[gmx-users] Neutral simulation box

David spoel at xray.bmc.uu.se
Wed Nov 26 21:41:02 CET 2003

On Wed, 2003-11-26 at 21:32, Deepa Rajamani wrote:
> I am running a simulation on protein. I have
> the following questions.
> 1. Should I be neutralizing the simulation box if I use the PME for
> calculating long range electrostatics.

> 2. IF I do will the mobility of the charged side chains be affected by the
> counter ions added.

> 3. IF yes for my second question, how do I overcome this problem.
this is not a problem. If we assume for a moment that the force field is
perfect and sampling is very good as well, not adding the ions will have
an adverse effect. If on the other hand the force field is not perfect,
and sampling is limited as well, then what? In my opinion, if not adding
ions would make the results more reliable (however you would prove
that), then the whole simulation is useless (i.e. unreliable). My
conclusion therefore is to take the most accurate description that you
can afford, which means PME and realistic ionic strength.

> Thanks in advance.
> Deepa
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David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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