Re: [AMBER] unwrap problem in the liquid water dynamics trajectory analysis

From: Matias Machado <>
Date: Sun, 16 Sep 2018 10:52:54 -0300 (UYT)

Dear Jinfeng,

Which water model are you using? Depending on the model some properties are better described than others... In particular TIP3P is known to have a self diffusion coefficient ~twice the experimental value, check this web as a reference:


I don't get what do you mean by "shows a gradual increasion versus the time"... does the MSD vs time curve show two (or more) slopes? how long was your simulation?



----- Mensaje original -----
De: "jinfeng liu" <>
Para: "AMBER Mailing List" <>
Enviados: Domingo, 16 de Septiembre 2018 2:43:13
Asunto: [AMBER] unwrap problem in the liquid water dynamics trajectory analysis

Dear Amber users,

       Recently I performed liquid water dynamics under the periodic
boundary condition in the NVT ensemble using the "iwrap=1". The unit cell
of water box contains 128 SPC/FW water molecules. I need to remove the
effect of "iwrap=1" in the trajectory before the diffusion coefficient is
calculated. I want to make it using the cpptraj, and my cpptraj input is
the following

trajin md1.crd
trajin md2.crd
trajin md3.crd
trajin md4.crd
trajin md5.crd
trajin md6.crd
unwrap :1-128
center :1-128 mass origin
trajout md_unwrap.crd

However, the water diffusion constant calculated on the md_unwrap.crd
trajectory is larger than the experimental value, and shows a gradual
increasion versus the time. So I want to know if there is anything wrong in
my unwrapping input, and what it should be ?

Thanks a lot !

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