On 3/12/2011 4:42 PM, pragna lakshmi wrote:
Thank u for reply. I did energy minimization and equilibration step.
It converged in 696 steps which is shown below.
Step= 692, Dmax= 9.2e-03 nm, Epot= -7.12587e+05 Fmax= 7.62150e+03,
atom= 2099
Step= 693, Dmax= 1.1e-02 nm, Epot= -7.12588e+05 Fmax= 9.72038e+03,
atom= 2099
Step= 695, Dmax= 6.6e-03 nm, Epot= -7.12670e+05 Fmax= 9.39830e+02,
atom= 2099
writing lowest energy coordinates.
Steepest Descents converged to Fmax < 1000 in 696 steps
Potential Energy = -7.1266969e+05
Maximum force = 9.3982965e+02 on atom 2099
Norm of force = 2.1967674e+01
The atom that has the greatest force after EM is the same one for which
LINCS warnings arise later. That's worth paying attention to. Read the
advice about diagnosing unstable systems on the link Justin gave you
last time.
# md.mdp file
title = protein
cpp = /lib/cpp ; location of cpp on SGI
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps = 1000000 ; total 50 ps.
nstcomm = 1
nstxout = 500 ; output coordinates every 1.0 ps
nstvout = 0
nstfout = 0
nstlist = 10
ns_type = grid
rlist = 0.9
coulombtype = PME
rcoulomb = 0.9
rvdw = 1.0
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 6
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on in four groups
Tcoupl = berendsen
tau_t = 0.1 0.1 0.1 0.1 0.1
tc-grps = protein ZN IMP sol NA+
ref_t = 300 300 300 300 300
http://www.gromacs.org/Documentation/Terminology/Thermostats
; Pressure coupling is on
Pcoupl = berendsen
pcoupltype = isotropic
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
It's probably not useful to re-generate velocities after the
position-restrained step.
Mark
# pr.mdp file
title = protein
cpp = /lib/cpp ; location of cpp on SGI
define = -DPOSRES
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps = 50000 ; total 20.0 ps.
nstcomm = 1
nstxout = 250 ; output coordinates every 0.5 ps
nstvout = 1000 ; output velocities every 2.0 ps
nstfout = 0
nstlog = 10
nstenergy = 10
nstlist = 10
ns_type = grid
rlist = 0.9
coulombtype = PME
rcoulomb = 0.9
rvdw = 1.0
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 6
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on in four groups
Tcoupl = V-rescale
tau_t = 0.1 0.1 0.1 0.1 0.1
tc_grps = protein ZN sol IMP NA+
ref_t = 300 300 300 300 300
; Pressure coupling is on
Pcoupl = no
pcoupltype = isotropic
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
#em.mdp file
title = protein
cpp = /lib/cpp ; location of cpp on SGI
define = -DFLEX_SPC ; Use Ferguson's Flexible water model [4]
constraints = none
integrator = steep
dt = 0.002 ; ps !
nsteps = 2000
nstlist = 10
ns_type = grid
rlist = 0.9
coulombtype = PME ; Use particle-mesh ewald
rcoulomb = 0.9
rvdw = 1.0
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
;
; Energy minimizing stuff
;
emtol = 1000.0
emstep = 0.01
I need further help to trouble shoot this problem.
On Sat, Dec 3, 2011 at 10:46 AM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
pragna lakshmi wrote:
Hi,
I am trying to run protein-ligand complex simulation. At
the final MD run step it is showing the following error. Can
anybody tell me the solution for this error?
http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings
There are hundreds of threads in the archive with the same issue
and several possible solutions. Please consult the link above
(and referenced pages), as well as other posts.
If you need further help diagnosing the problem, please post a
complete .mdp file, as well as a description of prior minimization
and equilibration.
-Justin
--
========================================
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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