RE: Umbrella Sampling in PLUMED + NAMD

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Tue Apr 23 2019 - 09:53:12 CDT

Ok. Well in that case its pretty straightforward. Umbrella sampling depends on running a series of simulations with harmonic biases. With NAMD+PLUMED, the least-cost path to doing this is to run N independent simulations (N being the number of windows) with a slightly different plumed script for each run, which varies in the center of the harmonic bias.

-Josh

On 2019-04-23 02:34:48-06:00 Mikhail Suyetin wrote:

Dear Joshua,
Thank you for your response.
I successfully created a PLUMED script for calculating protein interaction with surface using metadynamics, and I did some simulations.
Now, I am kind of stacked with writing script for umbrella sampling implementation in PLUMED for peptide interaction with surface.
Therefore, I posted my question, trying to gather some more information for umbrella sampling.
Kind Regards,
Mikhail

On Mon, 22 Apr 2019 at 18:54, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov<mailto:Joshua.Vermaas_at_nrel.gov>> wrote:
Hi Mikhail,
What exactly are you trying to do? There are about a bazillion different things PLUMED can do, and the scripts to implement individual collective variables can look wildly different depending on what you want to do. At a basic level, the plumed scripts I write look something like this:

UNITS LENGTH=A ENERGY=kcal/mol
GROUP ATOMS=1,2,...snip out a bunch more indices...,N LABEL=thingx
GROUP ATOMS=114,115,...snip out a bunch more indices...,M LABEL=thingy
COORDINATION GROUPA=thingx GROUPB=thingy LABEL=coord
PRINT ARG=coord FILE=coord.dat

Depending on what you want to do, this basic template of select atoms, then calculate things on them is going to be basically the same no matter what, but depends on what your sampling coordinate is going to be.

-Josh

On 2019-04-22 00:39:17-06:00 owner-namd-l_at_ks.uiuc.edu<mailto:owner-namd-l_at_ks.uiuc.edu> wrote:

Dear All,
I would like to use Umbrella Sampling in PLUMED and NAMD for studying peptide interactions with surface. The problem is, I cannot find an example of usage Umbrella Sampling in Plumed for studying peptides (or amino acids) interactions with a surface. It would be great if somebody could share with me an example of PLUMED script. I do believe there are some simulation already performed/available in NAMD with involving umbrella sampling in PLUMED.
Thank you.
Kind Regards,
Mikhail

This archive was generated by hypermail 2.1.6 : Sun Dec 08 2019 - 23:20:39 CST