Hi,
The solvateoct and solvatebox commands both take as their third
argument a buffer size (in Angstroms) which is the desired clearance
from solute to box edges. A typical value is ~10 Angstroms, but the
main concern is to choose a large enough buffer that once your system
density has equilibrated your solute is not directly interacting with
its images.
-Dan
PS - Note you can also specify a list for independent XYZ buffer
distances but that is advanced and typically not needed.
On Fri, Dec 5, 2014 at 11:44 AM, Sylvester Tumusiime <stumusii.uno.edu> wrote:
> 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
--
-------------------------
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 - 11:00:04 PST
