Does anybody have a good test system for reproducing the PMF about a
dihedral? I believe that my procedure is correct, and I have
successfully reproduced a 1d dihedral PMF for a 4 atom chain system
simulated in the absence of nonbonded interactions.
However, my results using an oplsaa interpretation of the alanine
dipeptide ACE-ALA-NAC disagree with the literature both in unconstrained
runs and in a 2D phi-psi PMFs. For example my unconstrained runs of 25ns
only sample beta space and my PMF shows a 6kcal/mol barrier for
transition over psi from beta to alphaR. On the other hand
(Hu,Elstner,Hermans,Proteins 2003) show that 6ns is enough to
significantly sample both Beta and alphaR space and (Ponder,Case,
Adv.Prot.Chem 2003) indicates that the barrier for this beta-alphaR
transition should be between 1.5 and 2 kcal/mol.
If somebody has a good test system that would be greatly appreciated. I
am also including my alanine dipeptide topology file, but I am fairly
sure that it is correct. The only thing that I still question is the
difference between the C-N-CT-HC dihedral parameters (c-terminal in
alanine dipeptide) and C-N-CT_2-HC dihedral parameters (involved where
i+1 is an amino acid residue and not NAC) in ffoplsaabon.itp. However, I
have tested the system while modifying C-N-CT-HC to all zeroes and it
does not change the gross morphology of my results.
In addition I have defined the following types at the beginning of my
.top file to correspond to the CT=CT_2 case as I have previously posted
here:
http://www.gromacs.org/pipermail/gmx-users/2006-September/023875.html.
As a further test I have generated PMFs without the inclusion of these
additional parameters, allowing them to default to all zeroes and it
does not change the gross morphology of my results.
[ dihedraltypes ]
CT C N CT_2 3 30.28798 -4.81160 -25.47638
0.00000 0.00000 0.00000 ; peptide - V1 changed to 2.3
CT_2 C N CT 3 30.28798 -4.81160 -25.47638
0.00000 0.00000 0.00000 ; peptide - V1 changed to 2.3
Before moving on to my .itp file, here are a couple of other points of
interest for anybody embarking on a dihedral PMF determination:
(i) g_chi uses non-standard dihedrals, use g_rama instead.
(ii) the default xtc_precision=1000 may not be large enough to get the
most out of your data. The default value here is fine for distances, but
the precision in a dihedral will be less than the precision in the
coordinates when the dihedral is calculated from the saved coordinates.
Many thanks,
Chris.
$cat alaninedipeptide.itp
[ moleculetype ]
; Name nrexcl
dialanine 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
typeB chargeB massB
1 opls_135 1 ACE CH3 1 -0.18 12.011 ;
qtot -0.18
2 opls_140 1 ACE HH31 1 0.06 1.008 ;
qtot -0.12
3 opls_140 1 ACE HH32 1 0.06 1.008 ;
qtot -0.06
4 opls_140 1 ACE HH33 1 0.06 1.008 ;
qtot 0
5 opls_235 1 ACE C 2 0.5 12.011 ;
qtot 0.5
6 opls_236 1 ACE O 2 -0.5 15.9994 ;
qtot 0
7 opls_238 2 ALA N 3 -0.5 14.0067 ;
qtot -0.5
8 opls_241 2 ALA H 3 0.3 1.008 ;
qtot -0.2
9 opls_224B 2 ALA CA 3 0.14 12.011 ;
qtot -0.06
10 opls_140 2 ALA HA 3 0.06 1.008 ;
qtot 0
11 opls_135 2 ALA CB 4 -0.18 12.011 ;
qtot -0.18
12 opls_140 2 ALA HB1 4 0.06 1.008 ;
qtot -0.12
13 opls_140 2 ALA HB2 4 0.06 1.008 ;
qtot -0.06
14 opls_140 2 ALA HB3 4 0.06 1.008 ;
qtot 0
15 opls_235 2 ALA C 5 0.5 12.011 ;
qtot 0.5
16 opls_236 2 ALA O 5 -0.5 15.9994 ;
qtot 0
17 opls_238 3 NAC N 6 -0.5 14.0067 ;
qtot -0.5
18 opls_241 3 NAC H 6 0.3 1.008 ;
qtot -0.2
19 opls_242 3 NAC CH3 7 0.02 12.011 ;
qtot -0.18
20 opls_140 3 NAC HH31 7 0.06 1.008 ;
qtot -0.12
21 opls_140 3 NAC HH32 7 0.06 1.008 ;
qtot -0.06
22 opls_140 3 NAC HH33 7 0.06 1.008 ;
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
7 8 1
7 9 1
9 10 1
9 11 1
9 15 1
11 12 1
11 13 1
11 14 1
15 16 1
15 17 1
17 18 1
17 19 1
19 20 1
19 21 1
19 22 1
[ pairs ]
; ai aj funct c0 c1 c2 c3
1 8 1
1 9 1
2 6 1
2 7 1
3 6 1
3 7 1
4 6 1
4 7 1
5 10 1
5 11 1
5 15 1
6 8 1
6 9 1
7 12 1
7 13 1
7 14 1
7 16 1
7 17 1
8 10 1
8 11 1
8 15 1
9 18 1
9 19 1
10 12 1
10 13 1
10 14 1
10 16 1
10 17 1
11 16 1
11 17 1
12 15 1
13 15 1
14 15 1
15 20 1
15 21 1
15 22 1
16 18 1
16 19 1
18 20 1
18 21 1
18 22 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
6 5 7 1
5 7 8 1
5 7 9 1
8 7 9 1
7 9 10 1
7 9 11 1
7 9 15 1
10 9 11 1
10 9 15 1
11 9 15 1
9 11 12 1
9 11 13 1
9 11 14 1
12 11 13 1
12 11 14 1
13 11 14 1
9 15 16 1
9 15 17 1
16 15 17 1
15 17 18 1
15 17 19 1
18 17 19 1
17 19 20 1
17 19 21 1
17 19 22 1
20 19 21 1
20 19 22 1
21 19 22 1
[ dihedrals ]
; ai aj ak al funct c0 c1
c2 c3 c4 c5
2 1 5 6 3
2 1 5 7 3
3 1 5 6 3
3 1 5 7 3
4 1 5 6 3
4 1 5 7 3
1 5 7 8 3
1 5 7 9 3
6 5 7 8 3
6 5 7 9 3
5 7 9 10 3
5 7 9 11 3
5 7 9 15 3
8 7 9 10 3
8 7 9 11 3
8 7 9 15 3
7 9 11 12 3
7 9 11 13 3
7 9 11 14 3
10 9 11 12 3
10 9 11 13 3
10 9 11 14 3
15 9 11 12 3
15 9 11 13 3
15 9 11 14 3
7 9 15 16 3
7 9 15 17 3
10 9 15 16 3
10 9 15 17 3
11 9 15 16 3
11 9 15 17 3
9 15 17 18 3
9 15 17 19 3
16 15 17 18 3
16 15 17 19 3
15 17 19 20 3
15 17 19 21 3
15 17 19 22 3
18 17 19 20 3
18 17 19 21 3
18 17 19 22 3
[ dihedrals ]
; ai aj ak al funct c0 c1
c2 c3
1 7 5 6 1 improper_O_C_X_Y
5 9 7 8 1 improper_Z_N_X_Y
9 17 15 16 1 improper_O_C_X_Y
15 19 17 18 1 improper_Z_N_X_Y
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