VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Feb 03 2022 - 23:14:43 CST

Hi,
  I had to go read the code to check on this, and there are
likely a bunch of details that have to line up precisely in order
for you to be able to use periodic MSM. My colleague (the MSM developer)
has updated the MSM interface and the new version of the code no
longer pays attention to MSMPOT_PBCON from what I see, which could
be related to your issue, but it's hard for me to guess since you didn't
provide the precise commands you ran. If you can provide more information,
I'm happy to followup further.

Best regards,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Feb 02, 2022 at 10:08:16AM +0200, Subhasish Mallick wrote:
> Hello everyone,
> I would like to run periodic MSM calculations using the VolMap plugin in
> VMD. I was trying to apply the following trick to run the same:
>
> export MSMPOT_PBCON=1
> export VMDMSMUSEPBC=1
>
> in the Linux shell prior to launching the VMD.
>
> it was running the periodic MSM calculations, but I got some errors as
> follows:
>
> It returns error code 3 - Illegal Parameters.
> Unfortunately, I have no control over the choice of grid except the
> resolution.
> Any suggestions on how one can calculate the periodic MSM calculations
> using VolMap will be highly appreciated.
> Thanks in advance.
> Best wishes,
> Subhasish
> --
> -------------------------------
> Dr. Subhasish Mallick
> Post-Doctoral fellow
> Fritz Haber Center for Molecular Dynamics Research
> Institute of Chemistry
> The Hebrew University of Jerusalem
> -------------------------- 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
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http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/