From: Olya Kravchenko (ovkrav_at_gmail.com)
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.
Correct?
Olga
On Tue, Jan 24, 2017 at 3:50 PM, Giacomo Fiorin <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 <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.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
> 1925 North 12th Street (035-07), Room 704D
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>
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>
>
>
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