Re: [gmx-users] mdrun seems stuck

2009-06-02 Thread Jussi Lehtola
On Tue, 2009-06-02 at 11:13 +0100, Stefano Meliga wrote: > The simulation seems just very slow. > step 0 has appeared on the screen after several minutes and in the log > file there's only step zero as well. You have 43 000 atoms and are using Ewald summation which is O(N^2), so the simulation re

Re: [gmx-users] mdrun seems stuck

2009-06-02 Thread Stefano Meliga
The simulation seems just very slow. step 0 has appeared on the screen after several minutes and in the log file there's only step zero as well. Stefano Nuno Azoia ha scritto: Take a look to your .log file. Gromacs writes everything there. Nuno Azoia On Tue, 2009-06-02 at 10:45 +0100, Stefa

Re: [gmx-users] mdrun seems stuck

2009-06-02 Thread Nuno Azoia
Take a look to your .log file. Gromacs writes everything there. Nuno Azoia On Tue, 2009-06-02 at 10:45 +0100, Stefano Meliga wrote: > Hello, > > I'd like to run a position restrained MD of a protein in water with > 3000 (protein) + 4 (SOL) atoms. > > I preprocess the input with the command

[gmx-users] mdrun seems stuck

2009-06-02 Thread Stefano Meliga
Hello, I'd like to run a position restrained MD of a protein in water with 3000 (protein) + 4 (SOL) atoms. I preprocess the input with the command line: $grxdir/grompp -f 4AKEprePRMD.mdp -po 4AKE_PRMD.mdp -c 4AKE_EMcg.gro -p 4AKEallHion.top -pp 4AKEprePRMD.top -o 4AKE_PRMD.tpr 4AKEprePRMD.m