Re: How to extend an ABF simulation ?

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed May 01 2019 - 09:43:54 CDT

FYI in any of the most recent versions of NAMD you can also use "cv
configfile" and "cv load" in lieu of "colvarsConfig" and "colvarsInput".
The former are Tcl commands that can be executed any time before or after a
"run" command. If you are making changes to the configuration that will
invalidate the state file, the best approach would be:
cv configfile <old configuration>
cv load <last state file with old config>
cv configfile <new config, e.g. add new variables/biases>

Giacomo

On Wed, May 1, 2019 at 3:57 AM philippe Bourly <philippe.bourly20_at_gmail.com>
wrote:

> Thank you, this is very helpful!
>
> Best,
> Philippe
>
> On Tue, Apr 30, 2019 at 5:36 PM horacio poblete <elhoraki_at_gmail.com>
> wrote:
>
>> Hi Philippe.
>>
>> This is an option, but with it you will start a “new” abf simulation from
>> a previous one, what you are showing here is a good option (e.g.) if you
>> want to modify your colvars file and extend or decrease your transition
>> coordinate.
>>
>> You can add a run number at the beginning of your namd configuration
>> file:
>>
>> set run 2
>> set outFile $name.$run
>> set last $name.[expr $run-1]
>>
>> And you can read a restart colvars file using something like this to the
>> Colvars section on your namd configuration file:
>>
>> if {1} {
>> colvars on
>> colvarsConfig ../${colvarsConf}.colvars
>> if {$run > 1} {
>> colvarsInput $last.restart.colvars.state
>> }
>> }
>>
>> Now you can just increase your run number and restart easily your abf
>> calculation.
>>
>> Best!
>>
>> -------------------------------------------------------
>> Horacio Poblete Vilches PhD.
>> Principal Investigator
>> Center for Bioinformatics and Molecular Simulations
>> Escuela de Ingeneria en Bioinformática
>> Universidad de Talca
>> Phone: +56712203041
>> hopoblete_at_utalca.cl
>> -------------------------------------------------------
>>
>>
>>
>>
>>
>> On Apr 30, 2019, at 11:19 AM, philippe Bourly <
>> philippe.bourly20_at_gmail.com> wrote:
>>
>> Hello everyone !
>> I have a question about ABF simulations. I would like to extend my ABF
>> simulation. I have extended the simulation the same way as a regular
>> simulation and I have modified the abf block on the colvar file as the
>> following:
>>
>>
>> abf{
>> colvars CycloAngle
>> FullSamples 5000
>> Historyfreq 2000
>> *inputPrefix output/cyclo*
>> }
>>
>>
>> “cyclo” is the name of my previous simulation that I want to extend. Is
>> it ok? Is it the good way to extend an ABF simulation?
>>
>>
>> Best regards,
>> Philippe
>>
>>
>>

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin

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