[gmx-users] Error while performing a REMD simulation

[devicerandom]

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,
>
>


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