Hi Dan,
I tried the AddIonsRand it worked perfectly. Thank you for your suggestion.
I still am not sure about what you mean when you talked about the larger buffer size suggestion that you made in your previous email.
Thank you,
Sylvester
________________________________________
From: Daniel Roe [daniel.r.roe.gmail.com]
Sent: Friday, December 05, 2014 10:07 AM
To: AMBER Mailing List
Subject: Re: [AMBER] closeness
Hi,
On Fri, Dec 5, 2014 at 4:49 AM, Sylvester Tumusiime <stumusii.uno.edu> wrote:
> 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.
Just to expand on what Dave said, when leap builds in solvent the
starting system density is purposefully low to avoid creating bad
contacts. Also, when you run with periodic boundary conditions there
is no such thing as "leaving" the box, since you just end up in a
neighboring unit cell. If your solute is extending outside the box you
probably need you use a larger buffer size, since in most cases you
don't want your solute to be able to interact with itself.
> 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?
Have you tried using addionsrand? It typically does a decent job and
is faster anyway. You could also try 'autoimage' followed by
'randomizeions' command in cpptraj on any existing frames to spread
your ions out (although it's probably easier to just use addionsrand
in leap).
-Dan
>
> 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.
>> _______________________________________________
>> AMBER mailing list
>> 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)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> 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)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Dec 05 2014 - 11:00:03 PST
