[gmx-users] Umbrella sampling - chain A does not get pulled

Davide Mercadante dmer018 at aucklanduni.ac.nz
Tue Dec 11 08:40:21 CET 2012

Dear Justin,

I have been practicing umbrella sampling simulations following your tutorial
step by step. I have just finished to perform the pull simulations to
identify the configurations to use in the umbrella runs. I have used the
distances.pl script to run iteratively g_dist and the resulting file
(summary_distances.dat) is showing a distance between 2.62nm (for conf0.gro)
and 5.3nm (for conf500.gro). I don't seem to have the values reported in the
tutorial at all (in the tutorial is reported that the COM distance would be
something of an order of magnitude lowerŠ) and I am not sure if something is
gone wrong. 

I have also tried to visualize the trajectories but I am not able to see
chain_A moving away from the rest of the fibril. I have set, at the end of
the topol_Protein_chain_B.itp file, the lines suggested to restrain chain B.

#ifdef POSRES_B
#include "posre_Protein_chain_B.itp"

I have used all the input files given in the tutorial and the commands/files
extensions suggested.

Can you please help me to understand if I am doing something wrong?

Thank you very much for your help.

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