On 20/06/2011 3:29 PM, E. Nihal Korkmaz wrote:
I also checked the output of the minimization:
Steepest Descents converged to machine precision in 402 steps,
but did not reach the requested Fmax < 10.
Potential Energy = -1.81875038188621e+04
Maximum force = 3.20769543152855e+02 on atom 331
Norm of force = 2.04356801849931e+01
I assume the structure is not relaxed enough to start a simulation.
How can I get it minimize further? I increased the step size up to 0.1
ps, i still get the same result.
The minimization is probably OK, but a period of equilibration at a
short time step will probably help smooth the process out. Simulations
in implicit solvent have few explicit degrees of freedom compared to
explicit solvent, and might be rather more susceptible to equilibration
issues if the generated velocities are randomly not-quite-good-enough.
Mark
Thanks,
Nihal
On Sun, Jun 19, 2011 at 11:48 PM, E. Nihal Korkmaz
<enihalkork...@gmail.com <mailto:enihalkork...@gmail.com>> wrote:
Dear all,
I am trying to simulate a GB simulation of a 112 amino acid long
protein. I keep getting these errors,
Step 27718, time 55.436 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 33.319842, max 438.763717 (between atoms 79 and 81)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 27718, time 55.436 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.058237, max 1.390675 (between atoms 91 and 93)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
91 92 50.2 0.1016 0.1065 0.1010
91 93 90.0 0.1002 0.2415 0.1010
91 94 70.2 0.1025 0.1066 0.1010
79 80 90.0 0.1057 1.0667 0.1090
79 81 90.0 1.3066 47.9342 0.1090
85 86 90.0 0.1084 0.1758 0.1090
85 87 90.0 1.0654 0.1668 0.1090
88 89 90.0 0.1097 0.6994 0.1090
88 90 90.0 0.1125 0.1097 0.1090
91 92 50.2 0.1016 0.1065 0.1010
91 93 90.0 0.1002 0.2415 0.1010
91 94 70.2 0.1025 0.1066 0.1010
I am copying my mdp parameters below, I'd appreciate any
suggestions to fix that.
integrator = sd
tinit = 0
dt = 0.002
nsteps = 2500000
simulation_part = 1
init_step = 1
nstxout = 5000
nstvout = 5000
nstenergy = 500
nstxtcout = 500
nstlog = 500
xtc_grps = System
energygrps = System
comm_mode = Linear
; neighbor searching and vdw/pme setting up
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 2.0
implicit_solvent = GBSA
gb_algorithm = OBC
gb_saltconc = 0.15
rgbradii = 2.0
coulombtype = Cut-off
fourierspacing = 0.1
pme_order = 6
rcoulomb = 2.0
vdwtype = Cut-off
rvdw_switch = 1.0
rvdw = 2.0
; cpt control
tcoupl = V-rescale
tc-grps = System
tau_t = 0.1
ref_t = 300.0
Pcoupl = Berendsen
pcoupltype = isotropic
tau_p = 1.0
compressibility = 4.5e-5
ref_p = 1.0
; velocity & temperature control
gen_vel = yes
gen_temp = 300.0
annealing = no
constraints = hbonds
constraint_algorithm = lincs
morse = no
Thanks,
--
Elif Nihal Korkmaz
Research Assistant
University of Wisconsin - Biophysics
Member of Qiang Cui & Thomas Record Labs
1101 University Ave, Rm. 8359
Madison, WI 53706
Phone: 608-265-3644 <tel:608-265-3644>
Email: kork...@wisc.edu <mailto:kork...@wisc.edu>
--
Elif Nihal Korkmaz
Research Assistant
University of Wisconsin - Biophysics
Member of Qiang Cui & Thomas Record Labs
1101 University Ave, Rm. 8359
Madison, WI 53706
Phone: 608-265-3644 <tel:608-265-3644>
Email: kork...@wisc.edu <mailto:kork...@wisc.edu>
--
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