[gmx-users] output force
Петр Попов
magistrpetrus at gmail.com
Sun Oct 10 19:38:39 CEST 2010
And what if I have four helices in Protein and a,b,c,d group for each helix
in index.file and I want to get a-c pmf?
10 октября 2010 г. 21:20 пользователь Justin A. Lemkul <jalemkul at vt.edu>написал:
>
>
> Justin A. Lemkul wrote:
>
>>
>>
>> Петр Попов wrote:
>>
>>> Unfortunately I've got an error.
>>>
>>> This is .mdp file:
>>>
>>> title = title
>>> cpp = /lib/cpp
>>> integrator = md
>>> tinit = 0.0
>>> dt = 0.002 nsteps = 25000 nstcomm
>>> = 1
>>> comm_grps = System
>>> ld_seed = -1
>>> niter = 40
>>> nstxout = 10000
>>> nstvout = 0
>>> nstfout = 0
>>> nstlog = 500
>>> nstenergy = 100
>>> nstlist = 10
>>>
>>
> If this .mdp file is to be used for a rerun, please recall the advice I
> gave you earlier about the proper setting for nstlist.
>
> -Justin
>
>
> ns_type = grid
>>> rlist = 1.2
>>> coulombtype = PME
>>> rcoulomb = 1.2
>>> fourierspacing = 0.12
>>> pme_order = 4
>>> optimize_fft = yes
>>> pbc = xyz
>>> vdwtype = Cut-off
>>> rvdw = 1.2
>>> tcoupl = V-rescale
>>> tc_grps = System
>>> tau_t = 0.1
>>> ref_t = 300.0
>>> annealing = single
>>> annealing_npoints = 3
>>> annealing_time = 0 5 50
>>> annealing_temp = 5 300 300
>>> pcoupl = berendsen
>>> pcoupltype = isotropic
>>> compressibility = 4.5e-5
>>> tau_p = 10.0
>>> ref_p = 1.0
>>> gen_vel = yes
>>> gen_temp = 5.0
>>> gen_seed = -1
>>> constraints = all-bonds
>>> constraint_algorithm = Lincs
>>> lincs_order = 4
>>> disre = simple
>>> disre_weighting = conservative
>>> disre_mixed = no
>>> nstdisreout = 50000
>>> disre_tau = 0
>>> pull = constraint
>>> pull_geometry = distance
>>> pull_dim = Y Y Y
>>> pull_constr_tol = 1e-6
>>> pull_nstfout = 1
>>> pull_nstxout = 1
>>> pull_ngroups = 1
>>> pull_group0 = a
>>> pull_group1 = b
>>> pull_init1 = 0.700
>>> pull_start = no
>>> pull_k1 = 1000
>>> lincs_iter = 2
>>> energygrps = Protein Protein
>>>
>>> I just replace in .mdp file line energygrps = System and the error is:
>>>
>>> Fatal error:
>>> Atom 1 in multiple Energy Mon. groups (1 and 2)
>>>
>>> What should I do to avoid this?
>>>
>>>
>> You cannot use multiple energygrps if those groups overlap in any way, as
>> the error indicates. I thought you were setting "energygrps = Protein SOL"?
>> If you're trying to get protein-only terms, then just set "energygrps =
>> Protein"
>>
>> -Justin
>>
>>
>>>
>>> 10 октября 2010 г. 20:01 пользователь Петр Попов <
>>> magistrpetrus at gmail.com <mailto:magistrpetrus at gmail.com>> написал:
>>>
>>> Thank you very much!
>>>
>>> 10 октября 2010 г. 19:58 пользователь Justin A. Lemkul
>>> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>> написал:
>>>
>>>
>>>
>>> Петр Попов wrote:
>>>
>>> So if I want to get protein-solvent component I should add
>>> in .mdp:
>>>
>>> energygrps = Protein SOL
>>>
>>> ?
>>>
>>>
>>> Yes, and set nstlist = 1.
>>>
>>> -Justin
>>>
>>> 10 октября 2010 г. 16:41 пользователь Justin A. Lemkul
>>> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>>> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> написал:
>>>
>>>
>>>
>>>
>>> Петр Попов wrote:
>>>
>>> Thank you for response!
>>> One more question:
>>> How can I get file with energy groups? Should I use
>>> grompp with
>>> a -e ener.edr option? In this case, how to build
>>> ener.edr file?
>>>
>>>
>>> The "energrygrps" keyword is an .mdp option, so generate
>>> a new .tpr
>>> file with the desired groups and use the -rerun feature
>>> of mdrun on
>>> the trajectory that has already been produced.
>>>
>>> -Justin
>>>
>>> 9 октября 2010 г. 14:50 пользователь Mark Abraham
>>> <mark.abraham at anu.edu.au
>>> <mailto:mark.abraham at anu.edu.au>
>>> <mailto:mark.abraham at anu.edu.au
>>> <mailto:mark.abraham at anu.edu.au>>
>>> <mailto:mark.abraham at anu.edu.au
>>> <mailto:mark.abraham at anu.edu.au>
>>> <mailto:mark.abraham at anu.edu.au
>>> <mailto:mark.abraham at anu.edu.au>>>> написал:
>>>
>>>
>>> You can get that with cunning use of energy groups
>>> and mdrun
>>> -rerun,
>>> but not mid-simulation.
>>> Mark
>>>
>>> ----- Original Message -----
>>> From: Петр Попов <magistrpetrus at gmail.com
>>> <mailto:magistrpetrus at gmail.com>
>>> <mailto:magistrpetrus at gmail.com
>>> <mailto:magistrpetrus at gmail.com>>
>>> <mailto:magistrpetrus at gmail.com
>>> <mailto:magistrpetrus at gmail.com>
>>> <mailto:magistrpetrus at gmail.com
>>> <mailto:magistrpetrus at gmail.com>>>>
>>> Date: Saturday, October 9, 2010 21:41
>>> Subject: [gmx-users] output force
>>> To: gmx-users at gromacs.org
>>> <mailto:gmx-users at gromacs.org> <mailto:gmx-users at gromacs.org
>>> <mailto:gmx-users at gromacs.org>>
>>> <mailto:gmx-users at gromacs.org
>>> <mailto:gmx-users at gromacs.org> <mailto:gmx-users at gromacs.org
>>> <mailto:gmx-users at gromacs.org>>>
>>>
>>> > Hello dear gmx-users!
>>> >
>>> > When calculated forces in gromacs to produce
>>> pmf, we have
>>> the net
>>> force in output. For example:
>>> > ...
>>> > #
>>> > # Giving Russians Opium May Alter Current
>>> Situation
>>> > #
>>> > @ title "Pull force"
>>> > @ xaxis label "Time (ps)"
>>> > @ yaxis label "Force (kJ/mol/nm)"
>>> > @TYPE xy
>>> > 0.000000 1017490.761270
>>> > 0.002000 -253098.034916
>>> > 0.004000 -43856.400160
>>> > 0.006000 48980.619113
>>> > 0.008000 52103.053067
>>> > 0.010000 33788.090031
>>> > 0.012000 19096.388350
>>> > 0.014000 14094.738810
>>> > 0.016000 14027.621966
>>> > 0.018000 15162.993741
>>> > 0.020000 14136.978177
>>> > ... etc.
>>> >
>>> > What sould I do to get the net force of
>>> protein-solvent
>>> interactions or protein-protein interactions or
>>> solvent-solvent
>>> interactions instead and get output .xvg file in
>>> the form
>>> like this:
>>> >
>>> > time Force(type1) Force(type2)
>>> Force(type3)
>>> >
>>> > t1 f1 f1
>>> f1
>>> > t2 f2 f2
>>> f2
>>> > t3 f3 f3
>>> f3
>>> > ... ... ...
>>> ...
>>> > etc.
>>> >
>>> > Thank you for attention and I hope you will
>>> help me!
>>> > --
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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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