From: Olya Kravchenko (ovkrav_at_gmail.com)
Date: Wed Jan 25 2017 - 09:19:10 CST
Thank you very much, this is very helpful!
On Tue, Jan 24, 2017 at 5:26 PM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
wrote:
> 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
>
>
>
>
>
> --
> 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
>
>
>
>
>
>
> --
> 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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