From: Brian Radak (bradak_at_anl.gov)
Date: Wed May 31 2017 - 18:24:19 CDT
Are all of the alchemical atoms getting flagged? For C36 glutamate
(which is what I recall this mutation being), you should have 8 atoms in
both groups, right?
On 05/31/2017 01:37 PM, Sadegh Faramarzi Ganjabad wrote:
> Hi Josh,
>
> My simulation doesn't run that far to see those lines you mentioned. I
> think runFEPmin section of fep.tcl allows a minimization step prior to
> FEP. I tried that and it stops in the minimization step and gives the
> same 'nan' error. So it gives the same error even when FEP/TI flag is on.
>
> Also, there are some warnings in the output file
>
> Warning: ALCH: SUSPICIOUS BONDS BETWEEN INITIAL AND FINAL GROUPS WERE
> FOUND
> Info: ALCH: 6 DIHEDRALS LINKING INITIAL AND FINAL ATOMS DELETED
>
> The first one is probably because I used extrabond to connect the
> initial and final groups.
>
> I'm putting my configuration file here.
>
> Thanks,
> Sadegh
>
> # MD SETUP
>
> timestep 2.0
> numsteps 1
>
>
> # FLEXIBLE CELL
>
> useflexiblecell no
>
> set temperature 310
>
> # INPUT
>
> structure all-ion-beta.psf
> parameters par_all36m_prot.prm
> parameters par_cph36_prot.prm
> parameters par_all36_cgenff.prm
> parameters par_all36_na.prm
> parameters par_all36_carb.prm
> parameters par_all36_lipid.prm
> parameters toppar_water_ions_fixed.str
> parameters retinal-pro.str
> #parameters toppar_all36_lipid_model.str
>
> paraTypeCharmm on
> temperature $temperature
>
> coordinates all-ion-beta.pdb
> #bincoordinates equilibration.coor
> #binvelocities equilibration.vel
>
> #extendedSystem equilibration.xsc
>
>
> # OUTPUT
>
> outputenergies 100
> outputtiming 100
> outputpressure 100
> binaryoutput yes
>
> outputname forward-noshift-pr
> restartname forward-noshift-pr
> restartfreq 100
> binaryrestart yes
>
> XSTFreq 100
>
>
> # PME
>
> PME yes
> PMETolerance 10e-6
> PMEInterpOrder 4
>
> PMEGridSpacing 1.0
>
> # Periodic Boundary Conditions
> if {1} {
> cellBasisVector1 73.60 0.0 0.0
> cellBasisVector2 0.0 73.60 0.0
> cellBasisVector3 0.0 0 83.16
> cellOrigin 0.030350102111697197 -0.059581365436315536
> 0.2382895052433014
> }
>
> # WRAP WATER FOR OUTPUT
> wrapAll on
>
>
> # CONSTANT-T
>
> langevin on
> langevinTemp 310.0
> langevinDamping 1.0
>
>
> # CONSTANT-P
>
>
>
> # SPACE PARTITIONING
>
> splitpatch hydrogen
> hgroupcutoff 2.8
> stepspercycle 20
> margin 1.0
>
>
> # CUT-OFFS
>
> switching on
> switchdist 10.0
> cutoff 12.0
> pairlistdist 12.0
>
>
> # RESPA
>
> fullElectFrequency 2
> nonbondedFreq 1
>
>
> # 1-4 NON-BONDED
>
> exclude scaled1-4
> 1-4scaling 1.0
>
>
> # COM
>
> commotion no
>
>
> # SHAKE
>
> rigidbonds all
> rigidtolerance 0.000001
> rigiditerations 400
>
>
> #############extra bonds
>
> extraBonds on
> extraBondsFile ref
> ########################
>
> # FEP PARAMETERS
>
> source ../tools/fep.tcl
>
> alch on
> alchType TI
> alchFile all-ion-beta.pdb
> alchCol B
> alchOutFile forward-noshift-pr.fepout
> alchOutFreq 10
> alchBondDecouple on
> alchBondLambdaEnd 1.0
>
> alchVdwLambdaEnd 1.0
> alchElecLambdaStart 0.0
> alchVdWShiftCoeff 0.0
> alchDecouple on
>
> alchEquilSteps 100
> set numSteps 500
>
>
>
> runFEPmin 1.0 0.0 0.0625 20 20 310
-- Brian Radak Postdoctoral Appointee Leadership Computing Facility Argonne National Laboratory 9700 South Cass Avenue, Bldg. 240 Argonne, IL 60439-4854 (630) 252-8643 brian.radak_at_anl.gov
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