[gmx-users] Reg: Running Energy minimisation for dichloroethane (DCE)
Justin A. Lemkul
jalemkul at vt.edu
Thu Oct 21 13:55:59 CEST 2010
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>> 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>>> 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>>>> 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>>
> <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:
>
> 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> | (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)
> 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> | (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> | (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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