Re: pH in NAMD

From: Richard Wood (
Date: Thu Feb 08 2007 - 09:36:19 CST

Hi Mark, If, theoretically, your pH was 6, you'd have 1 x 10^-6 H3O+ ions per liter of solution. So, you'd need to know what the volume of your simulation was, i.e., how many liters (a really small number), meaning you'd have much less than 10^-6 H3O+ ions in your simulation!!! For example, I have a box of water that is 24A per side, which is a volume of about 13824 A^3. One 1 liter is 1000 mL, or 1000 cm^3. Conversely, 1 A is 1 x 10^-8 cm, so 1A^3 is 1 x 10^-24 cm^3. My box of water is therefore 1.3824 x 10^-20 cm^3. This turns out to be 1.3824 x 10^-23 L. Thus, I should have 1.3824 x 10^-29 H3O+ ions in my box to have a pH of 6. I'd obviously need to simulate a very large box in order to have the right pH, as my 24 A box of waters had 512 waters. I'd need to have a box of 3.7 x 10^31 waters in order to have ONE H3O+ for me to simulate. (I think I did the chemistry math correctly...) Richard Richard L. Wood, Ph. D. Computational Chemist Cockeysville, MD 21030 ----- Original Message ---- From: Mark Abraham <> To: Sent: Thursday, February 8, 2007 7:20:06 AM Subject: Re: namd-l: pH in NAMD > Hi > > Is it possible to change the pH in system for a NAMD simulation besides > changing the state of the acids/base amino acids residues? So if you wanted a pH of 6 in an explicit solvent MD simulation, say, how many hydronium ions would you have per simulation cell, and which physical model would you use? Mark ____________________________________________________________________________________ It's here! Your new message! Get new email alerts with the free Yahoo! Toolbar.

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