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
Thank you for your reply,
Really, I dont 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
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
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
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