Re: Non standar solvent

From: Roy Fernando (
Date: Tue Feb 18 2014 - 10:49:10 CST

I think in solvating with a solvent other than water, we need to have a
solvent box. (that is what the documentations implies)

I think if you have a box of solvent (other than water) you can insert a
protein in to it by removing the overlapping solvent molecules. In order to
create the box of solvent it is possible to use the method suggested in
topotools (

Once you have created the solvent box you can equilibrate the box in order
to bring in liquid like properties to the system. However you need to have
parameter files for the simulation.

I look forward to see other opinions about this problem as I myself am in
the process of running a simulation along this line.


On Tue, Feb 18, 2014 at 11:12 AM, MEHRAN MB <> wrote:

> Hi Javad,
> this is NAMD mailing list, you should post your question in VMD mailing
> list,
> -mehran
> On Sat, Feb 15, 2014 at 7:52 AM, Javad Noroozi <>wrote:
>> Does any one have experience with creating non standard solvent using VMD?
>> I have pdb,psf,top files in VMD's plugin directory besides original
>> files for water and i have also changed seg name to QQQ.
>> I want to know what option should be cheked or filled in the VMD
>> solvation window.
>> Javad Noroozi
>> Chemical Engineering Department
>> Sharif University of Technology
>> Email:

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