Re: vacuum simulation -Reg

From: Subbarao Kanchi (ksubbu85_at_gmail.com)
Date: Sun May 19 2019 - 10:32:33 CDT

Hi

Then you should look for one of the best implicit solvent models.

On Sun, May 19, 2019 at 10:27 AM Mani Kandan <manikandand5110_at_gmail.com>
wrote:

> 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
>>
>> Get Outlook for iOS <https://aka.ms/o0ukef>
>>
>> ------------------------------
>> *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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