On 5/13/13 4:44 AM, Sainitin Donakonda wrote:
Thank you very much for inputs but i forgot to mention in previous query i
got one error ..with other protein ligand simulation i used same MD file
saving 200 steps..
*Cannot write trajectory frame; maybe you are out of quota?*
*
*
Whats the solution for this error ? is this same problem with saving 200
steps? or some thing else
You already got an answer to this - you're saving full-precision output far too
often. The sysadmins of clusters typically put in place quotas (limits) on how
much disk space any one user can occupy, to prevent one person from sucking up
all the available resources. Or, if you're running on a local workstation or
small cluster, you're just filling up your hard disk. Just because it "worked"
before doesn't mean it will again - you have run out of available room to write
data. Consider whether you need full-precision output every 0.4 ps - the answer
is almost certainly "no."
-Justin
On Mon, May 13, 2013 at 10:25 AM, Broadbent, Richard <
richard.broadben...@imperial.ac.uk> wrote:
On 13/05/2013 08:46, "Sainitin Donakonda" <saigr...@gmail.com> wrote:
Hello,
I am trying to run 20 ns protein ligand simulation on cluster using
following MD.MDP file
; 7.3.3 Run Control
integrator = md ; leap-frog integrator
dt = 0.002 ; 2 fs
nsteps = 5000000 ; maximum number of steps
to integrate
; 7.3.8 Output Control
nstxout = 200 ; suppress .trr output
nstvout = 200 ; suppress .trr output
This writes out every 0.4 ps I doubt that¹s what you want
nstenergy = 1000 ; save energies every 2 ps
nstlog = 1000 ; update log file every 2 ps
nstxtcout = 1000 ; write .xtc trajectory every 2 ps
energygrps = Protein LIG
; 7.3.9 Neighbor Searching
nstlist = 5 ; [steps] freq to update neighbor
list
ns_type = grid ; method of updating neighbor list
pbc = xyz ; periodic boundary conditions in
all directions
rlist = 1.2 ; [nm] cut-off distance for the
short-range neighbor list
; 7.3.10 Electrostatics
coulombtype = PME ; Particle-Mesh Ewald
electrostatics
rcoulomb = 1.2 ; [nm] distance for Coulomb
cut-off
; 7.3.11 VdW
vdwtype = switch ; twin-range cut-off with rlist
where rvdw >= rlist
rvdw = 1.2 ; [nm] distance for LJ cut-off
rvdw_switch = 0.8 ; Start switching th LJ potential
DispCorr = EnerPres ; apply long range dispersion
corrections for energy
; 7.3.13 Ewald
fourierspacing = 0.12 ; [nm] grid spacing for FFT grid
when using PME
pme_order = 4 ; interpolation order for PME, 4 =
cubic
ewald_rtol = 1e-5 ; relative strength of
Ewald-shifted potential at rcoulomb
; 7.3.14 Temperature Coupling
tcoupl = V-rescale ; temperature
coupling with Berendsen-thermostat
tc_grps = Protein_LIG Water_and_ions ; groups to couple
seperately to temperature bath
tau_t = 0.1 0.1 ; [ps] time
constant for coupling
ref_t = 300 300 ; [K] reference
temperature for coupling
; Pressure coupling
pcoupl = Parrinello-Rahman ; pressure coupling is on for
NPT
pcoupltype = isotropic ; uniform scaling of box
vectors
tau_p = 2.0 ; time constant, in ps
ref_p = 1.0 ; reference pressure, in bar
compressibility = 4.5e-5 ; isothermal compressibility
of
water, bar^-1
refcoord_scaling = com
; 7.3.17 Velocity Generation
gen_vel = no ; velocity generation turned off
; 7.3.18 Bonds
constraints = all-bonds ; convert all bonds to constraints
constraint_algorithm = LINCS ; LINear Constraint Solver
continuation = yes ; apply constraints to the start
configuration
lincs_order = 4 ; highest order in the expansion
of
the contraint coupling matrix
lincs_iter = 1 ; number of iterations to correct
for rotational lengthening
lincs_warnangle = 30 ; [degrees] maximum angle that a
bond can rotate before LINCS will complain
*and im using following commands dividing 20 ns to 10 ns each via
extending
simulation*
*#This is the first simulation MD.mdp file contains 20 ns setup*
grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o
MD_first10.tpr
mpirun -n 16 mdrun -s MD_first10.tpr -deffnm MD_first10 -np 16
*#This extends 10 ns simulation*
tpbconv -s MD_first10.tpr -extend 10000 -o md_extended.tpr
mpirun -n 16 mdrun -s md_extended.tpr -deffnm MD_first10 -cpi
MD_first10.cpt -append -np 16
But it is crashed giving following error
*XTC error - maybe you are out of quota?*
*
*
*dont know why it happened it is because as im saving .trr file every
200ps? is it creating large files? or should i give different name in
extending simulation?*
No you are writing every 200 steps not ps this is explained in the
turtorials and the manual
You can check the file size by looking at ls -lh my guess is both the trr
and xtc will be gigantic
*
*
*Please help*
*
*
*Thanks,*
*Nitin*
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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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