[gmx-users] problem about compiling mdrun_mpi under cygwin

Hi, there: I met a problem when I try to compile mdrun_mpi using configure --enable-mpi, I have mpich2 installed. I got some error message like the following(sorry, it is too long, hope you do not mind). I am wondering if anyone could tell me how to deal with it. Thank you so much. Best wishe

Re: [gmx-users] question about parallel runing of gromacs

ark Abraham wrote: > > Xiang Mao wrote: > > My PC has a intel core2 cpu. I compiled gromacs under cygwin, and using > MPICH2. After mpiboot, I use mpirun -n 2 mdrun_mpi to run EM, MD. > > > OK that might be working right. Now you need to look in the log file for an > ind

Re: [gmx-users] question about parallel runing of gromacs

My PC has a intel core2 cpu. I compiled gromacs under cygwin, and using MPICH2. After mpiboot, I use mpirun -n 2 mdrun_mpi to run EM, MD. thanks. mao On Mon, Mar 9, 2009 at 11:56 AM, Mark Abraham wrote: > Xiang Mao wrote: > >> Hello, everyone: >>I hav

[gmx-users] question about parallel runing of gromacs

Hello, everyone: I have a question about mdrun_mpi, when I tried to run mdrun_mpi with two processors, the log file show everystep twice like the following, I am just wondering if that is normal. Thanks for help. Step=0, Dmax= 1.0e-02 nm, Epot= -2.08462e+06 Fmax= 1.93968e+04, atom= 8202

[gmx-users] question about ligand

Dear All: How are you. Sorry to bother you. I am trying do use gromacs to do MD on a protein- ligand complex. I am following Dr. Kerrigan's tutorial on simulation of protein-ligand complex. Here I have a question about the topology of ligandgenerated by prodrg. And when I run pdb2gmx on my