From: Sebastian Stolzenberg (ss629_at_cornell.edu)
Date: Fri Sep 12 2014 - 13:21:10 CDT
Dear All,
I think I found a possible answer to my question, but would highly
appreciate
, if somebody could explain this to me:
For practicality, I re-did the computations just for the annihiliation
of Na (i.e. without an extra water appearing):
Na2_to_vac dG_FEP correction corr. dG_FEP whatif
boxsize_67__q0=0_q1=-1 82.2 -7.0 75.2 89.2
boxsize_67_q0=1_q1=0 82.5 7.0 89.5 89.5
boxsize_128_q0=0_q1=-1 85.8 -3.7 82.1 89.5
Boxsize_128_q0=1_q1=0 85.8 3.7 89.5 89.5
all values are in kcal/mol.
In the "whatif" column in
boxsize_67__q0=0_q1=-1
and
boxsize_67__q0=0_q1=-1,
I simply *added* instead of subtracted the corrections, and ended up
with the same free energy values for different FEP experiments and
different box sizes.
Thank you, Best,
Sebastian
On 07.09.2014 17:23, Sebastian Stolzenberg wrote:
> Dear All,
>
> let me give you some free energy difference values (in kcal/mol) for
> the email below:
>
> FEP experiment 1 (L=67A):
> 75.96 (reverse run gives -75.50)
> cr=-7.03
>
> FEP experiment 2 (L=67A):
> 76.03 (reverse run gives -75.88)
> cr=7.03
>
> I also did the same FEP runs just for the annihilation of Na2 (i.e.
> without an H2O appearing) and get the same odd result.
>
> Can anybody tell me what I am conceptionally missing here?
>
> Much appreciation,
> Sebastian
>
>
> Am 02.09.14 um 22:12 schrieb Sebastian Stolzenberg:
>> Dear All,
>>
>> I stumbled over the following consistency check to see, whether I
>> fully understand the size-dependent charge correction derived in
>> Hummer, G.; Pratt, L. R.; Garcia, A. E. J. Phys. Chem. 1996, 100,
>> 1206–1215,
>> for FEP/TI with Ewald summation;
>> this correction I denote here as cr=0.5*ξ*(q1^2-q0^2), where q0 and
>> q1 are the total charges of the simulated system in the reference and
>> target state, respectively, ξ=−2.837/L, and L is the length of the
>> cubic simulation box.
>>
>> Given:
>> - cubic water box with length L=67A (or 128A) with 0.15mM NaCl,
>> neutral net charge
>> - standard CHARMM36 ff, NPT, PME, NAMD 2.9
>>
>> FEP experiment 1:
>> annihilate an Na ion, and let appear a water molecule
>> (the Na and OH2 atoms are harmonically restrained to the same {x y z}
>> position)
>> => q0=0, q1=-1
>> => cr<0
>>
>> FEP experiment 2:
>> prior to FEP, delete a CL ion in the box, then
>> annihilate an Na ion, and let appear a water molecule
>> (the Na and OH2 atoms are harmonically restrained to the same {x y z}
>> position
>> => q0=+1, q1=0
>> => cr>0
>>
>> I understand that the corrected free energy difference DG_cr is
>> obtained from the computed DG (e.g. via NAMD FEP) via:
>> DG_cr=DG+cr
>> I am confused because in my FEP simulations, DG is nearly identical
>> for both FEP experiments stated above (to the second digit).
>> Therefore, I would receive different values of DG_cr for the same
>> alchemical transformation (Na to water).
>>
>> Is there something I missed along the lines?
>>
>> With Thanks and Best Regards,
>> Sebastian
>>
>
This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:22:51 CST