RE: Umbrella Sampling in PLUMED + NAMD

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Mon Apr 22 2019 - 11:50:56 CDT

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 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

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