VMD-L Mailing List

From: maxim todoru (mtodoru_at_gmail.com)
Date: Thu Aug 31 2023 - 04:16:04 CDT

Dear Pr. Sarkar,
No no, the situation isn't like that, i'm not looking for simulation, the
whole matter is i perform a topological analysis of an organic molecule,
and the results i get is like what i explained before (some bonds are much
longer than the normal), i need to adjusted for nicer visualisation, and i
think VMD is the only program i know can help me (instead of Gaussview).

Le jeudi 31 août 2023, Daipayan Sarkar <sdaipayan_at_gmail.com> a écrit :

> Hi,
>
>
>
> Are you sure the molecule is built correctly? Said differently, this could
> easily be due to your psfgen script where I assume you have topology files
> for the molecule you are working with. For that more specific information
> about the molecule would be necessary. This is of course if you are
> planning to simulate the molecule.
>
>
>
> “i need the reduce their length to a specific value” - I personally do
> not recommend, even if you are using VMD only for visualization purposes.
>
>
>
> -Daipayan
>
>
>
> *From: *"owner-vmd-l_at_ks.uiuc.edu" <owner-vmd-l_at_ks.uiuc.edu> on behalf of
> maxim todoru <mtodoru_at_gmail.com>
> *Date: *Thursday, August 31, 2023 at 3:35 AM
> *To: *"vmd-l_at_ks.uiuc.edu" <vmd-l_at_ks.uiuc.edu>
> *Subject: *vmd-l: How to shortening bonds length in a molecule ?
>
>
>
> Hi VMD community,
>
> I used VMD to perform the visualisation of some organic molecules, but it
> appears that some bonds length are little tall from normal, and i need the
> reduce their length to a specific value. I failed to figure out a solution,
> and i need some help.
>