Re: vacuum simulation -Reg

From: Mani Kandan (manikandand5110_at_gmail.com)
Date: Sun May 19 2019 - 11:23:23 CDT

Thanks for the tip! But implicit solvent model the effect of the ions and
solvent. I want to model ions explicitly but water as implicitly or by some
potential between the ions.

On Sun, May 19, 2019, 9:02 PM Subbarao Kanchi <ksubbu85_at_gmail.com> wrote:

> 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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