Re: [AMBER] Interesting findings regarding water density, ntf values, and total potential energy

From: Matias Machado <>
Date: Tue, 23 Nov 2021 19:06:10 -0300 (UYT)

According to AMBER 2020 reference manual:

"For water models, a special "three-point" algorithm is used.[420] Consequently,
to employ TIP3P set NTF = NTC = 2." (page 349)

Hope this helps...



----- Mensaje original -----
De: "Liao" <>
Para: "AMBER Mailing List" <>
Enviados: Martes, 23 de Noviembre 2021 5:23:35
Asunto: [AMBER] Interesting findings regarding water density, ntf values, and total potential energy

Dear Amber community,
Today I was investigating some water behavior with a box of pure TIP3P water. I was doing so because I noticed in my research projects the water density was around 0.96 at 300K. I thought it should be around 1.
Anyway, I found out that the water density is affected by ntf values. The following are results from 3 trials each of ntf=1, ntf=2, ntf=8. I need to use ntf=8 as part of my binding studies.
ntf=8 0.9630 0.9614 0.9643
ntf=2 0.9854 0.9852 0.9837
ntf=1 1.0253 1.0257 1.0239
The potential energy values are also affected:
ntf=8 -59576.5082 -59610.5461 -59626.2363
ntf=2 -59916.4938 -59959.9350 -59926.4898
ntf=1 -60732.8611 -60657.8262 -60669.2797

Since in all cases the intramolecular and 1-4 interaction energies are all 0, and that TIP3P water is rigid. In theory I believe all values of ntf should give the same result? But somehow it didn't. And, when I turned off SHAKE and used 0.002 as the timestep, the simulation still crashed-but there are no solute atoms at all. It probably doesn't matter in many scenarios, but I'm not sure for every single scenario. I'm just very curious of the reason this is happening. Were there forces and interactions of a pure box of TIP3P water I missed out, or does has something to do with how the simulation code is written?

Thank you!
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