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

[Lili Zhang]

Hi Victor,

Thank you for your reply.
In my original post, I meant to say POPC_chlo_slov.gro looks normal without
Cl-Cl bonds, not npt.gro.

After EM, I tried the NVT, but it failed reporting LINCS warning,

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.012074, max 0.486350 (between atoms 18047 and 18043)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  18047  18043  166.8    0.0977   0.0565      0.1100
starting mdrun '128 POPC w 200 chloroform in TIP3 water at 298 K'
50000 steps,     50.0 ps.

It seems the spurious bond of Cl-Cl causing this warning, so I can not
proceed on with NVT or NPT...

Lili





On Fri, Oct 5, 2018 at 8:40 AM Victor Rosas Garcia <rosas.victor at gmail.com>
wrote:

> 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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