Date: Mon, 17 Sep 2018 09:21:31 +0800
Dear Matias,
Thanks for your reply. I have sourced the SPC/FW parameters in leap, and
I checked that the SPC/FW simulated water diffusion coefficient should be
0.232 A^2/ps, which is very close to the experimental value. However, my
calculated value is slightly larger (0.26 A^2/ps), and the diffusion
coefficient (not MSD) vs time shows a slightly increasion at the late stage
of the trajectory, which is shown in the attachment.
1) I want to make sure whether there is something wrong in my cpptraj
input for unwraping the trajectory ?
2) I find that, in the .out file of the MD simulation, there are many
output like the following:
wrapping first mol.: -0.00000 -15.93530 0.00000
wrapping first mol.: -0.00000 -15.93530 0.00000
Does this destroy the continuity of the trajectory ?
Thanks again !
Best,
Jinfeng
Matias Machado <mmachado.pasteur.edu.uy> 於 2018年9月16日 週日 下午10:05寫道：
> 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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(image/jpeg attachment: diffusion.jpg)
