Hi InSuk
Thank you for your comments regarding to my question.
I have few more questions about your answer.
First, number of ions is determined from the water box volume. For example, 113 NaCl ions gives me 0.3M salt concentration based on the water box volume, which is generated from "solvatebox mol TIP3PBOX 12.0 0.832".
Now, if I put ions first (neutral ions, 113 Na+ and Cl-, each), and then solvate system with "solvatebox mol TIP3PBOX 12.0 0.832", the water box becomes too big and therefore, salt concentration drops to 0.07M.
If I use smallest water box with "solvatebox mol TIP3PBOX 0.1 0.832", it still gives me big water box and low salt concentration (0.12M).
Above all, big water box also causes to take longer MD simulation time.
Therefore, if we solvate system after we put ions, Amber11 looks like building too big water box and we can not obtain desired salt concentration.
So, is there any way we can let Amber11 (leap) know what is water box size limitation when we put ions around solute?
Thank you.
TJ
________________________________
From: InSuk Joung <i.joung.gmail.com>
To: TAEJIN KIM <liquidhelium4k.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Wednesday, February 1, 2012 2:19 PM
Subject: Re: [AMBER] Problems in ions in Amber11
Hi,
Try adding ions before you solvate your solute.
addions mol Na+ 0
addions mol Na+ 113
addions mol Cl- 113
solvatebox mol TIP3PBOX 12.0 0.832
On Wed, Feb 1, 2012 at 2:11 PM, TAEJIN KIM <liquidhelium4k.yahoo.com> wrote:
> Dear Amber users.
>
> I have some questions about initial locations of ion, which are placed by
> Amber11 leap.
> I am preparing MD simulation of RNA in high salt concentration (0.3M).
> I placed ions (neutral Na+ extra Na+, Cl-) around RNA with following
> procedures.
>
> $AMBERHOME/exe/xleap -s -f leaprc.ff10
>
> loadamberparams frcmod.ionsjc_tip3p
> mol=loadpdb RNA.pdb
> solvatebox mol TIP3PBOX 12.0 0.832
> addions mol Na+ 0
> addions mol Na+ 113
> addions mol Cl- 113
> savepdb mol RNA-sol.pdb
>
>
> When I checked final structure, RNA-sol.pdb, I found that some ions are
> outside of water box. I do not think this happed because of high salt
> concentration, since I could see ions outside of water box when I put
> 0.15M NaCl too.
>
> As for another test I also placed ions with
>
> mol2=loadpdb RNA.pdb
> solvatebox mol2 TIP3PBOX 12.0 0.832
> addions mol2 Na+ 113 Cl- 113
>
> and I found more weired configuration of ions which most of them located
> at the corner of water box.
>
>
> Is there any way to use leap or force filed to avoid these problems?
>
> For me, these ion configurations look wrong since ions outside of water
> box can collide to RNA by periodic boundary condition. In addition, Cl- ion
> cloud, which is placed outside of Na+ cloud may cause artificial
> electric filed.
> If someone know how to solve this problem, please let me know.
> Thank you.
>
> TJ
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Best,
InSuk Joung
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Received on Thu Feb 02 2012 - 15:30:02 PST
