[gmx-users] Reg: Running Energy minimisation for dichloroethane (DCE)
Justin A. Lemkul
jalemkul at vt.edu
Thu Oct 21 14:08:32 CEST 2010
vinothkumar mohanakrishnan wrote:
> Hi Justin
>
> Thank you for your suggestion. I am doing equilibration of DCE (108
> molecules) alone in a box and there is no water molecule inside the box.
> cant i use -DFLEXIBLE for DCE?. by the way i will try your suggestion
> about xmgrace.
>
In that case, -DFLEXBILE will have no effect. The bigger concern then is the
potential stability issues of not using constraints and using a 2-fs timestep.
It might be fine, but keep it in mind if you run into problems.
-Justin
> Regards
> Vinoth
>
> On Thu, Oct 21, 2010 at 5:25 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> vinothkumar mohanakrishnan wrote:
>
> Hi Justin
>
> Below is my nvt.mdp (nvt equilibration) file.i think probably
> you can have look at it and its not such big.
>
> define = -DFLEXIBLE
>
>
> You should never run MD with flexible water. All the water models
> included in Gromacs are meant to be rigid. -DFLEXIBLE should only
> be used during EM.
>
>
> integrator = md nsteps =
> 50000 dt =
> 0.002 nstxout = 100 nstvout
> = 100 nstenergy =
> 100 nstlog = 100
> constraint_algorithm = shake constraints =
> none
>
>
> If you're not using constraints, then a 2-fs timestep might be too
> large. If you encounter any later instability, this is likely the
> cause.
>
>
> unconstrained_start = yes shake_tol =
> 0.0001
> morse = no ns_type =
> grid nstlist = 5
> rlist = 1.0 coulombtype =
> PME rcoulomb = 1.0
> vdwtype = Cut-off rvdw =
> 1.0 pme_order = 4
> fourierspacing = 0.16 pbc =
> xyz tcoupl = V-rescale
> tc-grps = system tau_t =
> 0.1 ref_t = 300
> DispCorr = Ener gen_vel =
> yes gen_temp = 300 gen_seed =
> 173529
> regarding the plot i too know that one should use Xmgrace to
> plot. In the pressure Vs time(lysozyme tutorial) you have got
> two graphs. i to got the pressure Vs time (black line graph) my
> question is how to get the running average ( red line) and
> plot?. does i need any command to get the running average?. any
> help is highly appreciated.
>
>
> Data -> Transformations -> Running averages
>
> -Justin
>
> Regards
> Vinoth
>
>
> On Thu, Oct 21, 2010 at 4:56 PM, Justin A. Lemkul
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
>
>
>
> vinothkumar mohanakrishnan wrote:
>
> Hi justin
>
> I found what went wrong and i corrected my mdp file.now the
> system equilibrated to the desired temperature 300 K (plus r
> minus 30 K) is this ok?
>
>
> This is impossible to assess without seeing your .mdp
> settings. A
> fluctuation of 10% is probably fine.
>
>
> Apart from that i want to know how you plot the average
> running
> pressure and density in your tutorial for lyzosyme
> (redline). i
> just want to do that for DCE. any help is highly
> appreciated.
>
>
> Xmgrace.
>
> -Justin
>
> Regards
> Vinoth
>
>
> On Wed, Oct 20, 2010 at 5:33 PM, Justin A. Lemkul
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>>> wrote:
>
>
>
> vinothkumar mohanakrishnan wrote:
>
> 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
>
>
> VMD tries to guess where bonds should be, but does not
> always
> do a
> good job. Your topology defines bonds. These are the
> only bonds
> that there will be. None can be broken or formed in
> standard MD.
>
>
> 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.
>
>
> Without seeing your .mdp file, there's no way to know.
> The
> fluctuation does seem too high, though, unless your system
> really is
> just that unstable. Are other properties converged -
> potential
> energy, density, etc? What type of ensemble are you
> using?
>
> -Justin
>
> Regards
> Vinoth
>
>
> On Mon, Oct 18, 2010 at 6:09 PM, Justin A. Lemkul
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto: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>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
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> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>>>
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> <mailto:jalemkul at vt.edu>>
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> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto: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>
> <http://vt.edu>
> <http://vt.edu> <http://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 <http://vt.edu>
> <http://vt.edu> <http://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 <http://vt.edu> <http://vt.edu>
> <http://vt.edu> | (540)
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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 <http://vt.edu> <http://vt.edu> | (540)
> 231-9080
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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 <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
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