afsaneh maleki wrote:
Dear Justin,
I use version 4.0.7
I don't recall any specific bug related to this problem, but when using outdated
software (several years old in this case), the first step is to upgrade to the
newest version and try again. Development in the 4.0.x series is no longer
ongoing, so fixing any potential bugs there is not likely to happen. If the
problem is reproducible in the newest version, it will need to be investigated
further.
-Justin
Thanks
Afsaneh
On 3/25/12, Justin A. Lemkul <[email protected]> wrote:
afsaneh maleki wrote:
Thanks Dear Peter and Justin for reply,
I paste some text from .mdp for calculation of free energy. I have
done calculation of minimization energy before.
Which Gromacs version are you using? I can't reproduce your problem with
version 4.5.4 or 4.5.5, either with or without the free energy code. My
energy
outputs are always present at the nstenergy interval.
-Justin
title = production for ile-pro-SOL
; Run parameters
integrator = sd ; leap-frog integrator
nsteps = 1000000 ; 0.002* 1000000 = 2000 ps (2 ns)
dt = 0.002 ; 2 fs
tinit =0
; Output control
nstxout = 100000 ; save coordinates every 0.2 ps
nstvout =100000 ; save velocities every 0.2 ps
nstxtcout =100000 ; xtc compressed trajectory output every
2 ps
nstenergy = 10000 ; save energies every 0.2 ps
nstlog = 10000 ; update log file every 0.2 ps
xtc_precision =1000
; Bond parameters
constraint_algorithm = lincs ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H
bonds) constrained
lincs_iter = 2 ; accuracy of LINCS
unconstrained_start =no
lincs_order =12
lincs_warnangle =30
shake-tol =0.0001
; Neighborsearching
ns_type = grid ; search neighboring grid cels
nstlist = 10 ; 10 fs
rlist = 1.2 ; short-range neighborlist cutoff (in
nm)
rcoulomb = 1.2 ; short-range electrostatic cutoff (in
nm)
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon-r = 1.2
; Method for doing Van der Waals =
vdw-type = switch
; cut-off lengths =
rvdw-switch = 1.
rvdw =1.1
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range
electrostatics
; EWALD/PME/PPPM parameters =
pme_order = 6
ewald_rtol = 1e-06
epsilon_surface = 0
optimize_fft = no
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling is on
;tcoupl = Nose-Hoover ; More accurate thermostat
;pcoupl =Parrinello-Rahman ; Pressure coupling on in NPT
pcoupltype = isotropic
tau_p = 5.0 ; time constant, in ps
ref_p = 1.0 ; reference pressure, x-y, z
(in bar)
compressibility = 4.5e-5 ; isothermal compressibility,
bar^-1
;restraints
;dihre=simple
dihre-fc=1
nstdihreout=1000
disre=simple
disre_fc=1
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
Thanks,
Afsaneh
On 3/25/12, Justin A. Lemkul <[email protected]> wrote:
Peter C. Lai wrote:
In the .mdp file what is nstenergy set to?
I'd further ask what the rest of the .mdp file says, as well. If this is
the
output of energy minimization, it's totally normal. The output seems
irregular
but is due (I believe) to the potentially uneven step size taken during
EM.
-Justin
On 2012-03-25 04:37:59PM +0430, afsaneh maleki wrote:
Dear users,
When I got "total energy.xvg" file for plotting total energy via time,
data haven't saved in order time intervals. What command can control
time intervals in .mdp for .edr file? To better understand I pasted
some text from "total energy.xvg" file. As you see, time intervals
aren't same.
@ s0 legend "Total Energy"
0.000000 -274454.750000
12.420001 -274884.187500
18.060001 -274532.343750
20.000000 -274475.437500
29.360001 -275739.562500
35.000000 -274441.937500
40.000000 -274463.156250
46.280003 -273342.250000
51.920002 -273099.718750
57.580002 -274429.250000
60.000004 -274844.062500
68.860001 -273905.093750
74.500000 -273988.812500
80.000000 -276057.625000
Thanks very much in advance
Afsaneh
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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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========================================
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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--
========================================
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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