[gmx-users] Bonds of chloroform molecules messed up after EM

[Lili Zhang]

Hi Justin,

Thank you for your reply.
Yes, this is the chloroform based on DH model. The chlo.str file was kindly
shared with me by Dr. MacKerell. I noticed two bond force constant kb and angle
force constant ktheta are zero, in the str file.

BONDS
CCM   CLCM   500.0      1.758
CCM   HCM    500.0      1.100
CLCM  CLCM     0.0      2.9028314
HCM   CLCM     0.0      2.3383924

ANGLES
CLCM  CCM  CLCM    0.0    111.30
HCM   CCM  CLCM    0.0    107.57

I converted the force constant kb in the first two rows from kcal/mole/A**2
(CHARMM unit) to kJ/mole/nm**2 (Gromacs unit), so I did not assign
arbitrary values.

Lili

On Fri, Oct 5, 2018 at 9:36 AM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 10/4/18 6:38 PM, Lili Zhang wrote:
> > Hello Gromacs users,
> >
> > I am trying to run MD  simulation of chloroform in hydrated POPC in
> > CHARMM36 ff. I did not observe anything wrong with the bond structure of
> > chloroform after insert molecules or solvation. But after EM, when I
> looked
> > em.gro in VMD, there were Cl-Cl bonds or Cl-H bonds formed on some
> > chloroform molecules, which had not been there for npt.gro. I assume I
> need
> > to use SHAKE to constrain those bonds during EM, but no completely sure.
> >
> > And I also want check if my "Adding a residue to a force field" process
> is
> > done correctly. The following is what I did.
> >
> > ========================================================================
> > The chloroform atomtypes CCM HCM and CLCM are not included in the ff, so
> I
> > first added them to the atomtypes.atp as
> >    CLCM     35.45000 ;
> >     HCM      1.00800 ;
> >     CCM     12.01100 ;
> >
> > Second, I added LJ parameters to ffnonbonded.itp as
> > ;type atnum         mass   charge ptype           sigma  epsilon
> > CLCM     17    35.450000    0.000  A  0.172067736185  1.25520
> >   CCM      6    12.011000    0.000  A  0.170071301248  0.42677
> >   HCM      1     1.008000    0.000  A  0.110044563280  0.08368
> >
> > Third, I added bond info to ffbonded.itp as
> > [ bondtypes ]
> > ;      i        j  func           b0           kb
> >       CCM     CLCM     1   0.17580000    418400.00
> >      CCM       HCM     1   0.11000000    418400.00
> >
> > [ angletypes ]
> > ;      i        j        k  func       theta0       ktheta          ub0
> >       kub
> >      CLCM      CCM     CLCM     5   111.300000     0.000000   0.00000000
> >      0.00
> >       HCM      CCM     CLCM     5   107.570000     0.000000   0.00000000
> >      0.00
>
> The force constants on your angles are zero, so you effectively have no
> angle potential and your molecule will surely distort as a consequence.
>
> If this is the Dietz and Heininger model for CHCl3, it relies on a rigid
> geometry that includes constrained bonds between all atoms. As I recall
> we have discussed this before, it may not work in GROMACS. But if you're
> going to convert the topology to a "normal" approach of just covalent
> bonds and valence angles, you have to actually parametrize the bonds and
> angles, not just assign arbitrary values (which looks like the case for
> kb in the bonds, as well).
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
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