VMD-L Mailing List

From: JC Gumbart (gumbart_at_physics.gatech.edu)
Date: Fri Nov 06 2015 - 08:13:56 CST

Ah - the key missing bit of info was that they are called vx, vy, and vz. :)

Thanks!
JC

> On Nov 6, 2015, at 1:09 AM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> JC,
> You can set/get velocity components just like coordinates, like this:
>
> set sel [atomselect top all]
> $sel get { vx vy vz }
> $sel set vx 1.0
> $sel get { vx vy vz }
>
> As more trajectory formats add explicit support for velocity or other
> info, we'll continue to add them into VMD and the molfile plugins.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Fri, Nov 06, 2015 at 05:43:12AM +0000, JC Gumbart wrote:
>> Is there a way to access it using TCL commands though?A Or do we need c
>> code?
>>
>> Thanks!
>> JC
>>
>> On Thu, Nov 5, 2015, 9:51 PMA JC Gumbart <[1]gumbart_at_physics.gatech.edu>
>> wrote:
>>
>> Hi John et al.,
>>
>> We have a problem where we would like to store velocity data for a
>> molecule.A However, it seems this array only gets initialized if the
>> filetype already contains such data.A This is what I see in
>> MolFilePlugin.C
>>
>>> A A // allocate space for velocities only if
>>> A A // 1) the plugin implements read_timestep_metadata;
>>> A A // 2) metadata->has_velocities is TRUE.
>>> A A float *velocities = NULL;
>>
>> Is there any way around that?A Wea**d rather not have to use TCL lists
>> to store the data (too slow).
>>
>> Thanks!
>> JC
>>
>> References
>>
>> Visible links
>> 1. mailto:gumbart_at_physics.gatech.edu
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/