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

[Shi Li]

> 
>> 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

I would also change the etmol in your em.mdp file to 10 instead of 500. This should give you a better system before you pass it to NVT/NPT.

Shi
>> 
>> 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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> 
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