[Chimera-users] Run procedure

[Elaine Meng]

Hi Paul,
(1) please send questions to the chimera-users address, CC’d here.  Questions sent just to me may fall through the cracks.

(2) all I know about the Molecular Dynamics Simulation tool, I have written in its documentation.  You can see it by clicking the Help button on the dialog or viewing the copy at our website:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/md/md.html>

See the sentence containing “clicking Run” about 1/3 of the way down and the last sentence in the page starting with "After the completion of any MD run…”

I am guessing that you chose the recording option in the MD Movie dialog.  If you are not sure which data it is showing, Quit from the MD Movie dialog. Then from the Tools menu, restart MD Movie and specify the specific MMTK input (trajectory) file that you want, like we discussed earlier.  Although I said earlier that if you gave the same output name for both equilibration and production, the production might overwrite the equilibration, I’m no longer sure about whether it overwrites or just gets added to the end.  However, you should be able to tell by the number of frames in the output trajectory.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco




> On Jun 16, 2017, at 12:03 PM, pbuscemi <pbuscemi at q.com> wrote:
> 
> Elaine,
> 
> In doing a simulation, does it matter which screen is used to select "RUN"  ie,  minimize, equilibrium,production, or other.
> 
> i.e  If I select equlibrium,  is production also run ?  When a movie is recorded,  is it from equilibrium or production portion ?
> 
> thanks 
> Paul
> 
>