From: Ryan McGreevy (
Date: Wed Dec 30 2015 - 10:51:33 CST

If you are running VMD on windows, the issue you are having is likely due
to how Windows treats 32bit applications running on 64bit windows. If you
'ls' from the tkconsole, you should notice that the output file appears to
be there. You can load it or run commands on it from the tkconsole/VMD as
normal (i.e. mol new 4ake-target_autopsf.situs should work). However, if
you try to navigate to that file in windows explorer, it won't appear to be
there. The actual output file should be written to the
folder C:\Users\UserName\AppData\Local\VirtualStore\Program Files
(x86)\University of Illinois\VMD where UserName is your windows user name,
and assuming you performed a default install. This is the folder that
windows tricks VMD into thinking is the normal C:/ path.

I am not sure what you mean by "By the way neither is there any working
code available to anyone outside of the Schulten group." All MDFF code has
been publicly available in VMD and NAMD for many years now with many people
external to our group successfully using it. Along with the tutorial, you
can find more information about the MDFF plugin at or by typing each command
in the vmd console without any options to get its usage. The sim command
can generate .situs and .dx files, but you are correct that the
documentation lacks this information, which I will make sure is correctly
updated. Also, for more detailed information on the theoretical and
practical aspects of MDFF, you can read the MDFF methodological

On Wed, Dec 30, 2015 at 10:31 AM Rose, Stuart Wallace <>

> Hello,
> In the MDFF tutorial under "A simple MDFF example" the step requiring this
> command does not work using VMD for WIN32, version 1.9.2 (December 29,
> 2014):
> mdff sim $sel -res 5 -o 4ake-target autopsf.situs
> No situs file is generated and no alternative file extension/ types are
> referenced in documentation or posts in the context of the "sim" command or
> the "-o" option. By the way neither is there any working code available
> to anyone outside of the Schulten group.
> Earlier post mentions things like the inability to generate a situs
> formatted file and the situs web page for vmd mention vmd can read but not
> write this format. MDFF documentation is sparse regarding command
> examples, reasons for option and what anything does. Is there a special
> place to find out how this stuff works because the first steps of the
> tutorial fail so there is a high probability of a long path of problems.
> Brief description of file formats and context for MDFF are necessary for
> outsiders to gain actual knowledge of the tools use.
> Regards,
> Stuart
> *********************************************************************************
> Stuart W. Rose
> E-Mail:
> University of Illinois @ Urbana-Champaign Office: 153
> Davenport Hall
> 607 S. Mathews Avenue
> Urbana, IL 61801
> Lab Ph. (217)333-7407
> Center for Biophysics & Quantative Biology Office: Loomis,
> MC-704
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