[gmx-users] segmentation fault after mdrun

[Justin A. Lemkul]

Nikit sharan wrote:
> Dear justin,
> 
> As you suggested i have changed the coloumb type to PME and set
> pme_order to 5 as  said in the mailing list as it will increase the

Try an even number.

> accuracy.But then the simulation is not getting completed.Its taking
> hours together.Normally what's the running time for a lipid bilayer?I

Timings will be dependent on your hardware, especially the communication between 
nodes in a cluster.

-Justin

> dint find anything wrong with the topology as it is downloaded from
> tielman's website.it is also well equilibriated.Kindly give me your
> suggestions.My mdp.file is below:
> 
> 
> title                    = Yo
> cpp                      = cpp
> include                  =
> define                   =
> integrator               = md
> tinit                    = 0
> dt                       = 0.005
> nsteps                   = 50000
> init_step                = 0
> comm-mode                = Linear
> nstcomm                  = 1
> comm-grps                = system
> nstxout                  = 200
> nstvout                  = 0
> nstfout                  = 0
> nstcheckpoint            = 1000
> nstlog                   = 100
> nstenergy                = 100
> nstxtcout                = 1000
> xtc-precision            = 1000
> nstlist                  = 10
> ns_type                  = grid
> pbc                      = xyz
> rlist                    = 1.0
> domain-decomposition     = no
> coulombtype              = PME
> rcoulomb-switch          = 0
> rcoulomb                 = 1.0
> epsilon-r                = 1
> vdw-type                 = Cut-off
> rvdw-switch              = 0
> rvdw                     = 1.0
> DispCorr                 = EnerPres
> table-extension          = 1
> fourierspacing           = 0.12
> Pcoupl                   = berendsen
> Pcoupltype               = semiisotropic
> tau_p                    = 0.5 0.5 0.5
> compressibility          = 4.5e-5 4.5e-5 4.5e-5
> ref_p                    = 1.0 1.0 1.0
> andersen_seed            = 815131
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-- 
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Justin A. Lemkul
Graduate Research Assistant
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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