From: Olya Kravchenko (ovkrav_at_gmail.com)
Date: Tue Jan 24 2017 - 15:44:32 CST
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".
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
>
>
>
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