Just in case, check weather you have correctly source the SPC/FW parameters in leap:
source leaprc.water.spce
loadAmberParams frcmod.spcfw
Best,
Matias
----- Mensaje original -----
De: "Matias Machado" <mmachado.pasteur.edu.uy>
Para: "AMBER Mailing List" <amber.ambermd.org>
Enviados: Domingo, 16 de Septiembre 2018 10:52:54
Asunto: Re: [AMBER] unwrap problem in the liquid water dynamics trajectory analysis
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:
[
http://www1.lsbu.ac.uk/water/water_models.html]
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?
Best,
Matias
----- Mensaje original -----
De: "jinfeng liu" <jinfengliu1119.gmail.com>
Para: "AMBER Mailing List" <amber.ambermd.org>
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 !
Best,
Jinfeng
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Received on Sun Sep 16 2018 - 07:30:01 PDT
