for your reply.
After energy minimization, all carbon atoms are in true position,
inside box but again, both ends of cnt were deformed, same problem I
had before I add bond length to the
Dear Justin
I built CNT by nano tube modeller. Then, I put protein (fragment model with
15 residues) in appropriate distance of CNT manually.
I used force field parameters from following paper:
J. Phys. Chem. B 2001, 105, 9980-9987.
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If the system does not explode, everything is correct. Though your
solution is perhaps in the wrong place in relation to the tube.
Dr. Vitaly V. Chaban
On Tue, Dec 10, 2013 at 10:02 AM, Atila Petrosian
atila.petros...@gmail.com wrote:
Dear Justin
Based on your suggestion, I added C-C bond
On Tue, Dec 10, 2013 at 4:02 AM, Atila Petrosian
atila.petros...@gmail.comwrote:
Dear Justin
Based on your suggestion, I added C-C bond length to z dimension of box
(before: 5.5 3.5 3.5, now: 5.5 3.5 3.6418).
Then I used genion to neutralize system using replacing 2 water molecules
by 2
