[gmx-users] electrostatic forces

Hi, I would like to calculate the electrostatic forces on the atoms of an Indole group (in a TRP residue). I have performed two reruns of my simulation with two different topologies : a normal topology and a topology with all the Indole charges set equal to 0. I have also added energygrp_excl

R: [gmx-users] electrostatic forces

Thank you for your reply, Really, I don’t think that the difference come from the 1-4 interactions. I have excluded all the 1-4 interaction involving atoms in the indole group (deleting them from the pairs list). Furthermore, I have added the indole as an energygrps, and checking the 1-4 ener

[gmx-users] problems with nsgrid

Dear gmx users I'm simulating a system with 128 POPC, 5000 water (SPC) and 1 peptide with dummy hydrogens (option -vsite hydrogens in pdb2gmx) and 4fs of time step to reproduce the bilayer assembling, starting from molecules randomly placed inside the box. The system has been minimized and an

Re: [gmx-users] problems with nsgrid

The previous e-mail refers to simulation running with mdrun in double precision, using the single precision the problem is disappered. Regards Gianfranco - Original Message - From: "Gianfranco Bocchinfuso" <[EMAIL PROTECTED]> To: "Discussion list for GROMACS