VMD-L Mailing List

From: Ronald Cohen (rcohen_at_carnegiescience.edu)
Date: Wed Jul 31 2024 - 11:24:09 CDT

Sure I will be glad to. I have looked at the VASP plugins and all of them assume a fixed cell. Even the atomic positions are thus wrong, because it multiplies the fractional coordinates in the frames by the wrong cell. I just haven't had time to try to modify the plugins myself. It seems there is not a standard form for the plugins, so it is a bit complicated how to do it best. Here are two examples of iron liquid:

https://urldefense.com/v3/__https://www.dropbox.com/scl/fi/e5ydb9lsqddxvh9s8r42v/vasprun.xml.gz?rlkey=zdtmbuo8b5y2epb0jkigqjph2&dl=0__;!!DZ3fjg!52HwICqlX14LYCjP5C2Ww8cnnKczcygcBa1fU7akJpUKtGXaXybpcctP-xYoYmyv4ZmrjBLdL3zxhmWTJsEgQ2b_8w$
https://urldefense.com/v3/__https://www.dropbox.com/scl/fi/ay770hk9kj27egaltew9w/XDATCAR.gz?rlkey=74rdf2plofpbzqkqj975pcax8&dl=0__;!!DZ3fjg!52HwICqlX14LYCjP5C2Ww8cnnKczcygcBa1fU7akJpUKtGXaXybpcctP-xYoYmyv4ZmrjBLdL3zxhmWTJsGMvSS61A$

Sincerely,

Ron

> On Jul 31, 2024, at 11:10 AM, Diego Gomes <diego.enry_at_gmail.com> wrote:
>
> Hi Ronald,
> thank you for bringing this up.
>
> Can you send me a sample file and if you know details about the VASP file, a brief explanation of the expected result?
>
> Friendly,
> Diego.
>
> --
> Diego Enry. B. Gomes, PhD
> Department of Physics at Auburn University &
> NIH Center for Macromolecular Modeling and Visualization
> Leach Science Center - Ste. 3182
> Auburn, AL, 36849 - (334) 844-4264
> dgomes_at_auburn.edu <mailto:dgomes_at_auburn.edu>
> On Mon, Jul 29, 2024 at 2:58 PM Ronald Cohen <rcohen_at_carnegiescience.edu <mailto:rcohen_at_carnegiescience.edu>> wrote:
>> I have followed up this in the course of the plugins, and not only does vmd not read the cell parameters correctly with a variable cell, but it even reads the atomic positions wrong!
>> It converts them to cartesian coordinates (angstroms) using the cell of the first frame.
>>
>> Ronald Cohen
>>
>>
>
>
> --
> Diego Enry B. Gomes, PhD
> Department of Physics at Auburn University &
> NIH Center for Macromolecular Modeling and Visualization
> Leach Science Center - Ste. 3182 - Auburn, AL
> dgomes_at_auburn.edu <mailto:dgomes_at_auburn.edu>