[gmx-users] Issue running gromacs in Cluster

Justin Lemkul jalemkul at vt.edu
Mon May 13 13:46:05 CEST 2013 


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.broadbent09 at imperial.ac.uk> wrote:
>
>>
>>
>> On 13/05/2013 08:46, "Sainitin Donakonda" <saigro16 at 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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>>
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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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