VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Tue Nov 15 2016 - 09:10:39 CST

Hi

Excuse the previous incomplete email.

You have asked for 2 different things.
1) Finding out number of solvent molecules:
-------Assuming this solvent is water you can do this:
set sel [atomselect top "waters"]
expr [llength [$sel get index]]/3

the last line should return the exact number of water molecules.

2) Solvating a (big) system:

for the second you can go through this ::
http://www.ks.uiuc.edu/Research/vmd/minitutorials/largesystems/

Hope this helps.

Best,
/A

On Wed, Nov 16, 2016 at 4:07 AM, Ashar Malik <asharjm_at_gmail.com> wrote:

> Hi
>
> You have asked for 2 different things.
> 1) Finding out number of solvent molecules:
> -------Assuming this solvent is water you can do this:
>
>
> On Wed, Nov 16, 2016 at 3:20 AM, Raviteja Kurapati <tsii.ravi_at_gmail.com>
> wrote:
>
>> how to know exact number of solvent molecule in simulation box?
>> I have added solvent to protein using vmd solvate package. No matter what
>> the box size is, solvated pdb file shows around 9000 solvent molecules (
>> which is default number of molecules in wat.pdb file used in solvate
>> package).
>> how to place exact number of solvent molecules within desired box size?
>>
>>
>> Best Regards.
>>
>
>
>
> --
> Best,
> /A
> 

-- 
Best,
/A