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Re: generating parameters for pyruvate
RD2015 #24411 05/25/10 09:23 PM
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OK, I took a very close look at the whole case, and discovered that the line
Code:
IMPR C1   O11  O12  C2
is missing from your topology. Unfortunately, this means that you'll have to redo your dihedral fit. For starters, try 0.44 for your 2-fold and 0.06 for your 3-fold. Also, if you're still suffering asymmetry problems, a possible solution would be to not constrain CCCH while fitting OCCC.

Edit: beware: it is not impossible that CCCH needs to be re-fit as well.

Last edited by Kenno; 05/25/10 09:28 PM.
Re: generating parameters for pyruvate
Kenno #24412 05/25/10 09:40 PM
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I thought that improper was accounted for by

CG2O3 OG2D2 OG2D2 CG2O5 96.0000 0 0.00
.

Complete file is attached

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Re: generating parameters for pyruvate
RD2015 #24414 05/25/10 10:29 PM
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Originally Posted By: RD2015
I thought that improper was accounted for by
Code:
CG2O3  OG2D2  OG2D2  CG2O5     96.0000  0     0.00
Every improper needs to be defined both in the topology and in the parameter section of the stream file, as discussed elaborately earlier in this thread. If you don't believe me, just try it.

Re: generating parameters for pyruvate
Kenno #24416 05/25/10 11:04 PM
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Sorry I didn't even realize it was missing there.

The scan & rtf are attached.

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scan.jpg (98.48 KB, 636 downloads)
Last edited by RD2015; 05/26/10 12:16 AM. Reason: rotated pic
Re: generating parameters for pyruvate
RD2015 #24418 05/26/10 01:39 AM
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You see, the major asymmetry around the peaks is gone now. There is still a minor asymmetry around the minima, which most probably is caused by the small offset in the location of the minima in the CCCH scan, and which can be resolved by not constraining CCCH while scanning OCCC. I suggest you try that now. Once that problem is resolved, you might want to tweak your amplitudes a bit, although it may not be necessary.

Re: generating parameters for pyruvate
Kenno #24419 05/26/10 01:56 AM
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Ok I removed the other constraint. Picture is attached.

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Last edited by RD2015; 05/26/10 01:57 AM.
Re: generating parameters for pyruvate
RD2015 #24420 05/26/10 02:20 AM
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Nice! Next step in the procedure is to take the input file for the water interactions, change "stage" to 5, run it, and see if the water interaction energies are still as good. If not, the charges may be tweaked.

Re: generating parameters for pyruvate
Kenno #24426 05/26/10 05:06 AM
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stage 5 result is attached.

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Re: generating parameters for pyruvate
RD2015 #24427 05/26/10 04:14 PM
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Are there significant differences in the water interaction energies, compared to the constrained case? If yes, you might want to consider tweaking the charges. However, if you decide to do so, you'd have to tweak the dihedrals again after tweaking the charges. Then, you have to calculate the charges again and see if tweaking the dihedrals made any difference. Usually, you won't see big changes at that point (meaning that the force field is self-consistent).

Re: generating parameters for pyruvate
Kenno #24428 05/26/10 04:20 PM
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I'm not sure. I'll put the data inside of the post.

constrained:
Code:
PYRU WATER INTERACTION
######## USING MP2 GEOMETRY
QM DIPOLE (DEBYE)
MP2/6-31G*: X= 4.6182 Y= 1.9920 Z= 0.6033 TOT= 5.0655
EMPIRICAL DIPOLE: 6.08792 1.98516 0.682021 6.43962
1) O2...HOH, 180. DEGREES
A.I. -10.21 1.94
EMP. -9.51408 -10.7018 1.18769 1.7
ENE DIFF: 0.69592 DIST DIFF: -0.24
2) O2...HOH LINEAR, HOH: 90. DEGREES
A.I. -8.86 1.97
EMP. -9.51903 -10.7673 1.24829 1.68
ENE DIFF: -0.65903 DIST DIFF: -0.29
3) O11...HOH, 180. DEGREES
A.I. -13.45 1.87
EMP. -11.8093 -13.3237 1.51444 1.72
ENE DIFF: 1.6407 DIST DIFF: -0.15
4) O11...HOH LINEAR, HOH: 90. DEGREES
A.I. -12.97 1.84
EMP. -14.0462 -16.0888 2.04265 1.68
ENE DIFF: -1.0762 DIST DIFF: -0.16
5) O12...HOH, 0. DEGREES
A.I. -11.03 2.01
EMP. -9.8125 -11.1797 1.36724 1.77
ENE DIFF: 1.2175 DIST DIFF: -0.24
6) O12...HOH LINEAR, HOH: 90. DEGREES
A.I. -12.65 1.86
EMP. -14.0059 -16.1521 2.14621 1.68
ENE DIFF: -1.3559 DIST DIFF: -0.18
7) C3H..OHH 90.0 DEGREES
A.I. 0 4.50
EMP. 3.25087 3.3397 -8.882918E-02 4.49
ENE DIFF: 3.25087 DIST DIFF: -1E-02
8) C3H..OHH 90.0 DEGREES
A.I. 0 4.50
EMP. 3.07274 3.42676 -0.354018 2.89
ENE DIFF: 3.07274 DIST DIFF: -1.61
9) C3H..OHH 90.0 DEGREES
A.I. 0 4.50
EMP. 2.17095 2.23453 -6.357937E-02 4.49
ENE DIFF: 2.17095 DIST DIFF: -1E-02
AVEDIFF, RMSDIFF, AVERAGE ABSOLUTE ERROR
0.995283 1.62949 1.6822


unconstrained
Code:
PYRU WATER INTERACTION
QM DIPOLE (DEBYE)
MP2/6-31G*: X= 4.6182 Y= 1.9920 Z= 0.6033 TOT= 5.0655
EMPIRICAL DIPOLE: 6.51472 2.04064 0.629351 6.85579
1) O2...HOH, 180. DEGREES
A.I. -10.21 1.94
EMP. -9.10737 -10.4329 1.32555 1.72
ENE DIFF: 1.10263 DIST DIFF: -0.22
2) O2...HOH LINEAR, HOH: 90. DEGREES
A.I. -8.86 1.97
EMP. -9.37746 -10.6219 1.24447 1.68
ENE DIFF: -0.51746 DIST DIFF: -0.29
3) O11...HOH, 180. DEGREES
A.I. -13.45 1.87
EMP. -11.8425 -13.3543 1.51179 1.72
ENE DIFF: 1.6075 DIST DIFF: -0.15
4) O11...HOH LINEAR, HOH: 90. DEGREES
A.I. -12.97 1.84
EMP. -14.1356 -16.3738 2.23822 1.67
ENE DIFF: -1.1656 DIST DIFF: -0.17
5) O12...HOH, 0. DEGREES
A.I. -11.03 2.01
EMP. -10.4721 -11.9395 1.46745 1.74
ENE DIFF: 0.5579 DIST DIFF: -0.27
6) O12...HOH LINEAR, HOH: 90. DEGREES
A.I. -12.65 1.86
EMP. -14.1965 -16.3492 2.15268 1.68
ENE DIFF: -1.5465 DIST DIFF: -0.18
7) C3H..OHH 90.0 DEGREES
A.I. 0 4.50
EMP. 2.16734 2.23126 -6.391633E-02 4.49
ENE DIFF: 2.16734 DIST DIFF: -1E-02
8) C3H..OHH 90.0 DEGREES
A.I. 0 4.50
EMP. 2.75731 3.08851 -0.331209 2.82
ENE DIFF: 2.75731 DIST DIFF: -1.68
9) C3H..OHH 90.0 DEGREES
A.I. 0 4.50
EMP. 3.08129 3.16696 -8.56656E-02 4.49
ENE DIFF: 3.08129 DIST DIFF: -1E-02
AVEDIFF, RMSDIFF, AVERAGE ABSOLUTE ERROR
0.893823 1.58932 1.6115


So unconstrained is actually a little better?

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