From: priyodorshi satpati (psatpati_at_gmail.com)
Date: Thu Nov 26 2009 - 03:19:48 CST
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.
I have attached both the "test_const.log" (log file) and "test_const.namd"
(config file).
Please let me know what is going on.
Regards and thanks again
satpati
On Thu, Nov 26, 2009 at 3:16 AM, Wenyu Zhong <wenyuzhong_at_gmail.com> wrote:
> Satpatiļ¼
>
> You should add
>
> run NSTEPS
>
> with NSTEPS>=50001 in the config file as a normal simulation
>
> Wenyu
>
> 2009/11/25, priyodorshi satpati <psatpati_at_gmail.com>:
> > Dear all,
> >
> > I was trying to run a 100ps restraint-distance simulation. My input is
> given
> > below :
> >
> > ***************************
> > paraTypeCharmm on
> > parameters par_satpati_gdp_hpo4.prm
> >
> > exclude scaled1-4
> > 1-4scaling 1.0
> > switching on
> >
> > cutoff 16.
> > switchdist 15.
> >
> > pairlistdist 18.
> > stepspercycle 10
> > timestep 2.0
> > nonbondedFreq 1
> > fullElectFrequency 2
> >
> > #Harmonic restraint parameters
> > rigidBonds all
> > rigidTolerance 1.0e-8
> >
> > # periodic cell
> > cellBasisVector1 51.5 0 0
> > cellBasisVector2 0 51.1 0
> > cellBasisVector3 0 0 51.1
> > cellOrigin -0.13 0.03 0.01
> > extendedSystem $inputname.xsc
> > wrapAll on
> >
> > # full electrostatics
> > PME on
> > PMEGridSizeX 75
> > PMEGridSizeY 75
> > PMEGridSizeZ 75
> >
> > # Constant Temperature Control
> > langevin on
> > langevinDamping 5
> > langevinTemp $temperature
> > langevinHydrogen off
> >
> > # pressure control
> > useGroupPressure yes
> > useFlexibleCell no
> > useConstantArea no
> > langevinPiston on
> > langevinPistonTarget 1.01325
> > langevinPistonPeriod 200.
> > langevinPistonDecay 100.
> > langevinPistonTemp $temperature
> >
> > #output files
> > binaryoutput no
> > outputName $outputname ;# base name for output from this run
> > restartfreq 50 ;# 50 steps = every 0.1ps
> > dcdfreq 100
> > xstFreq 100
> > outputEnergies 100 ;# 100 steps = every 0.2 ps
> >
> > freeEnergy on
> > freeEnergyConfig {
> > urestraint {
> >
> > dist (LIGA,1,P1) (LIG2,2,MG) kf=20 ref=2.63
> >
> > }
> >
> > pmf {
> > task = stop
> > time = 100 ps
> > }
> >
> > }
> > ***************************************************************
> >
> > but I got the following error :
> >
> > Info: RELATIVE IMPRECISION IN VDWA TABLE ENERGY: 2.06776e-20 AT 21.9986
> > Info: FREE ENERGY PERTURBATION CONFIG
> > Info: ***********************************
> >
> > urestraint {
> >
> > dist (LIGA,1,P1) (LIG2,2,MG) kf=20 ref=2.63
> >
> > }
> >
> > pmf {
> > task = stop
> > time = 100 ps
> > }
> >
> >
> > Info: ***********************************
> > FreeEnergy: Not enough steps to complete pfm & mcti blocks
> > FreeEnergy: Num Steps Needed = 50001
> > FreeEnergy: Num Steps Requested = 0
> > FATAL ERROR: FreeEnergy: Fatal Run-Time Error
> > Stack Traceback:
> > [0] CmiAbort+0x20 [0x8ca446]
> > [1] _Z8NAMD_diePKc+0x65 [0x4bcf25]
> > [2] _ZN22GlobalMasterFreeEnergy15user_initializeEv+0x1e7 [0x702541]
> >
> > please let me know what should i do to overcome this problem.
> >
> > regards and best wishes
> >
> > satpati
> >
>
--
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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