[gmx-users] output force
Dallas Warren
Dallas.Warren at monash.edu
Mon Oct 11 04:33:33 CEST 2010
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.warren at 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-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of ???? ?????
Sent: Monday, 11 October 2010 4:13 AM
To: jalemkul at 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 <magistrpetrus at gmail.com> написал:
Thank you very much!
10 октября 2010 г. 19:58 пользователь Justin A. Lemkul <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>> 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>>> 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>>>
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>>
> 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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