VMD-L Mailing List

From: t.shivam_at_iitg.ernet.in
Date: Mon Mar 12 2018 - 05:57:21 CDT

> Is it necessary to create a topology file for a newly built system? If it
> is then ,how can we create a topology file from the existing pdb and psf
> file of newly built cnt(solvated)?

If you already have a psf file you don't need a topology file, topology
file is an intermediate file needed to create the psf file, you don't need
a topology file to run simulation.

one piece of suggestion i would like to give you is that, even i am also a
beginner and what i found helpful is that if you go through the basic
tutorials of both NAMD and VMD very carefully, you will find most of your
questions answered, with much better understanding.

regards
shivam

>
> On Fri, Mar 9, 2018 at 2:41 PM, <t.shivam_at_iitg.ernet.in> wrote:
>
>>
>>
>> > can't we create ourselves for newly built carbon nanotube?
>>
>> parameters in parameter file depends only on the topology of your
>> system,
>> that is which atom is bonded to which atom and which atoms have angle
>> etc.
>> so if you are using a carbon nanotube no matter what are its dimensions,
>> the parameter file will be the same.
>>
>> regards
>> shivam
>> >
>> > On Fri, Mar 9, 2018 at 1:49 PM, <t.shivam_at_iitg.ernet.in> wrote:
>> >
>> >>
>> >>
>> >> > Dear all,
>> >> >
>> >> > I have built a new carbon nanotube using vmd. I have got the pdb
>> and
>> >> psf
>> >> > file of this system after solvation. For the minimization of it,
>> how
>> >> can
>> >> I
>> >> > get the parameter file? I am using namd.
>> >> >
>> >> > Regards,
>> >> > Shyam
>> >> >
>> >>
>> >> you can get the parameters for carbon nanotube in the tutorials -
>> >> http://www.ks.uiuc.edu/Training/Tutorials/
>> >> under the title - Simulation of Water Permeation through Nanotubes.
>> >> here are the individual files of tutorials -
>> >> http://www.ks.uiuc.edu/Training/Tutorials/science/nanotubes/files/
>> >>
>> >
>>
>>
>