Re: [AMBER] Problem with initial complex structure for TI

From: Kalenkiewicz, Andrew (NIH/NICHD) [F] <"Kalenkiewicz,>
Date: Mon, 14 Dec 2015 21:37:56 +0000

Not sure if anyone saw this but I'm still getting the "vlimit exceeded" error whenever I try to run the vdw_bonded simulation with clambda=1. I tried other minimization schemes to no avail.

One thing I noticed is that for the vdw_bonded simulations, the heating step starts from the restart file that was generated from the initial complex structure, NOT the equilibrated complex generated in the setup stage. Hence I tried using the actual minimized structure but I still get a vlimit exceeded error.
From: Kalenkiewicz, Andrew (NIH/NICHD) [F]
Sent: Friday, December 11, 2015 6:17 PM
Subject: [AMBER] Problem with initial complex structure for TI

Dear Amber users,

I'm attempting to carry out thermodynamic integration on my system using Hannes Loeffler's T4-lysozyme tutorial as a template. Everything has proceeded fine except for the van der Waals simulation with lambda = 1. In that case I get a "vlimit exceeded" error, which I know is usually due to overlapping atoms. The receptor conformation isn't ideal for the V1 state (I used the bound conformation of V0), i.e. there do look to be some possible vdw clashes. I don't really understand why it would only lead to a crash for lambda = 1 whereas the other lambdas appear fine. Any help with this would be much appreciated!


Andrew Kalenkiewicz
Postbaccalaureate Fellow, NICHD
Molecular Biology BS '13
Biomedical Engineering MSE '15
University of Michigan, Ann Arbor
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Received on Mon Dec 14 2015 - 14:00:03 PST
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