VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Nov 22 2017 - 13:25:20 CST

On Wed, Nov 22, 2017 at 12:50 PM, Yesica Pena <yesicacastaneda_at_tamu.edu>
wrote:

> Hi, I'm new running vmd jobs, and have a lot of questions, could you help
> me please.
>
> If I use this pair_style
> pair_style hbond/dreiding/lj command
> what 's the force field that I need for running my job.
>
> I mean, when I use for example, pair_style reax, the pair_coeff is
> ffield_COHFLiS, and it's one the file that I need to run in a terminal.
>
> I hope be clear in my question.
>

​no, you are not clear. *nothing* you say here has anything to do with VMD.
also, it seems like you are in need of significant in-person advising​ and
tutoring. thus i recommend you talk to your adviser/supervisor and/or more
experienced colleagues. the kind of help you need cannot be taught via
e-mail.

​axel.​

>
> The second question is, If I have the files with extensions .car and .mdf,
> what other file do I need? Excluding the .data file
>
> Thank you, your help
>
> On Wed, Nov 22, 2017 at 12:41 AM, Axel Kohlmeyer <akohlmey_at_gmail.com>
> wrote:
>
> >
> >
> > On Wed, Nov 22, 2017 at 12:40 AM, Vaidyanathan Sethuraman <
> > vsethura_at_umn.edu> wrote:
> >
> >> Dear VMD Users
> >>
> >> I am using Materials Studio to generate the initial structure for a
> >> cellulose polymer. Then I export the PDB version to VMD and use
> topotools
> >> to generate the input structure for LAMMPS. Please note that the PDB
> output
> >> DO contain the CONNECT information (bond information).
> >>
> >> Q: Can I use topotools in such a way that it utilizes the CONNECT
> >> information from PDB file while guessing angles and dihedrals rather
> than
> >> using heuristics?
> >>
> >> When I use
> >>
> >> mol new inpfile.pdb autobonds yes waitfor all
> >> topo guessangles
> >> topo guessdihedrals
> >> topo writelammpsdata out.data full
> >>
> >> the output still uses heuristics to compute "BONDS" and generates more
> >> number of bonds than what is there in the CONNECT info. The reason why
> >> heuristics is giving more bonds is because of the funky structure that
> some
> >> atoms will look apparently close. So can I trick topotools in such a way
> >> that the angle and dihedral topology is guessed from the CONNECT info?
> >>
> >
> > ​this has nothing to do with topotools. topotools uses the information
> > that VMD provides, which in turn depends on the PDB reader molfile plugin
> 

-- 
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.