RE: Npt lipid simulation with electrostatics 2

From: Radak, Brian K (
Date: Fri Feb 17 2017 - 09:26:20 CST

Is the volume well equilibrated? Sometimes the cell size errors go away once the volume is more stable and not changing so much.

Brian Radak
Postdoctoral Appointee
Leadership Computing Facility
Argonne National Laboratory

9700 South Cass Avenue, Bldg. 240
Argonne, IL 60439-4854
(630) 252-8643
From: [] on behalf of Life Sciences Inc []
Sent: Thursday, February 16, 2017 4:46 PM
Subject: namd-l: Npt lipid simulation with electrostatics 2

Hi All

I am facing a problem with Npt for the lipid system while giving 2 as full elect frequency in namd. It is returning an error of periodic cell becoming too short, I tried with 1 and the job is running fine. I have tried solutions given in the namd forum but still unable to run the job with 2. I tried changing margin tried also running the job with small time step but nothing is working. Althought with NVT simulation lipid system is running with 2 value but as I switch back again to NPT somehow electrostatics with 2 is not working. Can this problem be solved ?

Thanks in advance

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