[t-yama]

Hi all,

I’d like to perform gREST simulations with flat bottom restraints. Is there any way to define the restraint?
I mean the restraint something like this:
0 (when r less than r0)

k(r – r0)^2 (when r more than r0)

[oshima]

Hi t-yama,

The flat-bottom restraint is available as “FB” in the [RESTRAINTS] section in the GENESIS control file.
In GENESIS, FB is defined as:
U(R) = K (R-R_0)^2 if R > R_0,
U(R) = 0 otherwise.

I show an example of input for the FB restraint:

[SELECTION]
group1 = rno:1-2
group2 = rno:3-5

[RESTRAINTS]
nfunctions = 1
function1 = FB
reference1 = 10.0
constant1 = 1.0
select_index1 = 1 2

In the [SELECTION] section, please specify two groups which you want to apply the flat-bottom restraint. For example, two groups of residues are selected above. In the [RESTRAINTS] section, please specify “FB” for function1 to use the flat-bottom potential.”reference1″ and “constant1” correspond to R_0 and K, respectively. Two groups selected in the [SELECTION] section should be specified in “select_index1”. In this example, a FB restraint between two groups with R_0 = 10.0 and K = 1.0 is added to a system.

You can apply the flat-bottom restraint to the centers of mass by replacing “FB” with “FBMASS”. Similar to other restraint functions, “MASS” indicates that the force is applied to the center of mass of the selected group. When “MASS” is omitted, the force is applied to the geometric center of the coordinates.

Thank you,
Hiraku Oshima

[t-yama]

Hello oshima,

Thanks for your response. I have tried it and it seems to work fine with my system.
Thank you again for your kind support.

Regards,
t-yama

[monahan]

Hi,

I want to know whether the flat-bottom position restraints can be applied only for the pull code in umbrella sampling or it can be use for NPT or MD simulation of GROMACS (not umbrella sampling), If yes, please guide me how to use.

[jwjung]

Now, flat-bottom style position restraints are not available in genesis.