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

[Lili Zhang]

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

Last, I added the following to the merged.rtp as
[ chlo ]
  [ atoms ]
       C     CCM          0.179    0
     CL1     CLCM        -0.087     1
     CL2     CLCM        -0.087     2
     CL3     CLCM        -0.087    3
      HX     HCM          0.082     4

  [ bonds ]
      C    CL1
      C     HX
      C    CL2
      C    CL3
========================================================================
The result from EM was
Steepest Descents converged to Fmax < 500 in 5462 steps
Potential Energy  = -1.8603069e+05
Maximum force     =  4.8871869e+02 on atom 18043
Norm of force     =  1.0274749e+01

atom 18043 is the carbon of the chloroform that has weird Cl-Cl bond
connected visually in VMD.


Could anyone point out where I did wrong ? Thank you in advance.

Lili Zhang