AMBER Archive (2003)

Subject: Re: Simulation under physiological conditions

From: Andreas Svrcek-Seiler (svrci_at_tbi.univie.ac.at)
Date: Thu May 15 2003 - 11:11:13 CDT

Hi,
> could you recommend me, please, the easiest way to build .top and .crd
> file in Xleap for simulation with 0.15M - NaCl?

...This following reasoning might be a bit crude, but maybe it helps:
One liter of H2O is contains about 55.6 mols. Therefore,
if your original waterbox contains N_w H2Os, by adding
N_w/55.6 Na+ and N_w/55.6 Cl- ions, you should get an *approximately*
1M concentration of NaCl. (N_w/55.6)*0.15 should
give you the number if Na+ and Cl- ions to add for 0.15M solution.

Since that's only what I just thought up, you might wait
for the experts to give their opinion, too.

In principle, replacing every '55.6th' water by Na+ and again for Cl-
seems more accurate, but it might make little difference since
55.6 is much larger than 1. I believe that
due to the small size of usual periodic boxes, there
should be no 'exactly right' number of Na and Cl to add
(the number of ions per 50A x 50A x 50A box of the 'real world'
should fluctuate anyway).

Good luck
Andreas 

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