Remove the ‘center’ from after ‘unwrap’. This is artificially shifting the
entire system.
-Dan
On Sun, Sep 16, 2018 at 1:43 AM jinfeng liu <jinfengliu1119.gmail.com>
wrote:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Sep 17 2018 - 04:30:01 PDT
