[gmx-users] Insert Molecules Settings

[tca1]

I sent this message on Friday, but I didn't see it show up in my  
digest, so I'm trying again. Here's the previous text:


Thanks all for your suggestions so far. I believe I've got things more  
or less functional but I want to refine how I'm constructing my  
initial simulation box.

In particular, I'm using a custom coarse-grained system, so I'd like  
to be able to tailor the effective vdW radii for use with  
insert-molecules and solvate commands to accommodate the typically  
larger sizes of the CG sites. However, many of my simulations are on  
clusters or other resources where I can't edit the vdwradii.dat file  
and not all CG particles in my simulation have the same radii, so just  
updating the default radius using the -radius option isn't completely  
satisfactory either.

  Is there a way to tailor these values for each type of CG particle  
without editing the database file, or some other similar workaround to  
this issue?

Thanks,
Tom