# AMBER: Umbrella sampling

From: Jena M <jeninhas.hotmail.com>
Date: Fri, 26 Oct 2007 14:48:26 +0100

Dear amber users,

I have some questions related with the umbrella sampling method. I want to approach an atom of a ligand (C5) to an atom of a residue (OD1) from a distance of ~6 A to 4 A using a step of 0.2 A to study a reaction mechanism. So, after each equilibration I look for the distance C5-OD1 and subtract 0.2 to obtain the value of r2/r3 to be used in the restraint file for the next production MD. However, at the end of each production MD I always obtain a final structure with a distance C5-OD1 higher than that specified in the r2/r3. For instance, for the third step:
-Third MD (20 ps) to equilibrate the system
final distance (C5-OD1)= 5.809
-Third MD (50 ps) to approach the atoms
r2/r3=5.609
final distance (C5-OD1)= 5.625

Then I started the fourth equilibration using the rst file of the third production and I obtained a final distance C5-OD1 of 5.518. In this equilibration I had to use a force of 50 to restraint the heavy atoms otherwise the atoms were separated by a distance higher than 5.625. For the fourth production:
r2/r3= 5.318
final distance (C5-OD1)= 5.462

Is it correct the way the way I am doing the umbrella sampling? Is it expected that the value of the distance obtained at the end of each production be different of that specified in r2/r3 ?
My input is:
&rst iat=461,569, r1=0.0, r2=5.609, r3=5.609, r4=100.0, rk2=100., rk3=100.,
iresid=1,
ATNAM(1)='OD1',
ATNAM(2)='C5',
/
Should I increase the force? I think it is already high…