[gmx-users] printing a trajectory file in readable format starting from a specific frame other than zero

Hello, Is there a function that allows users to read a trajectory file and print it in a readable format (like gmxdump) but starting from a user- specified frame rather than from 0? Thanks in advance, Silvia Crivelli -- gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] Fwd: gmx-users Digest, Vol 79, Issue 102

users gmx-users@gromacs.org Message-ID: 4cdee7ac.9020...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 14/11/2010 5:58 AM, Silvia Crivelli wrote: Hello, When I run energy minimization, I'd like to obtain the energy per atom in addition to the (potential) energy

[gmx-users] how to calculate per-atom energies

Hello, When I run energy minimization, I'd like to obtain the energy per atom in addition to the (potential) energy value for the entire protein. Is there a way to do this? Thanks in advance, Silvia Crivelli -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman

[gmx-users] Question about building and testing on imac

Hello, I built gromacs4.5.1 on my new imac (OS X 10.6.4) without problems using the command sequence: ./configure --enable-shared make make install Before that, I built fftw (3.2.2) by following the following sequence: ./configure --enable-threads --enable-float make make install However,

[gmx-users] force evaluation

Hello, I need to calculate the forces (derivatives) for every atom in a protein as this is being locally minimized using mdrun. When I run mdrun I can get the maximum force F-max and the atom on which this force is evaluated printed in the log file (for example, F-max =