VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Aug 18 2010 - 19:16:17 CDT

Hi Demet,
If you're just trying to CG a system once, I recommend just adding CG
solvent rather than trying to CG the all-atom water. You can use a box
of CG water as a nonstandard solvent in VMD's Solvate plugin. If you
need to repeatedly switch between representations, you'll want to write
a script to shuffle the residue numbering so that the closest 6 waters
are always the ones that get included; CGTools wasn't really designed
with that situation in mind.
Best,
Peter

On 08/18/2010 04:06 PM, John Stone wrote:
> Hi,
> If you haven't already, I would suggest contacting
> Peter Freddolino or Anton Arkhipov about your question as they developed
> all of the RBCG plugins and the associated scripts you're using.
> (they have both graduated and are at different institutions now,
> but I'm CCing them in hopes they catch your question this way)
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Mon, Aug 09, 2010 at 01:34:26PM +0300, Demet Akten wrote:
>
>> Dear All,
>>
>> I have a system which contains about 40 Na+Cl ions. I know that that
>> an ion with its first hydration shell becomes an ``ion'' bead. But how
>> do you specify which water molecule will be a part of that bead? I
>> would appreciate any help on that.
>>
>> Best regards,
>>
>> Demet
>>
>