Re: vacuum simulation -Reg

From: Ashkan Shekaari (
Date: Sun May 19 2019 - 09:08:11 CDT

Dear Mani,
langevinDamping 2.5 would be much better. How about the strength of the electric field?
If "timestep 1 fs", then "rigidbonds water".

Ashkan Shekaari, 
Ph.D Candidate in Solid State Physics, 
K. N. Toosi University of Technology, 
Tehran, Iran 
From: "Mani Kandan" <> 
To: "namd-l" <> 
Sent: Sunday, May 19, 2019 6:25:02 PM 
Subject: namd-l: vacuum simulation -Reg 
Hello all, 
I am running the vacuum simulation to study ion transport through the nanopore. During this run, the ions are forming the cluster i.e anions and cations are attracted to each other and forms a cluster. But I don't want to form this kind of cluster of atoms. How can I avoid this problem? Simulation details are given below: 
Simulation details: 
NVT using Langevin thermostat of 1 1/ps 
timestep of 1fs 
Kindly help me in this regard. 
With regards 
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