Fwd: [gmx-users] SD integrator

[Dr. Vitaly Chaban]

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 <
hanniballecter13 at gmail.com> wrote:

> 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?
>> >>> --
>> >>> gmx-users mailing list    gmx-users at gromacs.org
>> >>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> >>> * Please search the archive at
>> >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> >>> * Please don't post (un)subscribe requests to the list. Use the
>> >>> www interface or send it to gmx-users-request at gromacs.org.
>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >>> --
>> >>> gmx-users mailing list    gmx-users at gromacs.org
>> >>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> >>> * Please search the archive at
>> >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> >>> * Please don't post (un)subscribe requests to the list. Use the
>> >>> www interface or send it to gmx-users-request at gromacs.org.
>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >>>
>> >>
>> >
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> * Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>