Dr Steinbrecher,
I used the following protocol from the example in tutorial A9.
V0 = Cl- + H20
V1 = H20
Step1:
for V0: prmtop of V0 and crgmask = '' & scmask = ''
for V1 prmtop of V0 and crgmask = 'Cl-.Cl-' and scmask = ''
Step2:
for V0: prmtop of V0 and crgmask = 'Cl-.Cl-' scmask = 'Cl-.Cl-'
for V1: prmtop of V1 and crgmask = '' scmask = ''
Since I dont have any atoms or charges to be added, I dont have step3. Am I
right in assuming this?
Results:
I used lambda = 0.01, 0.02, 0.03, 0.04, 0.05, 0.10, 0.15, 0.20, 0.25, 0.30,
0.35, 0.40, 0.45, 0.50, 0.55, 0.60, 0.65, 0.70, 0.75, 0.80, 0.85, 0.90,
0.95, 0.96, 0.97, 0.98, 0.99
For Step1:
Cl- ---> Cl0
DeltaG = 89.4425 kcal/mol
Step2:
Cl0 ---> Neutral atom
DeltaG = -4.78013 kcal/mol
The values are close to your JCC paper titled "Soft-core Potentials in
Thermodynamic Integration: Comparing One- and Two-Step Transformations", in
which your DG(Step1) = -93.97 kcal/mol and DG(step2) = 4.75 kcal/mol. I
used TIP3P water model where as you used TIP4P-EW water model.
Further, my values are shifted in sign for step 1 and step 2.
Am I doing something wrong here?
Thanks for your time.
Regards
Sai
On Wed, Jan 4, 2012 at 2:27 PM, Sai Kumar Ramadugu <sramadugu.gmail.com>wrote:
> Thanks Dr Steinbrecher.
> Currently I'm doing these calculations as you suggested.
>
> Regards
> Sai
>
>
> On Tue, Jan 3, 2012 at 2:37 PM, <steinbrt.rci.rutgers.edu> wrote:
>
>> Hi,
>>
>> > When I was going through your tutorial, using softcore potential, you
>> dont
>> > need to have same number of atoms that are undergoing the
>> transformation.
>> > But in my case I have only one atom/ion in the transformation. How can I
>> > achieve the transformation of a neutral atom to K+ or Cl-? Should I use
>> > dummy atoms instead? If so, can you point me how to use the dummy atoms
>> > for
>> > the necessary transformation?
>> > I did not understand how to use/include dummy atoms using ff99SB force
>> > field.
>>
>> Hi,
>>
>> there is no need to use dummy atoms in the type of calculation you plan.
>> Just set up your system as:
>>
>> System 1 System 2
>> Ion + Water just Water
>>
>> and set scmask in our input files to the Ion residue(s). Make sure all
>> water molecules have the same coordinates in Systems 1 and 2 or your sim
>> will halt with an error.
>>
>> This decouples both the (in this case very dominant) Coulomb as well as
>> vdW interactions and gives you (with some caveats) the free energy of
>> solvation.
>>
>> Check out the Steinbrecher, Joung and Case J. Comp. Chem. paper for an
>> example using Cl-.
>>
>> Kind Regards,
>>
>> Thomas
>>
>> Dr. Thomas Steinbrecher
>> formerly at the
>> BioMaps Institute
>> Rutgers University
>> 610 Taylor Rd.
>> Piscataway, NJ 08854
>>
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>>
>
>
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Received on Thu Jan 12 2012 - 11:30:02 PST
