AMBER Archive (2004)

Subject: Re: AMBER: MD at different pH !!

From: Bimo Ario Tejo (bimo7_at_gmx.de)
Date: Sat Mar 06 2004 - 06:18:15 CST

Hi Jiten,

You should neutralize your system, particularly if you use PBC. If the
system doesn't have a neutral charge, then when you replicate it using PBC, the
total charge would become infinity.

Cheers,
Bimo

> Thanks for the discussion on MD at different pH. When we assign the
> charges
> on the residues at different pH the total charge of the protein would be
> changed. According the sander MD simulations, it would force plasma charge
> neutrailty. In such case should we need to neutalise the systems with
> counterions before the simulation - I mean using xleap.
>
> Your advice to me would be highly appreciated, Thanks in advance.
>
> Jiten 

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