From: priyodorshi satpati (psatpati_at_gmail.com)
Date: Fri Nov 27 2009 - 03:26:01 CST
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--0015174c1d0a538e55047956e135--
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:53:33 CST