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.cgl.ucsf.edu>
Subject: Re: [AMBER] drying of solvent possible ?
To: amber.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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Aug 19 2009 - 22:35:47 PDT
