Re: how do I restart umbrella sampling calculations?

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue Jan 24 2017 - 16:09:13 CST

On Tue, Jan 24, 2017 at 4:44 PM, Olya Kravchenko <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>
> 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 <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 <(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 <(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

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