Thanks. From your publications it seems that you have been simulating with
infinite CNTs. I am trying to use finite CNTs and I am generating my
topology files according to
http://chembytes.wikidot.com/grocnt.
I am modeling the peripheral Carbon atoms with two bonds by specifying it
in the
Are you sure that the source of instability is the CNT, not the protein? If
yes, what makes you to think so?
If you freeze all the atoms of the CNT, does it work well?
Dr. Vitaly V. Chaban
On Sun, Sep 15, 2013 at 11:07 PM, HANNIBAL LECTER
hanniballecte...@gmail.com wrote:
Thanks. From your
There must be some problem with degrees of freedom in your system...
Dr. Vitaly V. Chaban
-- Forwarded message --
From: HANNIBAL LECTER hanniballecte...@gmail.com
Date: Fri, Sep 13, 2013 at 7:15 PM
Subject: [gmx-users] SD integrator
To: Discussion list for GROMACS users
Do you couple CNT as a separate T-group? It should be done so.
I think your systems blows up because of incorrectly defined bonded
parameters for the tube, not due to thermostatting. For instance, you might
not define all the valence angles and dihedrals.
See my papers for the parameters for
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