[gmx-users] scalar correlation matrix

Hello, everyone, Do anybody knows how to calculate the scalar correlation matrix across the alpha carbon atoms, where the correlation function is defined as: Cij=delta_ri*delta_rj/squart(delta_ri^2delta_rj^2). Is there any direct command can do this in gromacs? Thanks. * *

[gmx-users] protein running out of box

Hello, every body. I have running a MD for 10ns. However, after 5ns part of protein will running out of the box and be located at other part of the water box. And the whole structure seems ver strange. It seems that it was caused by the mass translation but I have used the comm_mode=Linear. Any

[gmx-users] about parallel work

Hello, every body. I have a question about parallel running of mdrun_mpi. I doubt that sometimes the parallel running of mdrun_mpi can not utilize the domain decomposition. This is the case when I use the batch work in the computer cluster which install the MPICH2. In the case, I use commond

Re: [gmx-users] about parallel work

Höfling martin.hoefl...@gmx.de Am 21.04.2009 um 17:04 schrieb sheerychen: ... However, in my person computer which install the MPICH (not MPICH 2), I use the commond like this ''mpirun -np 3 /usr/bin/mdrun_mpi -deffnm *** -v''. It would show the domain decomposition and the speed is quicked

[gmx-users] about the restart of the mdrun

Hello, I have a problem when I restrat of mdrun (Gromacs 4.0) using the following command: mdrun -deffnm Asp -cpi -append. The errors like this: eading checkpoint file Asp_md.cpt generated: Wed Mar 11 19:16:24 2009 Build time mismatch, current program: Thu Mar 5 17:52:53 CET 2009