[gmx-users] Umbrella sampling with spherical coordinate

Yuno Lee yunolee1 at gmail.com
Tue Nov 24 13:25:16 CET 2015

Hi all,

To find out leaving pathway of metal ion from metal binding site of RNA,
I want to perform an umbrella sampling with spherical coordinate (r) as
reaction coordinate.
Specifically, In pulling simulation, I want to pull the metal ion from the
origin site to outside of RNA with only restraining r = ((x_i - X_i)^2 +
(y_i - Y_i)^2 + (z_i - Z_i)^2)^1/2 (not Cartesian axes) like metal ion
staying on the small shell to larger spherical shell.

Is there any way to do this in GROMACS?
If not, do you have any other methods recommended to solve this?

Thank you in advance

Thanks & Regards,

Yuno Lee, Ph.D.

School of Computational Sciences, Korea Institute for Advanced Study (KIAS)
85 Hoegiro, Dongdaemun-gu, Seoul 130-722, Korea
Tel: 82-2-958-3889, Mobile : 82-10-9396-2729
Fax: 82-2-958-3820
E-mail : yunolee1 at kias.re.kr; *yunolee1 at gmail.com <yunolee1 at gmail.com>*

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