AMBER Archive (2004)

Subject: Re: AMBER: LES Simulations

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Thu Jan 29 2004 - 11:20:45 CST

the copies will each have 1/5 the charge of the original,
so the net charge is not changed.
carlos

----- Original Message -----
From: "Vlad Cojocaru" <Vlad.Cojocaru_at_mpi-bpc.mpg.de>
To: "amber" <amber_at_scripps.edu>
Sent: Thursday, January 29, 2004 12:18 PM
Subject: AMBER: LES Simulations

> Dear Amber users,
> I want to run LES simulations on an RNA loop. I have the non-LES
> system equilibrated (water + ions ...PME) and I created the LES topology
> (starting from the equilibrated non-LES system) file by making 5 copies
> of my region. I copied 10 RNA residues so I introdused more negative
> charges. The question is: Do I have to add more Na+ in order to
> neutralize the new LES system or the neutrality of the system will be
> conserved after making the copies?
> Thank you very much for answers
> vlad
>
> --
> Vlad Cojocaru
> Max Planck Institute for Biophysical Chemistry
> Department: 060
> Am Fassberg 11, 37077 Goettingen, Germany
> tel: ++49-551-201.1327
> e-mail: Vlad.Cojocaru_at_mpi-bpc.mpg.de
> home tel: ++49-551-9963204
>
>
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu