Hello Dan,
Thank you for your insight. I do have some follow-up questions:
You said the volume will decrease during equilibration based on the low density of the system. My question is how may i prevent this from happening? I suspect that once my volume decreases my solutes will leave or extend out of the box which i do not want.
Secondly, I used the add-ons command and it showed the ions forming a dense cloud outside the box which i suspect is a problem (will the minimization and equilibration steps bring them in?). That is why i wanted to specify the position of the ions. You suggest adding the ions to my PDB file in a position i like but i may have to add thousands. Will this call for a special script to do this?
If i go ahead and add the ions to the position i want in the pdb file, am guessing i can use "TER" separator to place them between my solutes?
Thank you once again.
S.T
________________________________________
From: Daniel Roe [daniel.r.roe.gmail.com]
Sent: Thursday, December 04, 2014 11:32 PM
To: AMBER Mailing List
Subject: Re: [AMBER] closeness
Hi,
On Thu, Dec 4, 2014 at 10:12 PM, Sylvester Tumusiime <stumusii.uno.edu> wrote:
> Total vdw box size: 34.015 41.102 44.674 angstroms.
>
> Volume: 62457.939 A^3
>
> Total mass 26186.398 amu, Density 0.696 g/cc
> 1. Should i consider the stated volume (62457.939 A^3) as the true volume
> of the box? If not, what dimension can i use as a true reflection of my box
> volume?
This volume seems right for a rectangular box of the given dimensions.
However, since your density is so low you can expect the volume to
decrease during equilibration.
> 2. Secondly, I came across the "closeness" command in amber manual. Can i
> use this in conjunction with the solvate (cap/box) commands to specify the
> location of ions within my system as a substitute to the addions command and
> the RP RW arguments of AddToBox?
I assume you're referring to the 'closeness' parameter for the
solvatebox/solvateoct/etc commands? This only controls how close water
can come to solute atoms. If you really need specific locations for
ions your best bet is probably to add the ions to your PDB in
whichever places you want - just make sure you use residue names that
leap expects for ions. However, in most cases I think the addions or
addionsrand commands do a fine job (provided you do some subsequent
equilibration). Based on what you've said I don't think you want a
solvent cap...
-Dan
> Thanks,
> S.T.
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Fri Dec 05 2014 - 04:00:03 PST
