From: Jeff Comer (jeffcomer_at_gmail.com)
Date: Thu Nov 13 2014 - 15:11:10 CST
PS: I think with implicit solvent the diffusion coefficient of an atom
is usually estimated by D = kT/(6πηR), where η is the viscosity of the
medium and R is the atomic radius. But I'm mostly familiar with
implicit solvent simulations of ions. I got the diffusion coefficient
formula from the following reference:
http://dx.doi.org/10.1529/biophysj.104.044008
–––––––––––––––––––––––––––––––––––———————
Jeffrey Comer, PhD
Assistant Professor
Institute of Computational Comparative Medicine
Nanotechnology Innovation Center of Kansas State
Kansas State University
Office: P-213 Mosier Hall
Phone: 785-532-6311
On Thu, Nov 13, 2014 at 10:41 AM, Fidan Sumbul <fidansumbul_at_gmail.com> wrote:
> Thank you for your response Dr. Comer.
>
> I'd like to perform Langevin dynamics simulation (stochastic dynamis), but
> not overdamped as Brownian dynamics.
> If Langevin thermostat and Langevin dynamics are the same, why we call
> Molecular dynamics that NAMD MD runs do with langevin thermostat?
>
> Could you please help me to understand what is the real distinction between
> MD simulations with Langevin thermostat and Langevin dynamics simulations?
> Does MD with Langevin thermostat also have random force?
>
> Regards,
>
>
> On Thu, Nov 13, 2014 at 12:37 AM, Jeff Comer <jeffcomer_at_gmail.com> wrote:
>>
>> Hi,
>>
>> The Langevin thermostat and Langevin dynamics are really one in the
>> same, assuming you aren't talking about overdamped Langevin dynamics.
>> You can use generalized Born implicit solvent
>> (http://www.ks.uiuc.edu/Research/namd/2.10b1/ug/node31.html) coupled
>> with "langevin on"
>> (http://www.ks.uiuc.edu/Research/namd/2.10b1/ug/node36.html).
>>
>> I've used the "langevinFile" option to set different friction
>> coefficients for different particles. This means that you can set the
>> diffusion coefficient (in the long time limit) for your particles (or
>> molecules).
>>
>> Best wishes,
>> Jeff
>>
>> –––––––––––––––––––––––––––––––––––———————
>> Jeffrey Comer, PhD
>> Assistant Professor
>> Institute of Computational Comparative Medicine
>> Nanotechnology Innovation Center of Kansas State
>> Kansas State University
>> Office: P-213 Mosier Hall
>> Phone: 785-532-6311
>>
>>
>> On Wed, Nov 12, 2014 at 2:48 PM, Fidan Sumbul <fidansumbul_at_gmail.com>
>> wrote:
>> > Dear NAMD users,
>> >
>> > I'd like to perform an implicit solvent Langevin Dynamics simulation. I
>> > can
>> > do it in Amber, but I wonder if I can use NAMD for this job because I am
>> > familiar with NAMD. Could you provide me a tutorial or link to a
>> > tutorial if
>> > NAMD does Langevin dynamics simulations. I know NAMD uses Langevin
>> > dynamics
>> > in normal MD simulations to keep temperature constant.
>> >
>> > Thanks for your help.
>> >
>> > --
>> > Fidan Sumbul
>> > PhD Student and T.A.
>> > Polymer Research Center
>> > Department of Chemical Engineering
>> > Bogazici University
>
>
>
>
> --
> Fidan Sumbul
> PhD Student and T.A.
> Polymer Research Center
> Department of Chemical Engineering
> Bogazici University
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