Re: [gmx-users] segmantation default

2012-02-02 Thread Justin A. Lemkul
mehmet kıytak wrote: hi Justin... you were right.. my equilibration is ınsufficient...ı increase nsteps 520..now ı recieve this message.. Fatal error: The Z-size of the box (1.957000) times the triclinic skew factor (1.00) is smaller than the number of DD cells (2) times the

Re: [gmx-users] segmantation default

2012-02-02 Thread mehmet kıytak
hi Justin... you were right.. my equilibration is ınsufficient...ı increase nsteps 520..now ı recieve this message.. Fatal error: The Z-size of the box (1.957000) times the triclinic skew factor (1.00) is smaller than the number of DD cells (2) times the smallest allowed cell size

Re: [gmx-users] segmantation default

2012-02-01 Thread Justin A. Lemkul
mehmet kıytak wrote: hi justin ı used this mdp. file ..simulation box may be wrong.?..ı used dodecahedron distance edge 2.0 nm. No, that's almost certainly not the problem. Insufficient minimization/equilibration, or instability due to the use of the free energy code is more likely.

Re: [gmx-users] segmantation default

2012-02-01 Thread mehmet kıytak
hi justin ı used this mdp. file ..simulation box may be wrong.?..ı used dodecahedron distance edge 2.0 nm. ; Run control integrator = sd ; Langevin dynamics tinit= 0 dt = 0.002 nsteps = 250 ; 5 ns nstcomm

Re: [gmx-users] segmantation default

2012-02-01 Thread Justin A. Lemkul
mehmet kıytak wrote: hi all... ı have a problem.. ı got segmentation fault when run nvt equilibration.. ı use below mdp file Please post a complete .mdp file. The Unix 'cat' command can be used to print the contents of the text file, which can then be copied and pasted into an email.

[gmx-users] segmantation default

2012-02-01 Thread mehmet kıytak
hi all... ı have a problem.. ı got segmentation fault when run nvt equilibration.. ı use below mdp file ; Run control integrator = sd ; Langevin dynamics tinit= 0 dt = 0.002 nsteps = 5; 100 ps nstcomm