On 1/28/13 6:51 AM, Shima Arasteh wrote:
Am I supposed to skip this step?
Do not be tempted to think that there is a "standard" or "required" workflow.
The ensembles and environments you choose are dependent upon the task at hand.
There may be common workflows for proteins in water, but even those are not set
in stone.
-Justin
Thanks for your reply.
Sincerely,
Shima
_______________________________
From: Dr. Vitaly Chaban <[email protected]>
To: [email protected]
Sent: Monday, January 28, 2013 3:17 PM
Subject: [gmx-users] Re: Protein in vacum
Dear users,
I have done simulation with my protein in water earlier successfully using
CHARMM36 FF. Now, I am trying to simulate protein in vacum similar to the last
simulation of protein-water. When I go to the NPT equilibration, I get a fatal
error.
The commands I ran:
The npt.mdp file settings are:
; Parameters describing neighbors searching and details about interaction
calculations
ns_type = grid ; Neighbor list search method (simple, grid)
nstlist = 5 ; Neighbor list update frequency (after every given
number of steps)
rlist = 1.2 ; Neighbor list search cut-off distance (nm)
rlistlong = 1.4
rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)
rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
vdwtype = switch
rvdw_switch = 0.8
; Parameters for treating bonded interactions
continuation = no ; Whether a fresh start or a continuation from a
previous run (yes/no)
constraint_algorithm = LINCS ; Constraint algorithm (LINCS / SHAKE)
constraints = all-bonds ; Which bonds/angles to constrain (all-bonds /
hbonds / none / all-angles / h-angles)
lincs_iter = 1 ; Number of iterations to correct for rotational
lengthening in LINCS (related to accuracy)
lincs_order = 4 ; Highest order in the expansion of the constraint
coupling matrix (related to accuracy)
; Parameters for treating electrostatic interactions
coulombtype = PME ; Long range electrostatic interactions treatment
(cut-off, Ewald, PME)
pme_order = 4 ; Interpolation order for PME (cubic interpolation is
represented by 4)
fourierspacing = 0.16 ; Maximum grid spacing for FFT grid using PME
(nm)
; Temperature coupling parameters
tcoupl = Nose-Hoover ; Modified Berendsen thermostat using
velocity rescaling
tc-grps = Protein ; Define groups to be coupled separately to
temperature bath
tau_t = 0.5 ; Group-wise coupling time constant (ps)
ref_t = 310 ; Group-wise reference temperature (K)
; Pressure coupling parameters
pcoupl = Parrinello-Rahman ; Pressure coupler used under NPT
conditions
pcoupltype = isotropic ; Isotropic scaling in the x-y direction,
independent of the z direction
tau_p = 5.0 ; Coupling time constant (ps)
ref_p = 1.0 ; Reference pressure for coupling, x-y, z
directions (bar)
compressibility = 4.5e-5 4.5e-5 ; Isothermal compressibility (bar^-1)
refcoord_scaling = com
Vacuum is incompatible with pressure coupling.
Dr. Vitaly V. Chaban
MEMPHYS - Center for Biomembrane Physics
Department of Physics, Chemistry and Pharmacy
University of Southern Denmark
Campusvej 55, 5230 Odense M, Denmark
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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