VMD-L Mailing List

From: Yesica Pena (yesicacastaneda_at_tamu.edu)
Date: Wed Nov 22 2017 - 11:50:03 CST

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.

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--001a11407a8c0ca332055e95f3e5--