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

[Victor Rosas Garcia]

the extra bonds you observe could be an artifact of the visualizer.  Most
molecular visualizers determine where to put bonds by a simple maximum
distance  criterion.  It may be that your molecules are distorted so that
some atoms are so close that the visualizer thinks there is a bond.

Hope this helps

Victor

El jue., 4 oct. 2018 a las 17:38, Lili Zhang (<zhanl10 at mcmaster.ca>)
escribió:

> 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
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