Re: vacuum simulation -Reg

From: Subbarao Kanchi (
Date: Sun May 19 2019 - 09:33:18 CDT

Hi Mani,

You could set the dielectric constant to around 76 which is close to that of water. For default, it will be one.

Subbarao Kanchi

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From: on behalf of Mani Kandan <>
Sent: Sunday, May 19, 2019 9:28 AM
To: Ashkan Shekaari
Cc: namd-l
Subject: Re: namd-l: vacuum simulation -Reg

In these case, efied is around 0.04V/A.

And one more thing I missed in the previous email I sent. Here I am not considering any solvent and the system consists of ions and pore.

Formation of cluster happened due to absence of the solvent. Is there any way to include the effect of the solvent by adding some potential between the ions?

On Sun, May 19, 2019, 7:38 PM Ashkan Shekaari <<>> wrote:
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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