Re: FreeEnergy: Not enough steps to complete pfm & mcti blocks

From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Fri Nov 27 2009 - 06:42:59 CST

Dear Satpati,
You could also achieve the same effect with the collective variables
module (NAMD 2.7b1 and later). Just define a colvar corresponding to
the distance you want to restrain, and a "harmonic" block to create
the bias.
Jerome

2009/11/27 priyodorshi satpati <psatpati_at_gmail.com>:
> Dear Wenyu,
>
>  Thank you very much for your mail.
>
>  If I add "run 50020" after the free energy block I got the same error
> message (I mentioned in my first mail).
>
>  If I add "run 50020" before the free energy block the simulation start
> running without reading the constraint [I mentioned in my 2nd mail with
> attachments]
>
>  If I add "run 50020" in the following way :
>
> freeEnergy on
> freeEnergyConfig {
> urestraint {
> dist (LIGA,1,P1) (LIG2,2,MG) kf=20 ref=2.63
>
> }
> run 50020
> pmf {
>    task = stop
>    time = 100 ps
>  }
> }
>
>
> I got the following:
>
>
> Info:   FREE ENERGY PERTURBATION CONFIG
> Info: ***********************************
>
> urestraint {
> dist (LIGA,1,P1) (LIG2,2,MG) kf=20 ref=2.63
>
> }
> run 50020
> pmf {
>    task = stop
>    time = 100 ps
>  }
>
> Info: ***********************************
> FreeEnergy:
> FreeEnergy: Problem parsing input parameters
> FreeEnergy:   Warning:     Unable to Read Entire Input File
> FreeEnergy:   Read Until:  run 50020
> pmf {
>    task = stop
>    time = 100 ps
>  }
>
>
> FreeEnergy:
> Info: Entering startup phase 8 with 41132 kB of memory in use.
> Info: Finished startup with 44748 kB of memory in use.
> ETITLE:      TS           BOND          ANGLE          DIHED
> IMPRP               ELECT            VDW       BOUNDARY
> MISC        KINETIC               TOTAL           TEMP
> TOTAL2         TOTAL3        TEMPAVG            PRESSURE
> GPRESSURE         VOLUME       PRESSAVG      GPRESSAVG
>
> ENERGY:       0         3.2624        13.2535         0.1623
> 0.0000        -168214.1298     20534.9956         0.0000         0.0000
> 14832.4298        -132830.0261       189.3700   -132785.3757
> -132785.3757       189.3700           1371.7701      1385.9192
> 359376.6830      1371.7701      1385.9192
>
> OPENING EXTENDED SYSTEM TRAJECTORY FILE
> WRITING EXTENDED SYSTEM TO OUTPUT FILE AT STEP 0
> CLOSING EXTENDED SYSTEM TRAJECTORY FILE
>
>
> !!!! Warning: tracing not available with CMK_OPTIMIZE!
> WRITING COORDINATES TO OUTPUT FILE AT STEP 0
> COORDINATE DCD FILE WAS NOT CREATED
> WRITING VELOCITIES TO OUTPUT FILE AT STEP 0
> ==========================================
> WallClock: 5.285603  CPUTime: 5.285602  Memory: 68630 kB
> End of program
>
> Please comment on this. My target is to get a normal MD trajectory with a
> harmonic constraint between two atoms.
>
> Thanks again.
>
> Regards
>
> satpati
>
>
>
>
>
> On Fri, Nov 27, 2009 at 2:27 AM, Wenyu Zhong <wenyuzhong_at_gmail.com> wrote:
>
>> Dear Satpati,
>>
>> Seems you should add "run 50020" after the free energy bolck.
>> I'm sorry I have forgot the setting detail.
>>
>> Wenyu
>>
>> 2009/11/26, priyodorshi satpati <psatpati_at_gmail.com>:
>> > Deal all,
>> >
>> > Thank you very much for the prompt reply. I have added
>> > "run 50020" just before the free energy bolck (as mentioned by Wenyu).
>> The
>> > simulation has started without error message. But looking at the log file
>> it
>> > seems to me that the restraint specified by me is not active in the run

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