From: Olya Kravchenko (ovkrav_at_gmail.com)
Date: Tue Jan 24 2017 - 16:11:17 CST
Got it, thank you very much!
On Tue, Jan 24, 2017 at 5:09 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:
>
>
> 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
>
>
>
This archive was generated by hypermail 2.1.6 : Sun Dec 31 2017 - 23:21:01 CST