Re: [gmx-users] System blows up

2012-01-13 Thread Guido Leoni
highlight the problem? In your opinion the clash could be more probably due to solvent molecules or to my proteins perhaps too near each other? Thank you very much Guido 2012/1/11 Mark Abraham mark.abra...@anu.edu.au On 11/01/2012 8:35 PM, Guido Leoni wrote: Dear List I'm newbie to gromacs (sigh

[gmx-users] System blows up

2012-01-11 Thread Guido Leoni
Dear List I'm newbie to gromacs (sigh). I'm simulating the interaction between two proteins(chrystallographic structures) following the spider toxin tutorial. I'm able to correctly minimize ( E1000) and equilibrate (400 ps ) the system. No error message appears to me and I'm quite sure that my

[gmx-users] protein-protein simulation

2012-01-09 Thread Guido Leoni
300 ; Pressure coupling is off Pcoupl = no Pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 -- Guido Leoni National Research Institute on Food and Nutrition (I.N.R.A.N.) via Ardeatina 546 00178 Rome Italy tel + 39 06 51 49 41 (operator