[CP2K:1051] Re: Once again about periodic colvar

[Teodoro Laino]

Ilya,

sorry for the delay but this was a busy day...
After a careful inspection I'm happy to say that there are no bugs  
for the periodic colvar.
I will attach the following picture to show what you can get out of  
metadynamics after you've fully understood
the nature of your system and how the metadynamics works.
I won't give you the solution of the problem but keep in mind the  
following questions, they may help you in finding
the right solution:

(1) How big is my system and what kind of fluctuations I should expect?
(2) How large are the fluctuation of my COLVAR at the working  
temperature?
(3) Am I keeping under control the temperature of my system or is it  
just going everywhere?
(4) Do I have an idea of the barrier that I want to represent?

In the attached picture the potential energy surface (obtained  
keeping fixed the dihedral and optimizing all the
other DOF, calculation done with MOPAC2007) of the rotational barrier  
of butane and the free energy (calculation
performed with CP2K soon CP3K ;-) ) obtained with metadynamics at 100 K.

Have Fun!
Teo

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On 16 May 2008, at 09:52, ilya wrote:

>
> Here is the input with one of many parameter values for metadynamics
> I've tried.
> (Sorry, it's not as attachment. Google FAQs says that to attach a file
> you have to send e-mail to group's address. How to make it to appear
> here?)
>
>
> &GLOBAL
>   PROJECT_NAME BUTANE
>   RUN_TYPE MD
>   PRINT_LEVEL LOW
> &END GLOBAL
> &FORCE_EVAL
>   METHOD QS
>   &DFT
>     &QS
>       METHOD PM6
>       &SE
>       &END SE
>     &END QS
>     &SCF
>       SCF_GUESS ATOMIC
>       &PRINT
>         &RESTART OFF
>         &END
>       &END
>     &END SCF
>   &END DFT
>   &SUBSYS
>     &CELL
>       ABC 20.0 20.0 20.0
>       UNIT ANGSTROM
>       PERIODIC NONE
>     &END CELL
>     &COORD
> C   -8.1866427536766317E-01   -9.8145723495914294E-01
> -1.9509803466736661E-01
> C   -5.8924914610730947E-02    2.3406403231329728E-01
> 3.6337090710811820E-01
> C   -5.0164001189101215E-01    1.5910014193467945E+00
> -2.8293078840561836E-01
> C    4.9476299744407765E-01    2.6396358566826095E+00
> 1.2828925703243602E-01
> H   -6.2244524884126584E-01   -1.9072903584365897E+00
> 2.9329726493504088E-01
> H   -1.9547736115885346E+00   -9.0139495866835251E-01
> -5.9918150655443085E-02
> H   -6.1937432334401399E-01   -9.4837844365638890E-01
> -1.2385015008153359E+00
> H   -1.7075737360002088E-01    2.9731209011422616E-01
> 1.4541336191929111E+00
> H    9.7457573875863202E-01    8.5636471630587491E-02
> 1.2656205437423565E-01
> H   -5.0131648636893655E-01    1.6371906515892005E+00
> -1.4111541759474644E+00
> H   -1.5467719258289738E+00    1.7278640292584959E+00
> -6.4073628967786178E-02
> H    1.1121698319311175E+00    2.9201730368212155E+00
> -7.3684782242081992E-01
> H    1.8360961237017401E-02    3.5103940802614222E+00
> 4.9963333677363780E-01
> H    1.1955573776036026E+00    2.3395752869018538E+00
> 9.7481281683867282E-01
>     &END COORD
>     &VELOCITY
>     -9.1145154536295919E-05   -1.7288597297829858E-04
> 5.2498054992999613E-06
>      1.6071166440413050E-06   -2.6329278272704861E-05
> 4.6405385077460174E-05
>      2.8139550923834489E-04   -9.0163993819247976E-05
> 7.6949734768254173E-05
>     -3.5140868375595375E-05    1.1591245497504604E-04
> 9.3441546132711488E-07
>     -6.5449810886309572E-04    1.2949138600657238E-04
> -9.6905572370049138E-05
>     -5.5880056343657911E-04   -7.6023320034826296E-04
> 4.5331781519918144E-04
>      7.8891547853511906E-05    3.9925263875885246E-04
> -6.3042129441400981E-04
>      3.8964847985305349E-05   -3.5437713203463964E-04
> -1.1152482653525371E-03
>      1.4947763296898738E-04   -3.9868429077368579E-04
> 1.7981274276414143E-04
>      1.6902752937549336E-05    3.8798443523281535E-04
> -1.6885685806997559E-04
>     -1.0427106459532161E-03    1.3857405676144231E-04
> 2.8224441261646684E-04
>      6.0553785519956553E-04    4.7716373383966196E-04
> -5.7712612804223390E-04
>     -7.8775588105202301E-04    1.2823159298612447E-03
> 7.1462951097974915E-05
>      2.8652761625418420E-04    7.6557360110276226E-04
> 5.8106345621775769E-05
>     &END VELOCITY
>     &COLVAR
>       &TORSION
>         ATOMS 1 2 3 4
>       &END TORSION
>     &END
>   &END SUBSYS
> &END FORCE_EVAL
> &MOTION
>   &MD
>     ENSEMBLE NVT
>     STEPS 100000
>     TIMESTEP 0.5
>     TEMPERATURE 300.0
>     &THERMOSTAT
>       TYPE CSVR
>       &CSVR
>         TIMECON 200.0
>       &END CSVR
>     &END THERMOSTAT
>   &END MD
>   &FREE_ENERGY
>     METHOD METADYN
>     &METADYN
>       DO_HILLS TRUE
>       LAGRANGE TRUE
>       WW 0.001
>       TEMPERATURE 0.0
>       NT_HILLS 100
>       &METAVAR
>         MASS 50.0
>         LAMBDA 0.5
>         COLVAR 1
>         SCALE [rad] 0.5
>       &END METAVAR
>       &PRINT
>         &COLVAR
>           FILENAME =colvar
>         &END COLVAR
>       &END PRINT
>     &END METADYN
>   &END FREE_ENERGY
>   &PRINT
>     &TRAJECTORY
>       &EACH
>         MD 20
>       &END
>     &END
>   &END
> &END MOTION
>
>
> On May 16, 10:34 am, Teodoro Laino <teodor... at gmail.com> wrote:
>> Would you mind show us your full input.
>>
>> Teo
>>
>> On 16 May 2008, at 08:33, ilya wrote:
>>
>>
>>
>>> Well, I mean that rotation begins independently of gaussian params
>>> when the filled depth of the potential well is no more than 1  
>>> kcal/mol
>>> (but should be about 7 for butane rotation).
>>> I thought about what is called "hill surfing" but after more
>>> experiments I don't think that it is the source of such behavior  
>>> (I've
>>> tried small hills and large stride).
>>
>>> Ilya.
>>
>>> On May 15, 8:47 pm, Axel <akoh... at gmail.com> wrote:
>>>> On May 15, 10:13 am, ilya <ily... at gmail.com> wrote:
>>
>>>>> Hello!
>>
>>>>> Well, I performed another test reaction which is Cl- + CH3Cl
>>>>> (from the
>>>>> article).
>>>>> I have successfully build a 3d fes which is very similar to  
>>>>> that one
>>>>> in the article and I think I've got the idea of choosing  
>>>>> parameters
>>>>> for metadynamics.
>>>>>    BUT
>>>>> For the case of butane I can't obtain any adequate free energy
>>>>> profile.
>>>>> I observed that after some point  the molecule starts spinning
>>>>> strangely around C2-C3 bond and I think the are still some bugs
>>>>> in the
>>
>>>> ilya,
>>
>>>> please describe "strangely".
>>>> once you have filled all minima
>>>> with gaussians you are supposed to
>>>> have the molecule rotating freely
>>>> around the C2-C3 bond (no more barrier
>>>> left!).
>>
>>>> cheers,
>>>>     axel.
>>
>>>>> case of periodic colvar in code.
>>>>> Maybe someone else with more experience in metadynamics would
>>>>> also try
>>>>> to do this? Maybe I am doing something wrong?
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