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From: <diego.soler.uam.es>

Date: Fri, 04 Nov 2016 11:02:04 +0100

Hi,

I would like to perform simulation with arbitrary bias potentials of

my choice. Let's say I have a particular reaction coordinate, Y, and

that I have a potential energy function V(Y) which I want to use as

bias potential.

In practice, this bias potential would be described in a file

"bias_pot.dat" whose format would be as follows: N+1 columns, with N

the dimensionality of the reaction coordinate Y; N first columns

specifying values of the reaction coordinate along a certain grid with

which I discretize the possible values of Y; and the (N+1)th column to

specify the values of V(Y) in each row.

Next, I would like to perform a MD simulation with the bias potential

specified in my file "bias_pot.dat". The idea would be that, at each

step of the MD simulation, the program would check the value of the

reaction coordinate, Y, and compute V by interpolation over the rows

of the file "bias_pot.dat"

Is this possible in AMBER? I don't know if it is, but it would

certainly be great, because it would add a great deal of flexibility

for Umbrella simulations.

Thanks,

Diego Soler Polo, PhD student

Universidad AutÃ³noma de Madrid

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Fri Nov 04 2016 - 03:30:02 PDT

Date: Fri, 04 Nov 2016 11:02:04 +0100

Hi,

I would like to perform simulation with arbitrary bias potentials of

my choice. Let's say I have a particular reaction coordinate, Y, and

that I have a potential energy function V(Y) which I want to use as

bias potential.

In practice, this bias potential would be described in a file

"bias_pot.dat" whose format would be as follows: N+1 columns, with N

the dimensionality of the reaction coordinate Y; N first columns

specifying values of the reaction coordinate along a certain grid with

which I discretize the possible values of Y; and the (N+1)th column to

specify the values of V(Y) in each row.

Next, I would like to perform a MD simulation with the bias potential

specified in my file "bias_pot.dat". The idea would be that, at each

step of the MD simulation, the program would check the value of the

reaction coordinate, Y, and compute V by interpolation over the rows

of the file "bias_pot.dat"

Is this possible in AMBER? I don't know if it is, but it would

certainly be great, because it would add a great deal of flexibility

for Umbrella simulations.

Thanks,

Diego Soler Polo, PhD student

Universidad AutÃ³noma de Madrid

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Fri Nov 04 2016 - 03:30:02 PDT

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