Re: how do I restart umbrella sampling calculations?

From: Olya Kravchenko (
Date: Tue Jan 24 2017 - 15:14:55 CST

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.


On Tue, Jan 24, 2017 at 3:50 PM, Giacomo Fiorin <>

> 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 <> 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.stat), 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
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