[gmx-users] Bonds of chloroform molecules messed up after EM
zhanl10 at mcmaster.ca
Fri Oct 5 16:07:52 CEST 2018
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.
CCM CLCM 500.0 1.758
CCM HCM 500.0 1.100
CLCM CLCM 0.0 2.9028314
HCM CLCM 0.0 2.3383924
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
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
> > 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
> > 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
> > done correctly. The following is what I did.
> > ========================================================================
> > The chloroform atomtypes CCM HCM and CLCM are not included in the ff, so
> > 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 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
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