[gmx-users] output force
Петр Попов
magistrpetrus at gmail.com
Sun Oct 10 19:12:50 CEST 2010
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!
>>> > --
>>> > gmx-users mailing list gmx-users at gromacs.org
>>> <mailto:gmx-users at gromacs.org>
>>> <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
>>>
>>>
>>> > http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> > Please search the archive at
>>> > http://www.gromacs.org/Support/Mailing_Lists/Search before
>>> posting!
>>> > Please don't post (un)subscribe requests to the list. Use
>>> the
>>> > www interface or send it to gmx-users-request at gromacs.org
>>> <mailto:gmx-users-request at gromacs.org>
>>> <mailto:gmx-users-request at gromacs.org
>>> <mailto:gmx-users-request at gromacs.org>>.
>>>
>>> > Can't post? Read
>>> http://www.gromacs.org/Support/Mailing_Lists
>>> --
>>> gmx-users mailing list gmx-users at gromacs.org
>>> <mailto:gmx-users at gromacs.org>
>>> <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
>>>
>>>
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/Search before
>>> posting!
>>> Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-request at gromacs.org
>>> <mailto:gmx-users-request at gromacs.org>
>>> <mailto:gmx-users-request at gromacs.org
>>> <mailto:gmx-users-request at gromacs.org>>.
>>>
>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>>
>>>
>>> -- ========================================
>>>
>>> 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
>>> <mailto:gmx-users at gromacs.org>
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>> Please don't post (un)subscribe requests to the list. Use the www
>>> interface or send it to gmx-users-request at gromacs.org
>>> <mailto:gmx-users-request at gromacs.org>.
>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>>
>>>
>> --
>> ========================================
>>
>> 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
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101010/ee756a9a/attachment.html>
More information about the gromacs.org_gmx-users
mailing list