[gmx-users] Why is there a difference between an angle of 0 or 180 deg. for a type 9 proper dihedral with multiplicity of 2?
Christopher Neale
chris.neale at alum.utoronto.ca
Mon Jul 6 02:22:03 CEST 2015
I see, thank you Justin. I guess that even though I did read the equation, which is:
K(1 + cos(n*phi - phi_s)
I was actually thinking:
K(1 + cos(n* [ phi - phi_s ] )
so everything is as it should be.
Thanks for all your help,
Chris.
________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin Lemkul <jalemkul at vt.edu>
Sent: 05 July 2015 13:12
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Why is there a difference between an angle of 0 or 180 deg. for a type 9 proper dihedral with multiplicity of 2?
On 7/5/15 9:10 AM, Christopher Neale wrote:
> Dear Justin:
>
> here is a topology followed by initial coordinates (in which the rings of both Phe are planar, straight out of molefacture/pdb2gmx). Run this in EM or MD and the SC ring of Phe #1 will distort. However, replace "0 15.1669998 2" by "180 15.1669998 2" and everything is groovy.
>
My initial gut reaction (and yours) was incorrect. Plot the cosine series of
15.167(1-cos(2*phi-180) vs. 15.167(1-cos(2*phi)) and you will see that the
minima that you obtain when the phase is 180 have become maxima. Hence when you
switch the phase angle between 0 and 180, you completely invert the energy
landscape. Really wild to watch a planar benzene convert to a chair,
pseudo-cyclohexane :)
-Justin
> Chris.
>
> ###########################################
> ### TOPOLOGY
> ;
> ; File 'topol.top' was generated
> ; By user: lh824914 (36108)
> ; On host: headnode.rit.albany.edu
> ; At date: Sat Jul 4 23:10:10 2015
> ;
> ; This is a standalone topology file
> ;
> ; It was generated using program:
> ; pdb2gmx - VERSION 4.6.3
> ;
> ; Command line was:
> ; pdb2gmx -f FF.gro -ignh
> ;
> ; Force field was read from the standard Gromacs share directory.
> ;
>
> ; Include forcefield parameters
> #include "amber99.ff/forcefield.itp"
>
> [ moleculetype ]
> ; Name nrexcl
> Protein 3
>
> [ atoms ]
> ; nr type resnr residue atom cgnr charge mass typeB chargeB massB
> ; residue 1 PHE rtp NPHE q +1.0
> 1 N3 1 PHE N 1 0.1737 14.01 ; qtot 0.1737
> 2 H 1 PHE H1 2 0.1921 1.008 ; qtot 0.3658
> 3 H 1 PHE H2 3 0.1921 1.008 ; qtot 0.5579
> 4 H 1 PHE H3 4 0.1921 1.008 ; qtot 0.75
> 5 CT 1 PHE CA 5 0.0733 12.01 ; qtot 0.8233
> 6 HP 1 PHE HA 6 0.1041 1.008 ; qtot 0.9274
> 7 CT 1 PHE CB 7 0.033 12.01 ; qtot 0.9604
> 8 HC 1 PHE HB1 8 0.0104 1.008 ; qtot 0.9708
> 9 HC 1 PHE HB2 9 0.0104 1.008 ; qtot 0.9812
> 10 CA 1 PHE CG 10 0.0031 12.01 ; qtot 0.9843
> 11 CA 1 PHE CD1 11 -0.1392 12.01 ; qtot 0.8451
> 12 HA 1 PHE HD1 12 0.1374 1.008 ; qtot 0.9825
> 13 CA 1 PHE CE1 13 -0.1602 12.01 ; qtot 0.8223
> 14 HA 1 PHE HE1 14 0.1433 1.008 ; qtot 0.9656
> 15 CA 1 PHE CZ 15 -0.1208 12.01 ; qtot 0.8448
> 16 HA 1 PHE HZ 16 0.1329 1.008 ; qtot 0.9777
> 17 CA 1 PHE CE2 17 -0.1603 12.01 ; qtot 0.8174
> 18 HA 1 PHE HE2 18 0.1433 1.008 ; qtot 0.9607
> 19 CA 1 PHE CD2 19 -0.1391 12.01 ; qtot 0.8216
> 20 HA 1 PHE HD2 20 0.1374 1.008 ; qtot 0.959
> 21 C 1 PHE C 21 0.6123 12.01 ; qtot 1.571
> 22 O 1 PHE O 22 -0.5713 16 ; qtot 1
> ; residue 2 PHE rtp CPHE q -1.0
> 23 N 2 PHE N 23 -0.3821 14.01 ; qtot 0.6179
> 24 H 2 PHE H 24 0.2681 1.008 ; qtot 0.886
> 25 CT 2 PHE CA 25 -0.1825 12.01 ; qtot 0.7035
> 26 H1 2 PHE HA 26 0.1098 1.008 ; qtot 0.8133
> 27 CT 2 PHE CB 27 -0.0959 12.01 ; qtot 0.7174
> 28 HC 2 PHE HB1 28 0.0443 1.008 ; qtot 0.7617
> 29 HC 2 PHE HB2 29 0.0443 1.008 ; qtot 0.806
> 30 CA 2 PHE CG 30 0.0552 12.01 ; qtot 0.8612
> 31 CA 2 PHE CD1 31 -0.13 12.01 ; qtot 0.7312
> 32 HA 2 PHE HD1 32 0.1408 1.008 ; qtot 0.872
> 33 CA 2 PHE CE1 33 -0.1847 12.01 ; qtot 0.6873
> 34 HA 2 PHE HE1 34 0.1461 1.008 ; qtot 0.8334
> 35 CA 2 PHE CZ 35 -0.0944 12.01 ; qtot 0.739
> 36 HA 2 PHE HZ 36 0.128 1.008 ; qtot 0.867
> 37 CA 2 PHE CE2 37 -0.1847 12.01 ; qtot 0.6823
> 38 HA 2 PHE HE2 38 0.1461 1.008 ; qtot 0.8284
> 39 CA 2 PHE CD2 39 -0.13 12.01 ; qtot 0.6984
> 40 HA 2 PHE HD2 40 0.1408 1.008 ; qtot 0.8392
> 41 C 2 PHE C 41 0.766 12.01 ; qtot 1.605
> 42 O2 2 PHE OC1 42 -0.8026 16 ; qtot 0.8026
> 43 O2 2 PHE OC2 43 -0.8026 16 ; qtot 0
>
> [ bonds ]
> ; ai aj funct c0 c1 c2 c3
> 1 2 1
> 1 3 1
> 1 4 1
> 1 5 1
> 5 6 1
> 5 7 1
> 5 21 1
> 7 8 1
> 7 9 1
> 7 10 1
> 10 11 1
> 10 19 1
> 11 12 1
> 11 13 1
> 13 14 1
> 13 15 1
> 15 16 1
> 15 17 1
> 17 18 1
> 17 19 1
> 19 20 1
> 21 22 1
> 21 23 1
> 23 24 1
> 23 25 1
> 25 26 1
> 25 27 1
> 25 41 1
> 27 28 1
> 27 29 1
> 27 30 1
> 30 31 1
> 30 39 1
> 31 32 1
> 31 33 1
> 33 34 1
> 33 35 1
> 35 36 1
> 35 37 1
> 37 38 1
> 37 39 1
> 39 40 1
> 41 42 1
> 41 43 1
>
> [ pairs ]
> ; ai aj funct c0 c1 c2 c3
> 1 8 1
> 1 9 1
> 1 10 1
> 1 22 1
> 1 23 1
> 2 6 1
> 2 7 1
> 2 21 1
> 3 6 1
> 3 7 1
> 3 21 1
> 4 6 1
> 4 7 1
> 4 21 1
> 5 11 1
> 5 19 1
> 5 24 1
> 5 25 1
> 6 8 1
> 6 9 1
> 6 10 1
> 6 22 1
> 6 23 1
> 7 12 1
> 7 13 1
> 7 17 1
> 7 20 1
> 7 22 1
> 7 23 1
> 8 11 1
> 8 19 1
> 8 21 1
> 9 11 1
> 9 19 1
> 9 21 1
> 10 14 1
> 10 15 1
> 10 18 1
> 10 21 1
> 11 16 1
> 11 17 1
> 11 20 1
> 12 14 1
> 12 15 1
> 12 19 1
> 13 18 1
> 13 19 1
> 14 16 1
> 14 17 1
> 15 20 1
> 16 18 1
> 16 19 1
> 18 20 1
> 21 26 1
> 21 27 1
> 21 41 1
> 22 24 1
> 22 25 1
> 23 28 1
> 23 29 1
> 23 30 1
> 23 42 1
> 23 43 1
> 24 26 1
> 24 27 1
> 24 41 1
> 25 31 1
> 25 39 1
> 26 28 1
> 26 29 1
> 26 30 1
> 26 42 1
> 26 43 1
> 27 32 1
> 27 33 1
> 27 37 1
> 27 40 1
> 27 42 1
> 27 43 1
> 28 31 1
> 28 39 1
> 28 41 1
> 29 31 1
> 29 39 1
> 29 41 1
> 30 34 1
> 30 35 1
> 30 38 1
> 30 41 1
> 31 36 1
> 31 37 1
> 31 40 1
> 32 34 1
> 32 35 1
> 32 39 1
> 33 38 1
> 33 39 1
> 34 36 1
> 34 37 1
> 35 40 1
> 36 38 1
> 36 39 1
> 38 40 1
>
> [ angles ]
> ; ai aj ak funct c0 c1 c2 c3
> 2 1 3 1
> 2 1 4 1
> 2 1 5 1
> 3 1 4 1
> 3 1 5 1
> 4 1 5 1
> 1 5 6 1
> 1 5 7 1
> 1 5 21 1
> 6 5 7 1
> 6 5 21 1
> 7 5 21 1
> 5 7 8 1
> 5 7 9 1
> 5 7 10 1
> 8 7 9 1
> 8 7 10 1
> 9 7 10 1
> 7 10 11 1
> 7 10 19 1
> 11 10 19 1
> 10 11 12 1
> 10 11 13 1
> 12 11 13 1
> 11 13 14 1
> 11 13 15 1
> 14 13 15 1
> 13 15 16 1
> 13 15 17 1
> 16 15 17 1
> 15 17 18 1
> 15 17 19 1
> 18 17 19 1
> 10 19 17 1
> 10 19 20 1
> 17 19 20 1
> 5 21 22 1
> 5 21 23 1
> 22 21 23 1
> 21 23 24 1
> 21 23 25 1
> 24 23 25 1
> 23 25 26 1
> 23 25 27 1
> 23 25 41 1
> 26 25 27 1
> 26 25 41 1
> 27 25 41 1
> 25 27 28 1
> 25 27 29 1
> 25 27 30 1
> 28 27 29 1
> 28 27 30 1
> 29 27 30 1
> 27 30 31 1
> 27 30 39 1
> 31 30 39 1
> 30 31 32 1
> 30 31 33 1
> 32 31 33 1
> 31 33 34 1
> 31 33 35 1
> 34 33 35 1
> 33 35 36 1
> 33 35 37 1
> 36 35 37 1
> 35 37 38 1
> 35 37 39 1
> 38 37 39 1
> 30 39 37 1
> 30 39 40 1
> 37 39 40 1
> 25 41 42 1
> 25 41 43 1
> 42 41 43 1
>
> [ dihedrals ]
> ; ai aj ak al funct c0 c1 c2 c3 c4 c5
> 2 1 5 6 9
> 2 1 5 7 9
> 2 1 5 21 9
> 3 1 5 6 9
> 3 1 5 7 9
> 3 1 5 21 9
> 4 1 5 6 9
> 4 1 5 7 9
> 4 1 5 21 9
> 1 5 7 8 9
> 1 5 7 9 9
> 1 5 7 10 9
> 6 5 7 8 9
> 6 5 7 9 9
> 6 5 7 10 9
> 21 5 7 8 9
> 21 5 7 9 9
> 21 5 7 10 9
> 1 5 21 22 9
> 1 5 21 23 9
> 6 5 21 22 9
> 6 5 21 23 9
> 7 5 21 22 9
> 7 5 21 23 9
> 5 7 10 11 9
> 5 7 10 19 9
> 8 7 10 11 9
> 8 7 10 19 9
> 9 7 10 11 9
> 9 7 10 19 9
> 7 10 11 12 9 0 15.1669998 2
> 7 10 11 13 9 0 15.1669998 2
> 19 10 11 12 9 0 15.1669998 2
> 19 10 11 13 9 0 15.1669998 2
> 7 10 19 17 9 0 15.1669998 2
> 7 10 19 20 9 0 15.1669998 2
> 11 10 19 17 9 0 15.1669998 2
> 11 10 19 20 9 0 15.1669998 2
> 10 11 13 14 9 0 15.1669998 2
> 10 11 13 15 9 0 15.1669998 2
> 12 11 13 14 9 0 15.1669998 2
> 12 11 13 15 9 0 15.1669998 2
> 11 13 15 16 9 0 15.1669998 2
> 11 13 15 17 9 0 15.1669998 2
> 14 13 15 16 9 0 15.1669998 2
> 14 13 15 17 9 0 15.1669998 2
> 13 15 17 18 9 0 15.1669998 2
> 13 15 17 19 9 0 15.1669998 2
> 16 15 17 18 9 0 15.1669998 2
> 16 15 17 19 9 0 15.1669998 2
> 15 17 19 10 9 0 15.1669998 2
> 15 17 19 20 9 0 15.1669998 2
> 18 17 19 10 9 0 15.1669998 2
> 18 17 19 20 9 0 15.1669998 2
> 5 21 23 24 9
> 5 21 23 25 9
> 22 21 23 24 9
> 22 21 23 25 9
> 21 23 25 26 9
> 21 23 25 27 9
> 21 23 25 41 9
> 24 23 25 26 9
> 24 23 25 27 9
> 24 23 25 41 9
> 23 25 27 28 9
> 23 25 27 29 9
> 23 25 27 30 9
> 26 25 27 28 9
> 26 25 27 29 9
> 26 25 27 30 9
> 41 25 27 28 9
> 41 25 27 29 9
> 41 25 27 30 9
> 23 25 41 42 9
> 23 25 41 43 9
> 26 25 41 42 9
> 26 25 41 43 9
> 27 25 41 42 9
> 27 25 41 43 9
> 25 27 30 31 9
> 25 27 30 39 9
> 28 27 30 31 9
> 28 27 30 39 9
> 29 27 30 31 9
> 29 27 30 39 9
> 27 30 31 32 9
> 27 30 31 33 9
> 39 30 31 32 9
> 39 30 31 33 9
> 27 30 39 37 9
> 27 30 39 40 9
> 31 30 39 37 9
> 31 30 39 40 9
> 30 31 33 34 9
> 30 31 33 35 9
> 32 31 33 34 9
> 32 31 33 35 9
> 31 33 35 36 9
> 31 33 35 37 9
> 34 33 35 36 9
> 34 33 35 37 9
> 33 35 37 38 9
> 33 35 37 39 9
> 36 35 37 38 9
> 36 35 37 39 9
> 35 37 39 30 9
> 35 37 39 40 9
> 38 37 39 30 9
> 38 37 39 40 9
>
> [ dihedrals ]
> ; ai aj ak al funct c0 c1 c2 c3
> 5 23 21 22 4
> 7 10 19 11 4
> 10 13 11 12 4
> 10 17 19 20 4
> 11 15 13 14 4
> 13 17 15 16 4
> 15 19 17 18 4
> 21 25 23 24 4
> 25 42 41 43 4
> 27 30 39 31 4
> 30 33 31 32 4
> 30 37 39 40 4
> 31 35 33 34 4
> 33 37 35 36 4
> 35 39 37 38 4
>
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
>
> ; Include water topology
> #include "amber99.ff/tip3p.itp"
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ; i funct fcx fcy fcz
> 1 1 1000 1000 1000
> #endif
>
> ; Include topology for ions
> #include "amber99.ff/ions.itp"
>
> [ system ]
> ; Name
> Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
>
> [ molecules ]
> ; Compound #mols
> Protein 1
>
>
>
> ###########################################
> ### INITIAL COORDINATES
>
> Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
> 43
> 1PHE N 1 -0.013 0.245 -0.011
> 1PHE H1 2 -0.082 0.296 0.040
> 1PHE H2 3 0.064 0.225 0.049
> 1PHE H3 4 0.018 0.300 -0.088
> 1PHE CA 5 -0.070 0.121 -0.060
> 1PHE HA 6 -0.146 0.146 -0.120
> 1PHE CB 7 0.036 0.047 -0.136
> 1PHE HB1 8 0.122 0.085 -0.102
> 1PHE HB2 9 0.023 0.076 -0.231
> 1PHE CG 10 0.058 -0.104 -0.142
> 1PHE CD1 11 -0.017 -0.189 -0.060
> 1PHE HD1 12 -0.085 -0.151 0.003
> 1PHE CE1 13 0.003 -0.327 -0.067
> 1PHE HE1 14 -0.051 -0.388 -0.009
> 1PHE CZ 15 0.098 -0.380 -0.155
> 1PHE HZ 16 0.112 -0.479 -0.160
> 1PHE CE2 17 0.173 -0.294 -0.237
> 1PHE HE2 18 0.241 -0.331 -0.300
> 1PHE CD2 19 0.152 -0.155 -0.230
> 1PHE HD2 20 0.205 -0.093 -0.288
> 1PHE C 21 -0.122 0.034 0.054
> 1PHE O 22 -0.052 -0.053 0.105
> 2PHE N 23 -0.243 0.056 0.096
> 2PHE H 24 -0.298 0.127 0.053
> 2PHE CA 25 -0.300 -0.022 0.206
> 2PHE HA 26 -0.301 -0.118 0.177
> 2PHE CB 27 -0.214 -0.007 0.327
> 2PHE HB1 28 -0.258 0.067 0.379
> 2PHE HB2 29 -0.127 0.025 0.291
> 2PHE CG 30 -0.179 -0.115 0.430
> 2PHE CD1 31 -0.241 -0.240 0.424
> 2PHE HD1 32 -0.309 -0.259 0.353
> 2PHE CE1 33 -0.208 -0.338 0.518
> 2PHE HE1 34 -0.252 -0.428 0.514
> 2PHE CZ 35 -0.113 -0.311 0.618
> 2PHE HZ 36 -0.090 -0.381 0.685
> 2PHE CE2 37 -0.051 -0.185 0.623
> 2PHE HE2 38 0.016 -0.165 0.694
> 2PHE CD2 39 -0.084 -0.087 0.528
> 2PHE HD2 40 -0.040 0.003 0.531
> 2PHE C 41 -0.442 0.022 0.236
> 2PHE OC1 42 -0.493 -0.024 0.309
> 2PHE OC2 43 -0.496 0.113 0.173
> 10.00000 10.00000 10.00000
>
>
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin Lemkul <jalemkul at vt.edu>
> Sent: 05 July 2015 08:52
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Why is there a difference between an angle of 0 or 180 deg. for a type 9 proper dihedral with multiplicity of 2?
>
> On 7/5/15 12:56 AM, Christopher Neale wrote:
>> Dear Justin:
>>
>> Thank you for your help. I am glad to see that I was not way out to lunch in my interpretation of multiplicity and proper dihedral angles.
>>
>> First, the out-of-plane motions are not minor. Even just in EM, the dihedral angles along the main ring convert from near 0 deg to about 50 deg, so I think that we're into the neighbourhood of major problems here. Second, my test system was a single ring, like benzene but with a couple of substituents. However, I can reproduce this issue in a standard molecule as follows, so I do not think that the issue has anything to do with my exotic molecule. Take any peptide/protein with a phenylalanine. There are 24 proper dihedral angles around the PHE sidechain ring in the amber99 force field. In this force field, these dihedral angles are all 180 deg / Fc=15.1669998 / mult=2. I take my toplogy out of pdb2gmx and specify these parameters in the .top file and run EM and I still get the planar ring, as expected. Now I simply change those N=24 occurrences of 180 deg to 0 deg (still multiplicity=2) and I run EM and I get these ~50 deg dihedral angles around the ring. This is still wi!
t!
> h g
>> romacs 4.6.3. I have not checked with other versions of gromacs.
>>
>> If you make a PHE-PHE peptide in VMD with molefacture (2 aa's to avoid the problem amber has with a single amino acid and the termini), then run it through pdb2gmx (v. 4.6.3) the lines in the [ dihedrals ] section that need modification to adjust the proper dihedral angles in the ring of the first PHE sidechain are:
>>
>> 7 10 11 12 9 0 15.1669998 2
>> 7 10 11 13 9 0 15.1669998 2
>> 19 10 11 12 9 0 15.1669998 2
>> 19 10 11 13 9 0 15.1669998 2
>> 7 10 19 17 9 0 15.1669998 2
>> 7 10 19 20 9 0 15.1669998 2
>> 11 10 19 17 9 0 15.1669998 2
>> 11 10 19 20 9 0 15.1669998 2
>> 10 11 13 14 9 0 15.1669998 2
>> 10 11 13 15 9 0 15.1669998 2
>> 12 11 13 14 9 0 15.1669998 2
>> 12 11 13 15 9 0 15.1669998 2
>> 11 13 15 16 9 0 15.1669998 2
>> 11 13 15 17 9 0 15.1669998 2
>> 14 13 15 16 9 0 15.1669998 2
>> 14 13 15 17 9 0 15.1669998 2
>> 13 15 17 18 9 0 15.1669998 2
>> 13 15 17 19 9 0 15.1669998 2
>> 16 15 17 18 9 0 15.1669998 2
>> 16 15 17 19 9 0 15.1669998 2
>> 15 17 19 10 9 0 15.1669998 2
>> 15 17 19 20 9 0 15.1669998 2
>> 18 17 19 10 9 0 15.1669998 2
>> 18 17 19 20 9 0 15.1669998 2
>>
>
> Can you send the full topology, or at least the [atoms] section? I can't
> decipher what these actually should be.
>
> -Justin
>
>> where I get the bizarre conformations when I use the above, but if I switch the "0"'s to "180"'s (recovering the original force field) then I get a planar ring.
>>
>> Therefore, I think that either I am misunderstanding something about proper dihedrals and multiplicity = 2 or there is a more serious problem. What I don't understand at this point is that the force fields (amber at least) actually contain quite a few proper dihedrals that do use angle = 0 and multiplicity = 2, so what is special aboutthe PHE test case outlined above that leads them to not work whereas they are obviously intended to work.
>>
>> I'll take a look into other gromacs versions when I have a chance and will report back.
>>
>> Thank you,
>> Chris.
>>
>> ________________________________________
>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin Lemkul <jalemkul at vt.edu>
>> Sent: 04 July 2015 09:41
>> To: gmx-users at gromacs.org
>> Subject: Re: [gmx-users] Why is there a difference between an angle of 0 or 180 deg. for a type 9 proper dihedral with multiplicity of 2?
>>
>> On 7/4/15 3:32 AM, Christopher Neale wrote:
>>> Dear Gromacs users:
>>>
>>> I have been working on creating a topology for an exotic molecule. It
>>> contains aromatic rings and my parameters always seemed to allow the rings to
>>> buckle and become non-planer, much like a glucose ring would (though a little
>>> less extensively). However, I have managed to solve the problem by switching
>>> my proper (type 9) dihedral angles from angle = 0 degrees, multiplicity = 2
>>> to angle = 180 degrees, multiplicity = 2. I thought that those two conditions
>>> should be equivalent and it was only by seriously simplifying the molecule
>>> down to a single ring and then toying with every conceivable parameter that I
>>> even hit on this. I am using gromacs 4.6.3 and have not tried other versions
>>> of gromacs, but this makes so little sense to me that I thought I would ask
>>> about it here. There are lots of proper dihedrals in the available force
>>> fields that use dihedrals with a set angle of zero degrees, though I do note
>>> that for any aromatic ring that I have seen they are always 180 deg (with
>>> mul tiplicity of 2 so that they can handle both cis and trans). Presumably I
>>> have just missed some obvious definition, but at least I can verify that if I
>>> switch even one proper dihedral from angle = 180 back to angle = 0 (with
>>> multiplicity = 2 in each case), then I start to see deformation of the ring's
>>> planarity.
>>>
>>
>> Some deformation is not necessarily unphysical. Aromatic rings in CHARMM are
>> treated like this, for instance. It shouldn't be substantial, but it shouldn't
>> remain exactly planar, either. What are the parameters you're using? The
>> choice of 0 vs. 180 here for multiplicity = 2 should indeed be irrelevant. Have
>> you gone down to something as simple as, e.g. benzene?
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
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>>
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
>
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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