[gmx-users] question about preferred values in itp files

abhishek khetan askhetan at gmail.com
Wed Apr 13 19:54:00 CEST 2016

Dear gmx-users,

I have the opls-aa forcefield file for acetonitrile. It looks something
 [ moleculetype ]
 ; Name            nrexcl
 ACN                 3

 [ atoms ]
 ;   nr       type  resnr residue  atom   cgnr     charge       mass
      1   opls_755      1    ACN      C1      1      -0.08    12.01100
      2   opls_759      2    ACN      H2      1       0.06     1.00800
      3   opls_759      3    ACN      H3      1       0.06     1.00800
      4   opls_759      4    ACN      H4      1       0.06     1.00800
      5   opls_754      5    ACN      C5      2       0.46    12.01100
      6   opls_753      6    ACN      N6      3      -0.56    14.00670

My topol.top file looks like
#include "./oplsaa.ff/forcefield.itp"
#include "./oplsaa.ff/acn.itp"

[ system ]
; Name

[ molecules ]
; Compound        #mols
ACN              216

And the forcefield.itp looks like
[ defaults ]
; nbfunc    comb-rule    gen-pairs    fudgeLJ    fudgeQQ
1        3        yes        0.5    0.5

#include "ffnonbonded.itp"
#include "ffbonded.itp"

Needless to mention, that the ffbonded.itp and ffnonbonded.itp are the
standard files from the oplsaa.ff directory in which the opls_XYZ
[atomtypes]/[bondtypes]/[dihedraltypes] etc are defined.

My questions now are these:

1. When the charge and mass are already mentioned in the ffbonded.itp and
ffnonbonded.itp files for each of the opls_XYZ entries, then why do we
specify it again in the acn.itp file? Which values are read in the
simulations? the one from ffnonbonded.itp or the ones from acn.itp ? In
acse the acn.itp values are preferred, does it mean that the epsilon and
sigma value are still read from the ffnonbonded.itp file ?

2. BIGGER QUESTION: When i look at the ffnonbonded and ffbonded files - the
bondtypes are specified in terms of the atom symbols from atomtpes, instead
of the . The ffnonbonded and non bonded have entries like:
[ atomtypes ]
 opls_001   C    6      12.01100     0.500       A    3.75000e-01
4.39320e-01 ; SIG
 opls_017   C    6      12.01100     0.700       A    3.75000e-01
4.39320e-01 ; SIG
 opls_026   C    6      12.01100     0.265       A    3.75000e-01
4.60240e-01 ; SIG
[ bondtypes ]
  C     C3      1    0.15220   265265.6   ; END
  C     CA      1    0.14900   334720.0   ; wlj 8/97
  C     CB      1    0.14190   374049.6   ; GUA
  C     CM      1    0.14440   343088.0   ; THY
  C     CS      1    0.14900   334720.0   ;

As you see all the bondtypes involve C as one of the atom types - how does
gromacs know which atomtype to choose ?? there are multiple atomtypes
corresponding to the same symbol. Or are have the symbols been chosen in
such a way that when wither if opls 001/017/026 bonds with C3 then the bond

3. EVEN BIGGER QUESTION: From what I understand, once I specify the
opls_XYZ type for a certain atom in a given molecule along with
[bonds]/[dihedrals]/etc in the acn.itp, it reads all specifications along
with the equilibrium bond distances, the angles and all that stuff from the
ffbonded.itp and ffnonbonded.itp files and constructs the equilibrium
geometry of the molecule by itself. Does that mean that any geometry
specified by me for a single molecule is henceforth irrelevant ? I have
geometry for acetonitrile, calculated at a very high level of quantum
chemistry, perhaps more accurate than the one supplied in the pdb file that
came with the forcefield. However, this accurate geometry may not be
exactly the same as that constructed by gromacs from the ffbonded.itp and
ffnonbonded.itp. Why do then, people always provide a *pdb or *gro file for
the molecule along with the itp. if one has the acn.itp and the
ffbonded.itp and ffnonbonded.itp files, the geometry can already be
constructed... or ?

Thanks for your patience in reading these and taking the time to answer.


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