Re: how do I restart umbrella sampling calculations?

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue Jan 24 2017 - 15:20:38 CST

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 <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 <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
>> Philadelphia, PA 19122-1801
>> Phone: +1-215-204-4213 <(215)%20204-4213>
>>
>> Scholar: http://goo.gl/Q3TBQU
>> Personal: http://giacomofiorin.github.io/
>> Lab page: 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
Scholar: http://goo.gl/Q3TBQU
Personal: http://giacomofiorin.github.io/
Lab page: 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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