[gmx-users] Re: Membrane Runs Crashing

[Justin Lemkul]

On 6/19/13 9:25 AM, Neha wrote:
> Here's the full mdp file. Please let me know if you need anymore information
> and thank you so much for helping!
>
> ; RUN CONTROL PARAMETERS =
> integrator               = md
> ; start time and timestep in ps =
> tinit                    = 0.0
> dt                       = 0.02
> nsteps                   = 50000000
> ; number of steps for center of mass motion removal =
> nstcomm                  = 1
> comm-grps                = DPPC W
>
> ; OUTPUT CONTROL OPTIONS =
> ; Output frequency for coords (x), velocities (v) and forces (f) =
> nstxout                  = 50000
> nstvout                  = 50000
> nstfout                  = 0
> ; Output frequency for energies to log file and energy file =
> nstlog                   = 10000
> nstenergy                = 500
> ; Output frequency and precision for xtc file =
> nstxtcout                = 10000
> 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               = DPPC W
>
> ; NEIGHBORSEARCHING PARAMETERS =
> ; nblist update frequency =
> nstlist                  = 10
> ; ns algorithm (simple or grid) =
> ns_type                  = grid
> ; Periodic boundary conditions: xyz or none =
> pbc                      = xyz
> ; nblist cut-off         =
> rlist                    = 1.2
>
> ; OPTIONS FOR ELECTROSTATICS AND VDW =
> ; Method for doing electrostatics =
> coulombtype              = Shift
> rcoulomb_switch          = 0.0
> rcoulomb                 = 1.2
> ; Dielectric constant (DC) for cut-off or DC of reaction field =
> epsilon_r                = 15
> ; Method for doing Van der Waals =
> vdw_type                 = Shift
> ; cut-off lengths        =
> rvdw_switch              = 0.9
> rvdw                     = 1.2
> ; Apply long range dispersion corrections for Energy and Pressure =
> DispCorr                 = No
>
> ; OPTIONS FOR WEAK COUPLING ALGORITHMS =
> ; Temperature coupling   =
> tcoupl                   = Berendsen
> ; Groups to couple separately =
> tc-grps                  = DPPC W
> ; Time constant (ps) and reference temperature (K) =
> tau_t                    = 1.0 1.0
> ref_t                    = 325 325
> ; Pressure coupling      =
> Pcoupl                   = berendsen
> Pcoupltype               = semiisotropic
> ; Time constant (ps), compressibility (1/bar) and reference P (bar) =
> tau_p                    = 1.0  1.0
> compressibility          = 5e-6 0.0
> ref_p                    = 0.0  0.0
>
> ; GENERATE VELOCITIES FOR STARTUP RUN =
> gen_vel                  = yes
> gen_temp                 = 325
> gen_seed                 = 473529
>
> ; OPTIONS FOR BONDS     =
> constraints              = none
> ; Type of constraint algorithm =
> constraint_algorithm     = Lincs
> ; Do not constrain the start configuration =
> unconstrained_start      = no
> ; Highest order in the expansion of the constraint coupling matrix =
> lincs_order              = 4
> ; Lincs will write a warning to the stderr if in one step a bond =
> ; rotates over more degrees than =
> lincs_warnangle          = 30
>

What was the outcome of EM before this?  What if you try NVT before NPT?  Have 
you tried reducing the timestep or the value of nstlist?

I would try everything with ref_p = 1.0 instead of zero to make sure you can get 
a "normal" setup to work.

-Justin

-- 
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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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