From: priyodorshi satpati (psatpati_at_gmail.com)
Date: Wed Dec 02 2009 - 10:28:44 CST
Dear Jerome,
Thank you very much. I have followed your suggestions.
thanks again
regards
satpati
On Fri, Nov 27, 2009 at 1:42 PM, Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr>wrote:
> 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
>
--
Dr. Priyadarshi Satpati
Biocomputing and Structure research Group,
Laboratoire de Biochimie,
Ecole Polytechnique,
91128 Palaiseau, France
Phone :
(Off) : +33/(0)1 69 33 48 94
(Mob) : +33/(0)6 27 75 56 49
(Res) : +33/(0)177069139
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