Hi Luis,
First of all, NEVER REPLY IN PRIVATE when dealing with a mailing list
thread. It's a serious breach of netiquette.
Mailing lists are designed to be public and searchable. People help
other people on a mailing list so that the answer is public and other
people can look for the solution by googling. To write directly is not
only rude towards me (I am not your free private technical support,
sorry), but also indirectly towards people who would want to look at the
solution to avoid your same problems in the future.
It is also stupid for the poster, because by writing only to me you make
it impossible for other (possibly more skilled) people to help you.
In short: NEVER. DO. IT. AGAIN. Reply always to the mailing list, not in
private.
Now, let's come to your problem.
On 10/04/11 01:50, Luis Miguel Medina Solano wrote:
thanks a lot for your fast reply.
I'm sorry, the problem isn't that the simulation box is displaced, but
that the water molecules returns to the initial positions (positions
they had just after filling the simulation box with water).
Ok, this is quite different.
However molecules shouldn't magically come back to "initial positions".
Are you sure you're using the correct input files -that is, the
minimized ones and not the just-solvated ones?
Could you copy and paste all the commands you give so that we can see
your simulation protocol?
I've done the REMD simulation using a time step of 0.004 and 0.001 and
the problem persist.
Yes, I agree at this point, since it seems you're using non-minimized
starting structures by mistake.
m.
the error I obtain is the following (and always happen after the first
successful exchange, it doesn't matter if the exchange is at low or high
Temperatures):
Step 2001, time 2.001 (ps) LINCS WARNING
1: relative constraint deviation after LINCS:
1: rms 0.074171, max 0.781368 (between atoms 99 and 100)
2:
1: bonds that rotated more than 30 degrees:
2: step 2001: Water molecule starting at atom 6062 can not be settled.
1: atom 1 atom 2 angle previous, current, constraint length
2: Check for bad contacts and/or reduce the timestep if appropriate.
1: 99 100 90.0 0.1090 0.1942 0.1090
1:
1: step 2001: Water molecule starting at atom 6017 can not be settled.
1: Check for bad contacts and/or reduce the timestep if appropriate.
1: Wrote pdb files with previous and current coordinates
2: Wrote pdb files with previous and current coordinates
1:
1: Step 2002, time 2.002 (ps) LINCS WARNING
1: relative constraint deviation after LINCS:
1: rms 0.005479, max 0.057528 (between atoms 99 and 100)
1: bonds that rotated more than 30 degrees:
1: atom 1 atom 2 angle previous, current, constraint length
1: 99 100 90.1 0.1942 0.1153 0.1090
2:
2: step 2002: Water molecule starting at atom 7388 can not be settled.
2: Check for bad contacts and/or reduce the timestep if appropriate.
2: Wrote pdb files with previous and current coordinates
rank 2 in job 69 luis-GA-880GM-UD2H_40565 caused collective abort of all
ranks
exit status of rank 2: killed by signal 11
my .mdp file is the next:
; VARIOUS PREPROCESSING OPTIONS
title =
cpp = /lib/cpp
include =
define =
; RUN CONTROL PARAMETERS
integrator = md
; Start time and timestep in ps
tinit = 0
dt = 0.004
nsteps = 2
; For exact run continuation or redoing part of a run
init_step = 0
; mode for center of mass motion removal
comm-mode = Linear
; number of steps for center of mass motion removal
nstcomm = 1
; group(s) for center of mass motion removal
comm-grps =
; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout = 10000
nstvout = 10000
nstfout = 0
; Checkpointing helps you continue after crashes
nstcheckpoint = 1000
; Output frequency for energies to log file and energy file
nstlog = 100
nstenergy = 100
; Output frequency and precision for xtc file
nstxtcout = 100
xtc-precision = 1000
; This selects the subset of atoms for the xtc file. You can
; select multiple groups. By default all atoms will be written.
xtc-grps =
; Selection of energy groups
energygrps =
; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist = 5
; ns algorithm (simple or grid)
ns-type = grid
; Periodic boundary conditions: xyz (default), no (vacuum)
; or full (infinite systems only)
pbc = xyz
; nblist cut-off
rlist = 1.4
domain-decomposition = no
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = PME
rcoulomb-switch = 0
rcoulomb = 1.4
; Dielectric constant (DC) for cut-off or DC of reaction field
epsilon-r = 1.2
; Method for doing Van der Waals
vdw-type = Cut-off
; cut-off lengths
rvdw-switch = 0
rvdw = 1.4
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = EnerPres
; Extension of the potential lookup tables beyond the cut-off
table-extension = 1.4
; Spacing for the PME/PPPM FFT grid
fourierspacing = 0.24
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
; EWALD/PME/PPPM parameters
pme_order = 6
ewald_rtol = 1e-05
ewald_geometry = 3d
epsilon_surface = 0
optimize_fft = no
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
Tcoupl = V-rescale
; Groups to couple separately
tc-grps = protein sol
; Time constant (ps) and reference temperature (K)
tau-t = 0.1 0.1
ref-t = 300 300
; Pressure coupling
Pcoupl = Berendsen
Pcoupltype = Isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau-p = 1
compressibility = 5e-5
ref-p = 1
; Random seed for Andersen thermostat
andersen_seed = 815131
; GENERATE VELOCITIES FOR STARTUP RUN
gen-vel = yes
gen-temp = 300
gen-seed = 173529
; OPTIONS FOR BONDS
constraints = all-bonds
; Type of constraint algorithm
constraint-algorithm = Lincs
; Do not constrain the start configuration
continuation = yes
; Use successive overrelaxation to reduce the number of shake iterations
Shake-SOR = no
; Relative tolerance of shake
shake-tol = 1e-04
; Highest order in the expansion of the constraint coupling matrix
lincs-order = 4
; Number of iterations in the final step of LINCS. 1 is fine for
; normal simulations, but use 2 to conserve energy in NVE runs.
; For energy minimization with constraints it should be 4 to 8.
lincs-iter = 1
; Lincs will write a warning to the stderr if in one step a bond
; rotates over more degrees than
lincs-warnangle = 30
; Convert harmonic bonds to morse potentials
morse = no
Thanks in advance,
--
http://devicerandom.org
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