From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Wed Sep 13 2017 - 09:26:11 CDT
>From what I understand, salt concentration becomes irrelevant for implicit
solvent simulations, because implicit solvents assume infinite dilution.
Note that you don't have a periodic box. Even if you did have ions I am
guessing they would fly away as soon as you start the simulation. In my
understanding, this is one drawback of implicit solvent methods in that you
cannot choose an ionic strength.
Hope this helps,
On Wed, Sep 13, 2017 at 1:49 AM, Roshan Shrestha <roshanpra_at_gmail.com>
> If you use VMD, you can add KCl by using extensions/ modelling/add ions.
> On 9/13/17, Susmita Ghosh <g.susmita6_at_gmail.com> wrote:
> > Dear NAMD users,
> > In NAMD implicit solvent model how to specify the type of ION for
> > the system? If I use only the "ionConcentration" command then by default
> > it will take NA+ and CL- ions. Now I want to use KCL instead of NACL to
> > ionize the system. Is there any any way to do that with Implicit solvent
> > model?
> > Thanks in advance!
> Roshan Shrestha
> M.Sc (Physics)
> Central Department of Physics, Tribhuvan University
> Kathmandu, Nepal
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