[gmx-users] request for dihedral PMF test system or complete alanine dipeptide topology file

Chris Neale chris.neale at utoronto.ca
Thu Apr 26 01:19:54 CEST 2007

>I'll have to assume you know what you're doing with using impropers to
>calculate PMFs. I've done this using the dihedral restraints code.
>Have you double-checked that? That's the first place I would look.

Many thanks for your thoughtful reply.

I have included my .top file. The relevant section is in [ dihedral_restraints ]
This file is a template that I use like this: 
sed 's/PHI/${phi_value}/' template.top | sed 's/PSI/${psi_value}/' > phi${phi_value}_psi${psi_value}.top

I read in the gromacs manual 3.3 page 53 "Note that, since it is harmonic, periodicity is not taken into account, 
so it is best to define improper dihedrals to have a E0 as far away from ±180deg as you can manage."
However, I have not heeded this advice for two reasons. First is entirely practical: there is only one reaction coordinate
and so there can only be one dihedral definition e.g. Phi: C'(i-1)-N(i)-CA(i)-C'(i) could be complimented by H(i)-N(i)-CA(i)-C'(i)
with a E0 modified appropriately, but that would not be exact unless the relevant angles were totally constrained 
(as is known for g_chi vs. g_rama). The second reason is that it doesn't quite make sense to me. It seems to me that what is 
actually required is that (E-E0) is always far from +/-180deg and not that E0 itself is far away from 180deg. If this is where I have 
gone wrong then how have you dealt with my concern regarding a strict definition of a reaction coordinate?

$cat template.top

; Include forcefield parameters
#include "/home/cneale/gromacs/top/ffoplsaa.itp"

; Add these in order that ACE - ALA - NAC works properly
[ dihedraltypes ]
;  i    j    k    l   func     coefficients
  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

; Include topologies
#include "/home/cneale/gromacs/proteintop/dialanine.itp"
[ dihedral_restraints ]
; ai   aj    ak    al  type  label  phi  dphi  kfac  power
; phi C'(n-1) - N - CA - C'
   5    7     9    15     1      1  PHI     0     1      2
; psi N - CA - C' - N(n+1)
   7    9    15    17     1      1  PSI     0     1      2

#include "/home/cneale/gromacs/top/tip4p.itp"
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000

[ system ]
; Name
alanine dipeptide solvated in TIP4p water

[ molecules ]
; Compound        #mols
dialanine           1
SOL               869

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