From: Chris Chipot (chipot_at_ks.uiuc.edu)
Date: Sat Apr 17 2010 - 19:34:24 CDT
Hello Whomever you are,
as Axel said it in the past, it would be a good idea, and also
the courteous thing to do, to introduce yourself, or at least sign
your e-mails.
Looking at your output, I can only surmise that the exclusion list
has not been properly generated. You should definitely check your
"cleaned" PSF file.
I have rewritten this tutorial, taking advantage of the new
functionalities of NAMD, specifically the possibility to scale
electrostatic and van-der-Waals interactions separately. Under
these premises, there is no longer any need for a dual topology.
One can then charge reversibly the spherical particle without
altering the van-der-Waals component of the potential energy.
The revised tutorial should be on line by now. Note that it reflects
the new lexicon used in 2.7b2 for FEP calculations.
Chris Chipot
张鋆 wrote:
> Hi everyone!
>
> I am performing the "Charging a spherical ion" exercise in the "A Tutorial on Alchemical Free Energy Perturbation Calculations in NAMD ", I have performed the exercise step by step with the tutorial, but my md died with:
>
> TCL: Running for 25000 steps
> FEP: RESETTING FOR NEW FEP WINDOW LAMBDA SET TO 0 LAMBDA2 0.0625
> FEP: WINDOW TO HAVE 5000 STEPS OF EQUILIBRATION PRIOR TO FEP DATA COLLECTION.
> FEP: USING CONSTANT TEMPERATURE OF 298 K FOR FEP CALCULATION
> PRESSURE: 0 nan nan nan nan nan nan nan nan nan
> GPRESSURE: 0 nan nan nan nan nan nan nan nan nan
> ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP POTENTIAL TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG
> ENERGY: 0 30.6528 74.5554 76.2156 0.0000 -25218.8767 9999999999.9999 0.0000 0.0000 nan nan nan 9999999999.9999 nan nan nan nan 27000.0000 nan nan
> OPENING FEP ENERGY OUTPUT FILE
> OPENING EXTENDED SYSTEM TRAJECTORY FILE
> [2] Stack Traceback:
> [0] /lib/libc.so.6 [0x7f0fa172bf60]
> [1] _ZN12PmeRealSpace12fill_chargesEPPdPcS2_P11PmeParticle+0x901 [0x8f6731]
> [2] _ZN10ComputePme6doWorkEv+0x103f [0x715f0f]
> [3] _ZN11WorkDistrib18messageEnqueueWorkEP7Compute+0xb2 [0x950852]
> [4] _ZN7Compute10patchReadyEiii+0x87 [0x4f3867]
> [5] _ZN5Patch14positionsReadyEi+0x410 [0x8dfef0]
> [6] _ZN9HomePatch14positionsReadyEi+0x111a [0x86517a]
> [7] _ZN9Sequencer17runComputeObjectsEii+0xbe [0x9288de]
> [8] _ZN9Sequencer9integrateEv+0xc7b [0x92372b]
> [9] _ZN9Sequencer9threadRunEPS_+0x2ef [0x92f3ff]
> [10] CthStartThread+0x20 [0x9cff60]
> [11] /lib/libc.so.6 [0x7f0fa173d7c0]
>
> I guess this is due to the infinite energy ( SOD NA0 overlapping), my conf file is :
>
>
> #############################################################
> ## JOB DESCRIPTION ##
> #############################################################
> # FEP
>
> #############################################################
> ## ADJUSTABLE PARAMETERS ##
> #############################################################
> structure ./char.psf
> coordinates ./char.pdb
> set temperature 298
> set outputname char
>
> #############################################################
> ## SIMULATION PARAMETERS ##
> #############################################################
> # Input
> paraTypeCharmm on
> parameters ./par_all22_prot.inp
> temperature $temperature
>
> # Force-Field Parameters
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 12.
> switching on
> switchdist 10.
> pairlistdist 13.5
>
> # Integrator Parameters
> timestep 2.0 ;# 2fs/step
> rigidBonds all ;# needed for 2fs steps
> nonbondedFreq 1
> fullElectFrequency 2
> stepspercycle 10
>
> # Constant Temperature Control
> langevin on ;# do langevin dynamics
> langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
> langevinTemp $temperature
> langevinHydrogen off ;# don't couple langevin bath to hydrogens
>
> # Periodic Boundary Conditions
> cellBasisVector1 30. 0. 0.
> cellBasisVector2 0. 30. 0.
> cellBasisVector3 0. 0. 30.
> cellOrigin 25.7867336273 -20.6125450134 -12.3257799149
> wrapAll on
>
> # PME (for full-system periodic electrostatics)
> PME yes
> PMEGridSizeX 32
> PMEGridSizeY 32
> PMEGridSizeZ 32
>
> # Constant Pressure Control (variable volume)
> useGroupPressure yes ;# needed for rigidBonds
> useFlexibleCell no
> useConstantArea no
> langevinPiston on
> langevinPistonTarget 1.01325 ;# in bar -> 1 atm
> langevinPistonPeriod 100.
> langevinPistonDecay 50.
> langevinPistonTemp $temperature
>
> # Output
> outputName $outputname
> restartfreq 5000 ;# 500steps = every 1ps
> dcdfreq 2500
> xstFreq 2500
> outputEnergies 1000
> outputPressure 1000
> ##########################################################
> fixedAtoms on
> fixedAtomsFile char.fep
> fixedAtomsCol B
> #############################################################
> ## FEP PARAMETERS ##
> #############################################################
> source ./fep.tcl
> alch on
> alchtype fep
> alchFile char.fep
> alchCol B
> alchOutFile alchemy.alchOutFile
> alchOutFreq 10
> alchEquilSteps 1000
> set nSteps 11000
> set dLambda 0.1
> runFEP 0.0 1.0 $dLambda $nSteps
>
>
> the head of my char.fep is :
>
> REMARK original generated coordinate pdb file
> ATOM 1 SOD SOD 1 0.000 0.000 0.000 1.00 1.00 NA0
> ATOM 2 NA0 NA0 2 0.000 0.000 0.000 1.00 -1.00 NA0
> ATOM 3 OH2 TIP3 3 -17.244 23.344 -26.144 1.00 0.00 WT1 O
> ATOM 4 H1 TIP3 3 -17.473 23.366 -25.167 1.00 0.00 WT1 H
> ATOM 5 H2 TIP3 3 -17.961 23.747 -26.546 1.00 0.00 WT1 H
>
> the psf was generated by alchemify. NAMD is 2.7b2
>
> Can anyone give some ideas? Have I done something stupid? Thank you in advance. I can provide anything detail.
_______________________________________________________________________
Chris Chipot, Ph.D.
on leave from Nancy Université, CNRS
Theoretical and Computational Biophysics Group
Beckman Institute
University of Illinois at Urbana-Champaign
405 North Mathews Phone: (217) 244-5711
Urbana, Illinois 61801 Fax: (217) 244-6078
E-mail: chipot_at_ks.uiuc.edu
Christophe.Chipot_at_edam.uhp-nancy.fr
Web: http://www.ks.uiuc.edu/~chipot
http://www.edam.uhp-nancy.fr
I disapprove of what you say, but I will defend to the death your right
to say it
Evelyn Beatrice Hall
_______________________________________________________________________
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