[gmx-users] Fwd: What could be wrong with rdf plot?

[Lum Nforbi]

---------- Forwarded message ----------
From: Lum Nforbi <lumngwegia at gmail.com>
Date: Thu, Dec 31, 2009 at 12:33 PM
Subject: What could be wrong with rdf plot?
To: gmx-users at gromacs.org


Dear all,

     I am currently analyzing a system of 2000 molecules of TIP3P water on
which I performed a NPT simulation. The plot for g(OO) looks very good but
for some reason unknown to me, on the g(OH) plot there is an intense peak
coming before the normal peaks that are characteristic of a g(OH) plot.
Could someone tell me what is going on? I have attached the graphs for gOO
and gOH for viewing.
    Also, I have still not been able to figure out how to calculate the Cp
of my system and I have been struggling with this for over a month now.
g_energy for my system gives a wrong Cv (~12). Can someone explain to me or
give me hints on how to calculate the Cp of an NPT simulation of TIP3P
water, please?

Have a wonderful New Year 2010 and Decade (2010-2019)!

Thank you,
Lum
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