AMBER Archive (2009)

Subject: Re: [AMBER] drying of solvent possible ?

From: Jio M (jiomm_at_yahoo.com)
Date: Sat Aug 15 2009 - 00:59:08 CDT

Dear Bill Ross,

thanks for the reply for my second query. I will be glad to know if
someone has removed solvent gradualy from the system while running
dynamics

Regards

JIomm

From: Bill Ross <ross_at_cgl.ucsf.edu>
Subject: Re: [AMBER] drying of solvent possible ?
To: amber_at_ambermd.org
Date: Thursday, August 13, 2009, 4:21 PM

> 1) is there a way to slowly remove the water while running MD at low
> temperature that is  removing water only from the system keeping
> solute=A0 at last.  this can be considered
> as  "vacuum drying of a system at low temperature (say 10'C)"
>
> solute + Water=A0 -------Dynamics-Run-(at low temp.)-->> solute only

There isn't any way to do this, as far as I know.

> 2) other=A0 question (not related to above) I want to give
> environment of residue + water as a solvent to solute. Is this
> correctway to provide environment of residue + water to solute. I have
> run the dynamics it was successfull with no error, but I am not
> confident for my procedure. I used following:
>
>
> if my solute variable is "solu" and variable for residue molecule is
> "res" and both saved in abc.lib
>
> source leaprc.gaff (also loading the frcmod files of solv and solt)
>
> loadoff abc.lib
> solvateoct  solu res 8.0 {this adds=A0 res to solu }
> loadoff solvents.lib
> solvateoct solu TIP3PBOX 8.0
> edit solu { shows water and res environment around solu}
>
>
> Is this a correct method=20

It seems a good method for getting a mixed environment for your solute.

Bill

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