Re: vacuum simulation -Reg

From: Mani Kandan (manikandand5110_at_gmail.com)
Date: Sun May 19 2019 - 10:27:47 CDT

Hi,

Changing dielectric results in acceleration of the Dynamics as compared to
the system with water.

I want same Dynamics time as like a system having water. How can I
reproduce that

On Sun, May 19, 2019, 8:04 PM Subbarao Kanchi <ksubbu85_at_gmail.com> wrote:

> Hi Mani,
>
> You could set the dielectric constant to around 76 which is close to that
> of water. For default, it will be one.
>
>
> Best
> Subbarao Kanchi
>
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>
> ------------------------------
> *From:* owner-namd-l_at_ks.uiuc.edu on behalf of Mani Kandan <
> manikandand5110_at_gmail.com>
> *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 <shekaari_at_email.kntu.ac.ir>
> 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".
>> --
>> Regards,
>> Ashkan Shekaari,
>> Ph.D Candidate in Solid State Physics,
>> K. N. Toosi University of Technology,
>> Tehran, Iran
>>
>> ------------------------------
>> *From: *"Mani Kandan" <manikandand5110_at_gmail.com>
>> *To: *"namd-l" <namd-l_at_ks.uiuc.edu>
>> *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
>> MANIKANDAN
>>
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>

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