From: Chris Chipot (chipot_at_ks.uiuc.edu)
Date: Sat Nov 26 2011 - 10:51:57 CST
Bruno,
when you restart an aborted FEP calculation, NAMD does not know
anything about the net free energy that was reached when your run
stopped. Upon restarting, the net free energy is reset to zero. Then,
you will just need to add up the value of the free energy reached at
the starting value of ? in your new job.
Cheers,
Chris Chipot
On 11/26/11 10:15 AM, Bruno Luís Pinto de Oliveira wrote:
> Dear NAMD users,
>
> I would like to ask for your help in how to restart a FEP simulation.
>
> I found some related post in the forum but I still have some doubts.
>
> My calculation terminated almost at the end (lambda = 0.01).
>
> At lambda = 0.01 the net change is 28.58 kcal/mol. I did the restart
> at lambda = 0.1, however I found some problems in the overall dG
> calculation.
> After the first 120k steps the calculated net change is 3.29 kcal/mol
> instead of a value close to 28.58 kcal/mol.
>
> I am guessing that the restart at some point should give the same
> energy as before it aborted. Am I right?
>
> Below I attached my config file (my outputs have the name back.xxx).
>
> Can someone help me find what I'm doing wrong, please? Thanks in advance!
>
> Regards
>
> Bruno
>
> ###################################################
> # ALCHEMICAL TRANSFORMATION
> ###################################################
>
> # INPUT
>
> parameters MOL_par_all27_ISM.prm
>
> paraTypeCharmm on
>
> exclude scaled1-4
> 1-4scaling 1.0
>
> # TOPOLOGY
>
> structure solvated.psf
>
> # COORDINATES
>
> coordinates solvated.pdb (here I am not sure if I should
> use back.coor.old or solvated.pdb???!!!!!!!)
> bincoordinates back.coor
>
>
> # VELOCITIES
>
> #velocities alchemy_0.vel
> binvelocities back.vel
>
> # CELL
>
> extendedSystem back.xsc
>
> # OUTPUT FREQUENCIES
>
> outputenergies 1000
> outputtiming 1000
> outputpressure 1000
> restartfreq 1000
> XSTFreq 1000
> dcdfreq 1000
>
> # OUTPUT AND RESTART
>
> outputname back_rest_0
> restartname back_rest
>
> binaryoutput no
> binaryrestart yes
>
> # PME
>
> PME yes
> PMETolerance 10e-6
> PMEInterpOrder 4
>
> PMEGridSizeX 71
> PMEGridSizeY 55
> PMEGridSizeZ 71
> cellOrigin -53.7 131.5 -16.6
>
> # WRAP WATER FOR OUTPUT
>
> wrapAll on
>
> # CONSTANT-T
>
> langevin on
> langevinTemp 310.0
> langevinDamping 5.0
>
> # CONSTANT-P
>
> LangevinPiston on
> LangevinPistonTarget 1.01325
> LangevinPistonPeriod 200
> LangevinPistonDecay 50
> LangevinPistonTemp 310
>
> useGroupPressure yes
>
> useflexiblecell no
>
> # SPACE PARTITIONING
>
> splitpatch hydrogen
> hgroupcutoff 2.8
> stepspercycle 10
> margin 2.5
>
>
> # CUT-OFFS
>
> switching on
> switchdist 10.0
> cutoff 12.0
> pairlistdist 16.0
>
> # RESPA PROPAGATOR
>
> timestep 1.0
>
> fullElectFrequency 2
> nonbondedFreq 1
>
>
> # SHAKE
>
> rigidbonds all
> rigidtolerance 0.00000001
> rigiditerations 400
>
> # COM
>
> commotion no
>
>
> # FEP
>
> source fep.tcl
>
> alch on
> alchType fep
> alchFile solvated.fep
> alchCol B
> alchOutFile back_rest.fepout
> alchOutFreq 1
>
> alchVdwLambdaEnd 1.0
> alchElecLambdaStart 0.5
> alchVdwShiftCoeff 5.0
> alchDecouple yes
>
> # LOOP OVER LAMBDA-STATES
>
> alchEquilSteps 16000
> set nSteps 120000
>
> set dLambda 0.05
>
> #set init {1.0 0.9999999 0.999999 0.99999 0.9999 0.999
> 0.99 0.95 0.9}
> set end {0.05 0.01 0.001 0.0001 0.00001 0.000001
> 0.0000001 0.0}
>
> #runFEPlist $init $nSteps
> runFEP 0.1 0.05 $dLambda $nSteps
> runFEPlist $end $nSteps
>
>
--
_______________________________________________________________________
Chris Chipot, Ph.D.
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
The light shines in the darkness, and the darkness has not overcome it.
John 1:5.
_______________________________________________________________________
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:57:58 CST