Fwd: [gmx-users] SD integrator

[HANNIBAL LECTER]

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 atomname2type.n2t file. I am still not sure as to what is the source
of this discrepancy. After a few tests I think this can be caused by
improper parameterization of the bonds but I am not sure how to go about
correcting any discrepancies.


On Fri, Sep 13, 2013 at 5:53 PM, Dr. Vitaly Chaban <vvchaban at gmail.com>wrote:

> 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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