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
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
<magistrpet...@gmail.com <mailto:magistrpet...@gmail.com>> написал:
Thank you very much!
10 октября 2010 г. 19:58 пользователь Justin A. Lemkul
<jalem...@vt.edu <mailto: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>
<mailto: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>>
<mailto: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>>
<mailto: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>>
<mailto: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!
> --
> gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
<mailto:gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>
<mailto:gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org> <mailto:gmx-users@gromacs.org
<mailto:gmx-users@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-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>
<mailto:gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>>
<mailto:gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>
<mailto:gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>>>.
> Can't post? Read
http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
<mailto:gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>
<mailto:gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org> <mailto:gmx-users@gromacs.org
<mailto:gmx-users@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-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>
<mailto:gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>>
<mailto:gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>
<mailto:gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@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> <http://vt.edu> |
(540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
-- gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
<mailto:gmx-users@gromacs.org <mailto:gmx-users@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-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>
<mailto:gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@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@gromacs.org
<mailto:gmx-users@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-requ...@gromacs.org
<mailto:gmx-users-requ...@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@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-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
