[gmx-users] Insert Molecules Settings

Mark Abraham mark.j.abraham at gmail.com
Wed Nov 14 05:40:33 CET 2018


The tools look first in the working directory for such files, so copy it
there and modify however suits you.


On Mon, Nov 12, 2018 at 2:42 PM tca1 <tca1 at rice.edu> wrote:

> 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
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