Mahnam wrote:
In God We Trust
Hello everyone
We have a problem for equilibrate the system with a protein within
POPE. we have searched mailing list , we dident any good note. We have
used pope.pdb from Dr. Tielemans website. We have inserted our protein
into pope and minimized it and equilibrated it with NVT ensemble for 2
ns, and temperture was stable, but when we want to equilibrate our system
with NPT ensemble it dosen't accept lincs algoritm and says :
" *presure coupling more than 1% *" and also "* box was shifted at least
10 time*.
here is our npt file for position reastrant:
constraints = all-bonds
define = -DPOSRES -DPOSRES_pop
integrator = md
dt = 0.002; ps
nsteps = 2500000; .
nstcomm = 1
comm_mode = Linear
comm_grps = upper lower SOL
nstxout = 250
nstvout = 1000
nstfout = 0
nstlog = 10
nstenergy = 10
nstlist = 1
ns_type = grid
rlist = 1
coulombtype = cut-off
I can see no logical reason to use plain cutoff electrostatics, especially for a
membrane protein system. The artifacts are well-documented. You should be
using PME. I don't know if this is the root cause of your problem, but it
certainly won't lead to correct results.
rcoulomb = 1.4
rvdw = 1.4
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
niter = 20
pbc = xyz
nstcgsteep = 1000
nbfgscorr = 10
vdwtype = cut-off
DispCorr = EnerPres
freezegrps = Protein
freezedim = Y Y Y
emtol = 100
emstep = 0.01
energygrps = Protein
energygrp_excl = Protein Protein
What happens if you do not freeze your protein? Perhaps there are unresolved
clashes that freezing is keeping in place.
-Justin
; Berendsen temperature coupling is on in three groups
Tcoupl = Nose-Hoover
tau_t = 0.1 0.1 0.1
tc-grps = Protein POP bulk
ref_t = 100 100 100
; Pressure coupling is on
Pcoupl = Berendsen
Pcoupltype = semiisotropic
tau_p = 1 1
compressibility = 4.5e-05 4.5e-05
ref_p = 1 1
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 100.0
gen_seed = 173529
constraint-algorithm =lincs
lincs_iter = 1
lincs_order = 4
whould you please gide me
Many thanks in advance for your help and your reply.
Yours truly
Karim Mahnam
Institute of Biochemistry and Biophysics (IBB)
Tehran University
P.O.box 13145-1384
Tehran
Iran
http://www.ibb.ut.ac.ir/
--
========================================
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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