Re: [gmx-users] gmx 4.6 mpi installation through openmpi?

Hi, see installation instruction with CMAKE here: http://www.gromacs.org/Documentation/Installation_Instructions I guess that maybe you need to specify your Openmpi and FFTW installation directories using options CMAKE_PREFIX_PATH. For example, my Openmpi and FFTW were firstly installed in "/hom

[gmx-users] Inhomogeneity of water molecules insertion into the box

Hi all, I would like to add 484 water molecules into the box using command: genbox -cp newbox.gro -cs tip4p.gro -maxsol 484 -p topol.top -o solvated.gro What I expected is those water molecules would be randomly inserted into the box and the box should appear homogeneous. But the result disapp

Re: [gmx-users] How to have two proteins randomly positioned and oriented in the box

emkul wrote: > > > On 3/31/13 9:51 PM, Zhikun Cai wrote: > >> Hi everyone, >> >> I am trying to insert two same proteins in a simulation box. Now I have >> used pdb2gmx to convert one protein's pdb file to gro file. Then how >> should >> I do? How

[gmx-users] How to have two proteins randomly positioned and oriented in the box

Hi everyone, I am trying to insert two same proteins in a simulation box. Now I have used pdb2gmx to convert one protein's pdb file to gro file. Then how should I do? How could they be randomly positioned and oriented in the box? Thanks in advance. Zhikun -- gmx-users mailing listgmx-users@g