[gmx-users] Protein-ligand interactions
indira at ccbb.pitt.edu
Thu Aug 18 15:34:01 CEST 2005
I am having a similar problem as Ulrich below, regarding ligand-protein interactions. I get different behaviour of the ligand when I run it on one node and two nodes. So which one should I trust? the one-node simulation or two node-simulation? (the initial conditions are identical for both the simulations)
From: gmx-users-bounces at gromacs.org on behalf of Ulrich Omasits
Sent: Thu 8/18/2005 8:05 AM
To: gmx-users mailinglist
Subject: [gmx-users] stable trajectory?
I'm simulating a protein-ligand system in a 20A-SPC waterbox using the
gmx-ff and PME.
The ligand should be high-affinity but in two out of five
one-nanosecond-simulations the ligand detaches the protein!
In one simulation the ligand seems to be stable (RMSD & RMSF look nice)
but then the same simulation performed again (only starting velocities
differ) delivers totally different results (ligand even detaches!).
How can this happen!?! What can I do?
Should I change the forcefield, the water-type, the box-type, the
Could these changes affect the trajectory such drastically?
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