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Relaxed potential energy scans
#1255 04/14/04 03:33 AM
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I am trying to perform a relaxed PES to optimize a dihedral angle. I am beginning to question my strategy in conducting this. Basically, I am scanning from 0 to 360 degrees in 10 degree increments. I fix the desired angle at each step using
CONS DIHE FORCE 2000 ...

then minimize with
MINI CONJ NSTEP 1000 TOLGRD 0.0001 ...

I remove the constraint before taking a single point energy.

I then plot ?ENER vs. angle and comparing to the equivalent plot I obtain from my ab initio scan (Gaussian03 HF/6-31g* opt=modredundant)

I was thrilled when my optimized charmm surface fit the ab intio surface, but slightly less than thrilled when I found that the optimized structures differ by ninety degrees in the "optimized" torsion angle.

Is my approach completely wrong or do I just have a subtle bug?

I was concerned at first about using such a large force constant to hold the dihedral, but clearing it before the energy calc should prevent it from messing up the results, right? If I am understanding things correctly, this should be essentially what is happening in the ab initio scan.

Is minimizing with TOLGRD somehow a problem? I set it so slow because I have been looking at normal mode analysis as well and I was also trying to mimic the ab initio convergence.

If anybody has an epiphany to share, I would appreciate it, 'cause I am almost out of fresh ideas.


Joshua Ward Graduate Student Purdue University Department of Medicinal Chemistry and Pharmacology
Re: Relaxed potential energy scans
jmwict13 #1256 04/14/04 03:48 PM
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Why minimize at all? - if you want to do a MM-scan of the dihedral angle it might be easier just to rotate about the dihedral angle, assuming that adjacent groups are rigid, and then perform a single point energy calculation.

Re: Relaxed potential energy scans
jmwict13 #1257 04/15/04 06:04 PM
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Jeff,

First, you definetly have to do a relaxed PE scan in the MM calculation as this is what you are doing in the QM calculation. Remember to always use identical restraints in the QM and MM calculations.

Concerning your problem, you are assigning the restraints incorrectly or, perhaps,
not using "cons cldh" after each round of minimization to remove the old restraints.

There are a number of example inputs out there; see my web page for more information.

http://www.pharmacy.umaryland.edu/faculty/amackere/param/force_field_dev.htm

alex


School of Pharmacy
University of Maryland
20 Penn Street
Baltimore, MD, 21201
Re: Relaxed potential energy scans
jmwict13 #1258 04/16/04 01:17 PM
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How did you calculate the relaxed PES of a dihedral angle through GAUSSIAN, did you get the energies by the input file like this:
%CHK=G:/gal-dihedral-2/gal 14-12-16-18 torsion-2
%Mem=1000MB
#T HF/6-31G* opt=modredundant NoSymmetry

gal 14-12-16-18 torsion energy

0 1
C,0.4351957298,1.236891283,1.1583754
H,-0.4012189858,1.9246239069,1.09819828
O,1.2017089008,1.6624601161,2.2104512776
H,1.9504918787,1.0886980273,2.3120960291
C,-1.0813076781,-0.4537504411,0.5921886078
H,-1.8967305911,0.2541145419,0.728520529
O,-0.0127836597,-0.0632675116,1.4092419991
C,1.2000292197,1.1714754111,-0.1511498321
…

* 12 16 * R
14 12 16 18 0.0 S 12 30.0
or get the energies one by one independently with the corresponding fixed dihedral angle and the same initial structure every time? is it same between the different calculation methods? Thanks!


Re: Relaxed potential energy scans
shouqinlv #1259 04/16/04 02:05 PM
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One of my scan scripts:

$RunGauss
%chk=5431.chk (from optimized structure w/ opt command)
#hf/6-31g* geom=checkpoint opt=modredundant

partial optimization ( I wanted to make sure my torsion angle starts at zero degrees)

0 1

5 4 3 1 0.0 f

--Link1--
%chk=5431.chk
#hf/6-31g* geom=checkpoint opt=modredundant

relaxed PES c5-c4-c3-c1 torsion angle

0 1

5 4 3 1 s 36 10.0



I haven't tried it the other way. I assumed it would be a more time consuming method to do the same thing, but it would be a control I suppose. I have actually had improved results in the past few days. How likely is it that Gaussian will find a local instead of the global minimum of a small molecule? (I think that 10 haevy atoms can still be called a small molecule in Gaussian terms) I might have been using a partially optimized structure from Gaussian for comparison. Thanks to everbody for the thoughts and disussion. It's much more productive than talking to myself

Last edited by jmwict13; 04/16/04 02:06 PM.

Joshua Ward Graduate Student Purdue University Department of Medicinal Chemistry and Pharmacology
Re: Relaxed potential energy scans
jmwict13 #1260 04/16/04 04:08 PM
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It appears that the gaussian structure I was using for my comparsion was actually at a local minimum and not the global minimized structure. Both my structures and my surfaces are now aligning quite well.


Joshua Ward Graduate Student Purdue University Department of Medicinal Chemistry and Pharmacology

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