From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Jun 12 2014 - 05:46:33 CDT
On Jun 12, 2014 12:28 PM, "Z" <shenzldlut_at_gmail.com> wrote:
>
> 于2014/6/9 17:19, Axel Kohlmeyer :
>>
>>
>>
>>
>> On Mon, Jun 9, 2014 at 3:58 AM, Z <shenzldlut_at_gmail.com> wrote:
>>>
>>> Dear all,
>>> I built a single-wall boron nitride nanotube by Carbon/Boron Nitride
>>> Nanostructure Builder Plugin, Version 1.5. However, when I finished my
>>> model and run the simulation, the NAMD said "FATAL ERROR: DIDN'T FIND
>>> vdW PARAMETER FOR ATOM TYPE B".And then, I tired to find the vdW
>>> parameter for atom type B in the Internet, but I failed.
>>> What should I do that?
>>
>>
>> of *course* NAMD will say that, unless you use a file with parameters
set up particularly for boron nitride.
>>
>> the standard charmm parameter files are not set up for that. most
likely, you will have to look up publications that have done simulations of
such structures using charmm-like potential functions. not sure how well
this will work for you. many people i know use a manybody potential like
tersoff to model structures like that instead.
>>
>> axel.
>>
>>
>>
>>>
>>>
>>> Thanks,
>>> Z
>>>
>>
>>
>>
>> --
>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
>> College of Science & Technology, Temple University, Philadelphia PA, USA
>> International Centre for Theoretical Physics, Trieste. Italy.
>
>
> Dear profeesor,
> Thank you for your reply!
> I want to know how to use use a manybody potential like tersoff in
NAMD/VMD. Cna I use
You cannot.
topotools(VMD) to make a topology flie about boron nitride nanotubes?
>
> Tkanks,
> Z
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