VMD-L Mailing List

From: Diego Gomes (diego.enry_at_gmail.com)
Date: Wed Sep 07 2022 - 16:43:28 CDT

Hi Christos, QwikMD is evolving to accommodate user needs, thank you for
reaching out.
The crashing may be due to insufficient memory (RAM)

The trajectory processed with catDCD will not load because it was produced
outside QwikMD. Without water+ions it won't match the topology.

Right now, to solve your problems you may profit from automating VMD
actions with some TCL programming, and build your own script library.
Check the VMD manual and look at some example codes over here:
https://www.ks.uiuc.edu/Research/vmd/script_library/

If you really need to include water molecules in your analysis, and your PC
has a memory limitation, then "BigDCD" will be of great interest.
https://www.ks.uiuc.edu/Research/vmd/script_library/scripts/bigdcd/

The scripts used by QwikMD can be found @ qwickmd_func.tcl
You may browse the VMD folder to find it. The path should be something like
this:
vmd/plugins/noarch/tcl/qwikmd1.1/qwickmd_func.tcl

Cheers,
Diego.

On Thu, Sep 1, 2022 at 9:33 AM Efthymiou, Christos <
christos.dereschuk.20_at_ucl.ac.uk> wrote:

> Hi,
>
> I have two questions regarding QwikMD. I use a Windows 10 computer and VMD
> 1.9.3.
>
> First, is it possible to automate the analysis offered by QwikMD? For
> example, I would like to have a script that performs RMSD, RMSF, H-Bonds
> within the solute, between chains, etc. analyses so that I can run the
> script and generate .dat files for each characteristic rather than having
> to use the GUI. Is it possible to find the scripts/commands that QwikMD
> uses to calculate each of these? Ideally, I would like to use the GUI once
> for a trajectory, recording all the settings I use for each analysis, and
> then have a script that I can use on other trajectories.
>
> Second, it would be helpful to have such a script as currently I am only
> able to load the trajectory containing water molecules into QwikMD. I ran
> simulations using QwikMD/NAMD, but the trajectory is very large and causes
> VMD to crash. Right now, to be able to use QwikMD, I must set a high stride
> value to prevent crashing.
>
> I have used catdcd to reduce the size of the MD.dcd trajectory by removing
> all the water molecules and ions, but this edited trajectory does not show
> up as an option to load when I load the .qwikmd file. Is it possible to
> use the QwikMD analysis features with an edited dcd file?
>
> The only potential solution I can think of is to rename the dcd/psf/pdb
> files I created without water to the names of the solvated versions
> (thereby requiring me to change those to something else) to "trick" QwikMD
> into using the edited files. However, I would prefer to not have to go
> through this process every time I want to analyze my trajectories, so I
> appreciate any other workarounds to this problem.
>
> Thank you for any advice.
> 

-- 
Diego Enry B. Gomes, PhD
Department of Physics
Leach Science Center
Auburn University
dgomes_at_auburn.edu
+1 (334) 559-4016