[gmx-users] Error while performing a REMD simulation

Luis Miguel Medina Solano migu-med at uniandes.edu.co
Sun Apr 10 03:37:12 CEST 2011


I used a -maxwarn 5, but I only obtain 1 warning,  (about obsolete entries that the .mdp file has).
I used a solute-box distance of 0.34 in order to reduce the simulation box. I used before a solute-box distance of 1 nm and the problem persist. 

my .mdp file is the next:

title =
cpp = /lib/cpp
include =
define =

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 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 =

; 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

; 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

; 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

gen-vel = yes
gen-temp = 300
gen-seed = 173529

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,

Luis Miguel Medina Solano wrote:

I'm very sorry for the way I reply, the truth is that i didn't know how else to reply (it is my first time posting here).the script to generate the REMD is:

# ff opsla and water spc
echo -e "14\n4\n3\n3 0" |pdb2gmx -f 1.pdb -o inib4em.pdb -p topol.top -ignh -tereditconf -f inib4em.pdb -o inib4em.pdb -d 0.34 -bt dodecahedron
Using a solute-box distance of only 0.34 nm is probably unwise.  Why have you chosen such a short distance?grompp -v -f iniem.mdp -o em -c inib4em.pdb -maxwarn 5
Why are you using -maxwarn, especially to ignore up to five errors?  The notes that grompp prints are helpful in that they usually indicate sources of instability in your system by way of algorithm conflict.mdrun -v -s em -c ini_after_em.pdb -deffnm ini_after_em   editconf -f ini_after_em.pdb -o ini_after_em.pdb -d 0.34 -bt dodecahedrongenbox  -cp ini_after_em.pdb -cs spc216 -o sol_b4em.pdb -p topol.top
grompp -v -f em.mdp -c sol_b4em.pdb -o sol_em -p topol.top -maxwarn 5
mdrun -v -s sol_em -c sol_after_em.pdb -deffnm sol_after_em
grompp -v -f rp.mdp -c sol_after_em.pdb -o sol_rp -p topol.top -maxwarn 5
mdrun -v -s sol_rp -c sol_after_rp.pdb -deffnm sol_after_rp
# NVT and NPT runs for each replica
for ((i = 0; i<= 42 ; i ++))
grompp -v -f nvt$i.mdp -c sol_after_rp.pdb -o sol_nvt$i -p topol.top -maxwarn 5mdrun -v -s sol_nvt$i.tpr -c sol_after_nvt$i.pdb -deffnm sol_after_nvt$i
grompp -v -f npt$i.mdp -c sol_after_nvt$i.pdb -o sol_npt$i -p topol.top -maxwarn 5mdrun -v -s sol_npt$i.tpr -c sol_after_npt$i.pdb -deffnm sol_after_npt$i
editconf -f sol_after_npt$i.pdb -o sol_after_nptt$i.pdb  -c
grompp -v -f solv$i.mdp -c sol_after_nptt$i.pdb -o sol_solv$i -p topol.top -maxwarn 5Providing your .mdp files is probably useful for determining the source of your problems, but more likely either (or both) of the above points will have critical clues.-Justin

# REMD run
mpiexec -l -np 43 mdrun_mpi -v -s sol_solv.tpr -multi 43 -replex 500 -c Folded.pdb -deffnm FoldedBest regards


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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