Re: how do I restart umbrella sampling calculations?

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Tue Jan 24 2017 - 16:26:39 CST

For completeness, its probably also helpful to look at what the postprocessing algorithms expect. For Alan Grossfield's implementation of WHAM (http://membrane.urmc.rochester.edu/sites/default/files/wham/doc.html), you wouldn't need to concatenate by default, and could instead add both the original.colvars.traj and the original_restart.colvars.traj to the "metadata" file, with the caveat that you need to specify an autocorrelation time to get correct error estimates. If you decide to let g_wham (http://manual.gromacs.org/documentation/5.1/onlinehelp/gmx-wham.html) compute the autocorrelation time for you, you will need to concatenate the .traj files otherwise it can't compute a correct autocorrelation time.

-Josh

On 01/24/2017 03:15 PM, Olya Kravchenko wrote:
Got it, thank you very much!

On Tue, Jan 24, 2017 at 5:09 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com<mailto:giacomo.fiorin_at_gmail.com>> wrote:

On Tue, Jan 24, 2017 at 4:44 PM, Olya Kravchenko <ovkrav_at_gmail.com<mailto:ovkrav_at_gmail.com>> wrote:
Hmm, I don't quite understand then. In Joshua's reply he says: "you will also get a new colvars.traj file that you'd concatenate to the old one and get the data you need for post-processing the particular window".

That's true for the .traj file. I only wanted to make sure that you are not concatenating state files, since you mentioned only "output" files.

Colvars.traj <-> DCD file.
Colvars.state <> Coor, Vel, Xsc files.

I interpreted it this way: after I resubmit the job for a particular window 0, I will have win0.colvars.traj and win0_restart.colvars.traj, then I could add the output of win0_restart.colvars.traj into win0.colvars.traj and use this in wham (to obtain PMF). Am I missing something?

Olga

On Tue, Jan 24, 2017 at 4:20 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com<mailto:giacomo.fiorin_at_gmail.com>> wrote:
The state file is supposed to be self-contained, and you shouldn't concatenate multiple together. You don't concatenate .coor files, either.

Notice also that as Josh mentioned, fixed harmonic potentials don't carry a history, and the only use in your case for colvarsInput is to carry over the timestep number.

Giacomo

On Tue, Jan 24, 2017 at 4:14 PM, Olya Kravchenko <<mailto:ovkrav_at_gmail.com>ovkrav_at_gmail.com<mailto:ovkrav_at_gmail.com>> wrote:
Thank you both!! This is conventional umbrella sampling (not REMD).

Here is a portion of my *.conf file, does this look correct?

structure ../smd_start.psf
coordinates win0.pdb

# Continuing a job from the restart files

if {1} {
set inputname win0
binCoordinates $inputname.restart.coor
binVelocities $inputname.restart.vel
extendedSystem $inputname.restart.xsc
colvarsiInput $inputname.restart.colvars.state
}

set temperature 310
set outputname win0_restart

firsttimestep 2205900

I.e. there are will be new files for the output and in the end I will have to add the new colvar output to the old one when the job is finished. Correct?

Olga

On Tue, Jan 24, 2017 at 3:50 PM, Giacomo Fiorin <<mailto:giacomo.fiorin_at_gmail.com>giacomo.fiorin_at_gmail.com<mailto:giacomo.fiorin_at_gmail.com>> wrote:
Hello Olga, all of the above mentioned methods are provided by the same code (Colvars). The restart file is the same in all cases: you should only keep the colvars.state file (i.e. the argument of the next colvarsInput) synchronized with the .coor, .vel and .xsc files of NAMD.

Giacomo

On Tue, Jan 24, 2017 at 3:39 PM, Olya Kravchenko <<mailto:ovkrav_at_gmail.com>ovkrav_at_gmail.com<mailto:ovkrav_at_gmail.com>> wrote:
Hi all,

I have to restart my umbrella sampling calculations that quit due to hardware failure. What are the restart keywords for the colvars to use in the configuration file? I found one for ABF (colvarsInput <inputname>.restart.colvars.st<http://restart.colvars.st>at), but I don't see anything in tutorials or on this list about restarting US. Will the same option work for umbrella sampling? Is there anything else to change in the restart files so that colvar gets updated?

Does anyone have a sample restart file for US? (or ABF! I would appreciate that too for future reference.)

Thanks in advance!

Olga

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Giacomo Fiorin
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Institute for Computational Molecular Science (ICMS)
College of Science and Technology, Temple University
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"As computer programmers we have a responsibility to make sure that we run the computers instead of the computers running us."  - Steve Oualline
--
Giacomo Fiorin
Associate Professor of Research
Institute for Computational Molecular Science (ICMS)
College of Science and Technology, Temple University
1925 North 12th Street (035-07), Room 704D
Philadelphia, PA 19122-1801
Phone: +1-215-204-4213<tel:%28215%29%20204-4213>
Scholar: <http://goo.gl/Q3TBQU> http://goo.gl/Q3TBQU
Personal: <http://giacomofiorin.github.io/> http://giacomofiorin.github.io/
Lab page: <https://icms.cst.temple.edu/members.html> https://icms.cst.temple.edu/members.html
"As computer programmers we have a responsibility to make sure that we run the computers instead of the computers running us."  - Steve Oualline
--
Giacomo Fiorin
Associate Professor of Research
Institute for Computational Molecular Science (ICMS)
College of Science and Technology, Temple University
1925 North 12th Street (035-07), Room 704D
Philadelphia, PA 19122-1801
Phone: +1-215-204-4213<tel:%28215%29%20204-4213>
Scholar: <http://goo.gl/Q3TBQU> http://goo.gl/Q3TBQU
Personal: <http://giacomofiorin.github.io/> http://giacomofiorin.github.io/
Lab page: <https://icms.cst.temple.edu/members.html> https://icms.cst.temple.edu/members.html
"As computer programmers we have a responsibility to make sure that we run the computers instead of the computers running us."  - Steve Oualline

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