Hello dear gmx-users!
So, I run md and got all files md.cpt, .trr, .gro, mdf.xvg,... etc.
then I did: grompp_d -f sp.mdp -c md.gro -n index.ndx -p topol.top -o sp.tpr
where sp.mdp differ from md.mdp in one line: energygrps = Protein SOL (in
md.mdp: energygrps = System)
after that I did: mdrun_d -s sp.tpr -pf spf -rerun md.trr
and got file spf.xvg, but there was no forces:
@ title "Pull force"
@ xaxis label "Time (ps)"
@ yaxis label "Force (kJ/mol/nm)"
@TYPE xy
0.000000 0.000000
20.000000 0.000000
40.000000 0.000000
60.000000 0.000000
80.000000 0.000000
100.000000 0.000000
120.000000 0.000000
140.000000 0.000000
160.000000 0.000000
180.000000 0.000000
200.000000 0.000000
Also while reading frame I had a warning:
WARNING: Some frames do not contain velocities.
Ekin, temperature and pressure are incorrect,
the virial will be incorrect when constraints are present.
But I have no idea how to fix this.
Help me, please.
Sincerely.
Petr.
11 октября 2010 г. 6:33 пользователь Dallas Warren <dallas.war...@monash.edu
> написал:
> The error has told you, you have repeat energy groups, where at least one
> (and in your case all) of the atoms are placed within two energy groups.
>
>
>
> Solution, define your energy groups so that you don't have atoms in more
> than one.
>
>
>
> You currently have:
>
> energygrps = Protein Protein
>
>
>
> Should be something like
>
> energygrps = Protein SOL
>
>
>
> Catch ya,
>
> Dr. Dallas Warren
>
> Medicinal Chemistry and Drug Action
>
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.war...@monash.edu
>
> +61 3 9903 9304
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
>
>
> *From:* gmx-users-boun...@gromacs.org [mailto:
> gmx-users-boun...@gromacs.org] *On Behalf Of *???? ?????
> *Sent:* Monday, 11 October 2010 4:13 AM
> *To:* jalem...@vt.edu; Discussion list for GROMACS users
> *Subject:* Re: [gmx-users] output force
>
>
>
> 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
> 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?
>
>
> 10 октября 2010 г. 20:01 пользователь Петр Попов <magistrpet...@gmail.com>
> написал:
>
> Thank you very much!
>
> 10 октября 2010 г. 19:58 пользователь Justin A. Lemkul <jalem...@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
> <jalem...@vt.edu<mailto:
> jalem...@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.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au>
> <mailto:mark.abra...@anu.edu.au
> <mailto:mark.abra...@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 <magistrpet...@gmail.com
> <mailto:magistrpet...@gmail.com>
>
> <mailto:magistrpet...@gmail.com
> <mailto:magistrpet...@gmail.com>>>
> Date: Saturday, October 9, 2010 21:41
> Subject: [gmx-users] output force
> To: gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>
>
> <mailto:gmx-users@gromacs.org <mailto:gmx-users@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> | (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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