[gmx-users] CNT going outside during NVT

[Justin Lemkul]

On 3/5/15 11:50 AM, Naga Rajesh Tummala wrote:
> It is better to freeze the atoms of nanotube and make sure the one of the
> box dimension is same as the nanotube length (and the C-C bond length in
> the nanotube across the PBC is right), so that you have infinitely long
> nanotube.
>

In this case, one should use NVT so the box vectors don't change, but I would 
contend (as I usually do) that freezing anything is a pretty severe perturbation 
to the system.  Binding of anything to anything else in an MD simulation is not 
predicated upon a fixed absolute position in the simulation unit cell.  Given 
enough time, if the physical model describes the interactions appropriately, the 
right interactions will arise.  Of course, that assumes the model is good...

> If you want model flexible nanotube then you can unfreeze the atoms, but
> make sure the force-field parameters are right.
>

Agreed completely.  This is a non-trivial issue.

-Justin

>
>
> On Thu, Mar 5, 2015 at 11:31 AM, soumadwip ghosh <soumadwipghosh at gmail.com>
> wrote:
>
>> Dear Justin,
>>                   Thank u for your time. I would like to ask again about the
>> problem I'm facing. From my understanding, If the DNA is supposed to wrap
>> around the swCNT (i.e findings of other papers), should'nt I fix it inside
>> the box? I have a box in the center of which the DNA is kept and the CNT is
>> rather randomly placed along with the solvent molecules and ions. Do u
>> prefer me to use freeze group to fix the position of CNT or are you saying
>> that I should not worry about it since pbc is operative? Sorry I'm a newbie
>> and this CNT modelling is something I am unfamiliar with..
>>
>>
>> Regards,
>> Soumadwip Ghosh
>> IITB, Mumbai,
>> India
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>
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================