Fwd: [gmx-users] SD integrator

[Dr. Vitaly Chaban]

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 CNT, if you need such...


Dr. Vitaly V. Chaban


On Fri, Sep 13, 2013 at 8:55 PM, HANNIBAL LECTER <hanniballecter13 at gmail.com
> wrote:

> However, even if position restraints are not used, the error can be
> reproduced. I am constraining the bonds in my CNTs though.
>
> I was wondering if you could point me to some parameters for CNT.
>
>
> On Fri, Sep 13, 2013 at 1:50 PM, HANNIBAL LECTER <
> hanniballecter13 at gmail.com> wrote:
>
>> I am position restraining the CNT group. That affects the degrees of
>> freedom.
>> On Sep 13, 2013 1:43 PM, "Dr. Vitaly Chaban" <vvchaban at gmail.com> wrote:
>>
>>> 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
>>> tau-t?
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>>
>