[gmx-users] output force
Justin A. Lemkul
jalemkul at vt.edu
Sun Oct 10 19:20:58 CEST 2010
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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