[gmx-users] Saving velocities

Hi, Does anybody knows how to save the velocities of a group of particles every N time steps without having to write the .trr file for the whole system? I mean my system has two kinds of molecules say A and water what I want is to save the velocities for the atoms in the molecule A every certain n

[gmx-users] Installating GROMACS with MPI

GROMACS. thanks in advance for your help. Here it is the error message: /bin/sh ../../../../libtool --tag=CC --mode=compile mpicc -DHAVE_CONFIG_H -I. -I../../../../src -I/usr/include/libxml2 -I../../../../include -DGMXLIBDIR=\"/home/fb18/pojeda/bin/share/top\" -I/home/fb18/

[gmx-users] Metallic boundary conditions

Hi, thank you for your answer. What is then epsilon_r ? regards. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the lis

[gmx-users] Metallic boundary conditions

Hi, I want to use metallic boundary conditions in my problem. I think one can do that with the option epsilon_r =0 in gromacs. If I set epsilon_r =0 I get the output: Starting 2 threads Making 1D domain decomposition 2 x 1 x 1 starting mdrun 'Dipoles' 1000 steps, 5000.0 ps. Segmentation fau

[gmx-users] Reduced Units

Hi, I want to use the pme algorithm in GROMACS. Thge size of my box is 8.2x8.2x8.2 in reduced units. I am considering a collection of 1000 of CO2 molecules. If I am using reduced units, the values of the parameters "rcoulomb=0.9" I think should be converted to reduced units "rcoulomb=2.45" (my \si

[gmx-users] Hi

Hi, I am starting with GROMACS. About the units in GROMACS, I read in the manual that one can use the reduced units for lennard-jones systems. It means that if I want to use reduce units I just write the values of all the parameters (distance, mass, charge ...) in reduced units for all files (.mdp