Fwd: [gmx-users] SD integrator

Dr. Vitaly Chaban vvchaban at gmail.com
Fri Sep 13 19:42:20 CEST 2013

There must be some problem with degrees of freedom in your system...

Dr. Vitaly V. Chaban

---------- Forwarded message ----------
From: HANNIBAL LECTER <hanniballecter13 at gmail.com>
Date: Fri, Sep 13, 2013 at 7:15 PM
Subject: [gmx-users] SD integrator
To: Discussion list for GROMACS users <gmx-users at gromacs.org>

Hi all,

I have been posting for a while with my problems in simulating peptides
inside CNTs. After a lot of trials it seems like simulating the CNT with
bonds and angles seems like a wise thing to do.

I am using the SD integrator + PR barostat. It seems like improper
thermostatting can blow up the system. For example, when I am trying to
simulate with tau-t for CNT as 1.0 the system blows up for 300K. The output
temperatures (from g_energy) for CNT is about 150K for a ref-t of 300K.

 However, if a stronger coupling is used tau-t = 0.005, the system works
fine. Are there any artifacts for coupling the CNT group with such a low
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