Dear Bill,
Sorry for bothering you. I don't know why my E-mail format was changed. If
this problem is continued when you receive this mail, please tell me.
I am going to do equilibration, after making solvent box. As you mentioned
below, I made it much bigger for getting more residues. The box consists of
113 Tfo anions and 130 Emim cations.
Before doing equilibration, please check this input file below, then comment
on my input if there are some problems or some parameters are needed.
&cntrl
imin=0,
ntxo=1, ntrx=1,
cut=15.0,
ntpr=1000, ntwx=1000, ntwe=1000,
nstlim=50000,
dt=0.001, nscm=100,nsnb=10,
ntc=2, ntf=2, tol=0.00001,
ntx=1, irest=0,
ntb=2, ntp=1, pres0=1.0, taup=1.0
scee=1.2,
ntt=1, ntr=0,
&end
Thank you for your help ! I always appreciate it a lot
Regards,
Hoshin Kim
-----Original Message-----
The email format is encoded to a point that is hard for me to decrypt with
my primitive email setup, but I note:
> Added 2 residues.
You will probably need to make the box cutoff much bigger to get more
residues in there. Presumably the box will shrink a lot on equilibration
(constant pressure). However for test puroposes having a few residues might
be useful, so I would run some tests with what you have to see if things
blow up.
> my ion structures have been changed.
If you mean the coordinates have been changed, e.g. by shifting them into a
box, that is normal.
Bill
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-----Original Message-----
From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On Behalf
Of Bill Ross
Sent: Tuesday, May 04, 2010 5:06 AM
To: amber.ambermd.org
Subject: Re: [AMBER] How to make ionic liquid solvent box?
> I am trying to do dynamics regarding solvation sugar molecules in
> ionic liquids. Could anyone help me how to create the ionic liquid
> solvent box using xleap? Ionic liquid that I will try to use is
> [Emim][TfO] (1-ethyl-3-methylimidazolium Trifluoromethylsulfonate).
>
> Ionic liquid is the liquid that is only composed of anion and cation.
> In case of [Emim][TfO], Emim(1-ethyl-3-methylimidazolium) is
> cation(+1),
> [TfO](Trifluoromethylsulfonate) is anion(-1).
You could make an initial box by solvating a single molecule in
layers:
> init = copy mol1
> solvatebox init mol2 4
> solvatebox init mol1 2
> saveamberparm init iobox.top iobox.crd
Then equilibrate the box with constant pressure, convert to pdb, and
> solbox = loadpdb solbox.pdb
> solvatebox mymol solbox 10
Or you could build up the layers directly around your solute, then put a
cartestian restraint on the solute while equilibrating it (as would also be
necessary if using an intermediate box to solvate the solute).
Likely it will be tricky to get 1:1 ionic ratio, but this will not matter so
much if you are making an ion-only box to then solvate another molecule,
since arbitrary adjustments will still be needed after solvating the other
molecule because of losing the ionic balance. The adjustments can be made by
editing the system in xleap and deleting extra solute molecules of the
appropriate species.
You might want to consider debugging your solvent molecules by first running
each separately with Na+ and Cl- to neutralize.
Bill
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Received on Wed May 05 2010 - 14:00:03 PDT
