On 1/30/13 6:01 AM, Shima Arasteh wrote:
Dear users,
I' d like to know if I need to check the npt.gro file time by time? I mean is
it possible for npt.gro file to reach the equilibrated state and then again
become unequilibrated?
Unlikely, unless there's something wrong with your run parameters or topology.
If you've done a sufficient job of equilibrating, nothing should go haywire
unless there's something more fundamentally wrong.
-Justin
Thanks for your suggestions.
Sincerely,
Shima
________________________________
From: Mark Abraham <mark.j.abra...@gmail.com>
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Sent: Monday, January 28, 2013 2:32 PM
Subject: Re: [gmx-users] Fatal error: Number of atoms in Topology is not the
same as in Trajectory
http://www.gromacs.org/Documentation/Terminology/Blowing_Up contains the
ideas that will likely help you, e.g. smaller time step, more
equilibration-friendly pressure coupling.
Mark
On Sun, Jan 27, 2013 at 1:59 PM, Shima Arasteh
<shima_arasteh2...@yahoo.com>wrote:
It is 15 ns of NPT equilibration and I have not got a proper npt output
yet to go to the MDrun. Because when I run the -mdrun command, I get fatal
error as water molecule can not be settled.
I guess that the system might need more equilibration.
These are the settings of my npt.mdp file. The force field which I use is
C36.
integrator = md ; leap-frog integrator
nsteps =250000 ; 2 * 250000 = 500 ps
dt = 0.002 ; 2 fs
; Output control
nstxout = 1000 ; save coordinates every 0.2 ps
nstvout = 1000 ; save velocities every 0.2 ps
nstenergy = 1000 ; save energies every 0.2 ps
nstlog = 1000 ; update log file every 0.2 ps
continuation = yes ; first dynamics run
constraint_algorithm = lincs ; holonomic constraints
constraints = h-bonds ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid ; search neighboring grid cells
nstlist = 5 ; 10 fs
rlist = 1.2 ; short-range neighborlist cutoff (in 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
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range
electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = Nose-Hoover ; modified Berendsen thermostat
tc-grps = Protein POPC SOL_CL ; two coupling groups - more
accurate
tau_t = 0.5 0.5 0.5 ; time constant, in ps
ref_t = 310 310 310 ; reference temperature, one for each
group, in K
pcoupl = Parrinello-Rahman ; no pressure coupling in
NVT
pcoupltype = semiisotropic
tau_p = 4
ref_p = 1.01325 1.01325
compressibility = 4.5e-5 4.5e-5
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = no ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no ; assign velocities from Maxwell
distribution
;gen_temp = 310 ; temperature for Maxwell distribution
;gen_seed = -1 ; generate a random seed
nstcomm = 1
comm_mode = Linear
comm_grps = Protein_POPC SOL_CL
Would you please give me any sugestions? What are the possible problems
might be considered?
Thanks for your suggestions.
Sincerely,
Shima
________________________________
From: Justin Lemkul <jalem...@vt.edu>
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Sent: Sunday, January 6, 2013 9:15 AM
Subject: Re: [gmx-users] Fatal error: Number of atoms in Topology is not
the same as in Trajectory
On 1/6/13 12:33 AM, Shima Arasteh wrote:
Do you mean that I re-run NPT step with the new index file and npt.gro
(which I got from the last NPT equilibration)? That's not clear to me yet.
That's where I'd start. You may have to run the new configuration through
the entire equilibration protocol, though. Instability during MD often
indicates inadequate equilibration, so whatever your protocol is may not be
sufficient as is and may require greater time.
-Justin
-- ========================================
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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========================================
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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