[gmx-users] Reg: Running Energy minimisation for dichloroethane (DCE)
vinothkumar mohanakrishnan
kmvinoth at gmail.com
Wed Oct 20 11:10:34 CEST 2010
Hi Justin
I corrected the mistake what you said and i am able to run energy
minimisation and equilibration. but when i view my em.gro and
equilibration.gro in VMD it seems to me that the bonds between the atoms are
broken in molecules.I used g_energy to check weather the system has
equilibrated to the required temperature (300K) i found that the variation
in the temperature was 100K (plus r minus) . i am not able find out what
went wrong. any help is highly appreciated.
Regards
Vinoth
On Mon, Oct 18, 2010 at 6:09 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> vinothkumar mohanakrishnan wrote:
>
>> Dear Justin
>>
>> what corrections i should make to ffoplsaan.itp to make it correct. what i
>> should give instead of CAB and CLAA?.
>>
>>
> You must use atom types, not names. Unfortunately, you've chosen to use
> atom names, which are also types, which makes all of this quite confusing if
> you're not sure what you're doing.
>
> You defined two new atom types - opls_966 (CAB) and opls_967 (CLAA), which
> are the only indicators you are allowed to use if introducing new types.
> Thus, references to atom names (CAC, CLAD) will generate fatal errors.
>
>
> i copied the .rtp .atp .itp files from usr/local/gromacs/share/gromacs/top
>> to my working directory and added these parameters to the corresponding
>> files. what you mean is should i need to add these parameters to the source
>> directory ( usr/local/gromacs/share/gromacs/top)?
>>
>>
> Your topology needs to be consistent with whatever files need to be
> included. By default, Gromacs checks the working directory first, but if
> you've moved to a new (sub)directory to carry out further steps, the grompp
> will not find your modified files, but will instead locate only the default
> force field files in $GMXLIB. Either keep all your work in one directory
> (which can get messy), or make use of the "include" keyword in the .mdp
> file. Any directory specified there will be searched after the working
> directory, but before $GMXLIB.
>
> -Justin
>
> Regards
>> Vinoth
>>
>>
>> On Mon, Oct 18, 2010 at 5:27 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> jalemkul at vt.edu>> wrote:
>>
>>
>>
>> vinothkumar mohanakrishnan wrote:
>>
>> Hi all
>>
>> i added new atomtype for dichloroethane (DCE) and added the
>> corresponding parameters in the .rtp, .atp, .bon.itp, .nb.itp
>> respectively. given below are my additions to the corresponding
>> files respectively.
>>
>> *ffoplsaa.rtp*
>>
>> [ DCE ]
>> [ atoms ]
>> CLAA opls_967 -0.2270 1
>> CAB opls_966 0.2270 1
>> CAC opls_966 0.2270 2
>> CLAD opls_967 -0.2270 2
>>
>> [ bonds ]
>> CLAA CAB
>> CAB CAC
>> CAC CLAD
>>
>> [ angles ]
>> CLAA CAB CAC
>> CAB CAC CLAD
>>
>> [ dihedrals ]
>> CLAA CAB CAC CLAD
>>
>> *ffoplsaa.atp*
>>
>> opls_966 14.02700 ; CH2 for DCE
>> opls_967 35.45300 ; CL for DCE
>>
>> *ffoplsaabon.itp*
>>
>> [bondtypes]
>> CLAA CAB 1 0.17870 194137.6 ; CL-CH2 for DCE
>> CAB CAC 1 0.15300 259408.0 ; CH2-CH2 for DCE
>> CAC CLAD 1 0.17870 194137.6 ; CL-CH2 for DCE
>>
>> [angletypes]
>> CLAA CAB CAC 1 108.200 368.192 ; C-C-CL for DCE
>> CAB CAC CLAD 1 108.200 368.192 ; C-C-CL for DCE
>>
>> [dihedraltypes]
>> CLAA CAB CAC CLAD 3 20.76096 -0.4184
>> 27.011904 0.00000 0.00000 0.00000 ; for DCE
>>
>>
>> You shouldn't be using atom names in the [*types] directives. What
>> you should be using are the interpolated types from ffoplsaanb.itp,
>> thus you have only utilized opls_966 (CAB) and opls_967 (CLAA).
>>
>> *ffoplsaanb.itp*
>>
>>
>> opls_966 CAB 6 14.02700 0.227 A 3.98000e-01
>> 4.76976e-01 ; CH2 of DCE
>> opls_967 CLAA 17 35.45300 -0.227 A 3.16000e-01
>> 0.20920e+01 ; Cl of DCE
>>
>> *dce.pdb*
>>
>> HETATM 1 CLAA DCE 1 6.300 -2.280 1.360 1.00
>> 20.00 CL
>> HETATM 2 CAB DCE 1 5.060 -3.540 1.500 1.00
>> 20.00 C
>> HETATM 3 CAC DCE 1 4.320 -3.740 0.170 1.00
>> 20.00 C
>> HETATM 4 CLAD DCE 1 3.270 -2.350 -0.210 1.00
>> 20.00 CL
>>
>> After adding all this, when i run grompp i get the error as
>> *fatal error Unknown bond_atomtype CLAA*. can any one tell me
>> why this happens?.
>>
>>
>> Have you been sure to #include the correct (modified) force field
>> files? That is, if you made a local copy and adjusted them, these
>> won't be the files that pdb2gmx will #include by default.
>>
>> -Justin
>>
>> Regards
>> Vinoth
>>
>>
>> -- ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
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>>
>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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