[gmx-users] Reg: Running Energy minimisation for dichloroethane (DCE)
vinothkumar mohanakrishnan
kmvinoth at gmail.com
Thu Oct 21 13:52:49 CEST 2010
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
integrator = md
nsteps = 50000
dt = 0.002
nstxout = 100
nstvout = 100
nstenergy = 100
nstlog = 100
constraint_algorithm = shake
constraints = none
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.
Regards
Vinoth
On Thu, Oct 21, 2010 at 4:56 PM, Justin A. Lemkul <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>> 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>>> 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>>>> 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> | (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
>>
>> ========================================
>> -- gmx-users mailing list gmx-users at gromacs.org
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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
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