From: Jerome Henin (heninj_at_gmail.com)
Date: Tue Feb 24 2009 - 09:37:14 CST
Hi Chris,
I think the December 2008 build should be fine. Two questions:
1) did you run Alchemify on your PSF file?
2) did you look closely at the trajectories in VMD to see if anything
suspicious happens?
Best,
Jerome
On Mon, Feb 23, 2009 at 1:53 PM, Christopher Hartshorn
<cmhartshorn_at_wsu.edu> wrote:
> Hi everyone. After running an FEP calculation (see parameters below
> message),I am obtaining an FEP graph (dG vs Lambda step) which seems odd. I
> write to this forum because I think it is my system (or parameters) and not
> an actual physical result. Essentially I am seeing, as lambda goes from 0
> to 1, the dG drop below zero, hit a minimum (around -120), and then rises
> again to around lambda step 0.98. This is what I expect. But at around
> lambda step 0.98, it reverts going negative again (e.g it rises from -120 to
> about -44, at lambda=0.98, then reverts and ends around -50 at lambda=1).
> Is this one of those end point anomalies? Does my config. file seem okay
> (e.g using Langevin coupling to pressure/temp baths, etc.)? I'm using a CVS
> build from Dec 2, 2008 is this a good build for FEP? etc.
>
> Thank you to all for any help you can offer.
>
> Chris Hartshorn
> WSU
>
>
> structure dmpc_mid1.psf
> coordinates mdsim2ns_out.coor
> velocities mdsim2ns_out.vel
> extendedSystem mdsim2ns_out.xsc
> set outputname dmpcmid1FEPGA155ksteps04_out
>
> # firsttimestep 1000000
>
>
> #############################################################
> ## SIMULATION PARAMETERS ##
> #############################################################
>
> # Input parameters
> paraTypeCharmm on
> parameters par_all27_prot_lipid_sil.inp
> parameters par-extraterms.inp
>
> # Force-Field Parameters
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 10.0
> switching on
> switchdist 8.5
> pairlistdist 11.5
>
>
> # Integrator Parameters
> timestep 1.0 ;# 1fs/step
> nonbondedFreq 1
> fullElectFrequency 2
> stepspercycle 20
>
> margin 1
>
> wrapWater on
> wrapNearest off
>
> # PME (for full-system periodic electrostatics) only with PBC's
> # Must get cell dimensions from PBC basisvectors for accurate PME
> # Remember multiples of 2,3, and/or 5
> PME on
> PMEGridSizeX 120
> PMEGridSizeY 120
> PMEGridSizeZ 100
>
> # Constant Pressure Control (variable volume) only for PBC's
> useGroupPressure yes # smaller fluctuations
> useFlexibleCell no # allow dimensions to fluctuate independently
>
> # Constant Temperature Control
> langevin on ;# do langevin dynamics
> langevinDamping 10 ;# damping coefficient (gamma) of 10/ps
> langevinTemp 310
> langevinHydrogen off ;# don't couple langevin bath to hydrogens
>
> # Nos´e-Hoover Langevin piston pressure control
> langevinPiston on
> langevinPistonTarget 1.01325 ;# in bar -> 1 atm
> langevinPistonPeriod 200.0
> langevinPistonDecay 100.0
> langevinPistonTemp 310
>
> rigidbonds all
> rigidtolerance 0.000001
> rigiditerations 400
>
>
> fixedAtoms on
> fixedAtomsForces on
> fixedAtomsFile fixQ011.pdb
> fixedAtomsCol B
>
> #############################################################
> ## EXECUTION SCRIPT ##
> #############################################################
> # FEP
>
> source fep.tcl
>
> fep on
> fepFile dmpc_mid1_FEPGA1.fep
> fepCol B
> fepOutFile DMPCmid1GA155ksteps04.fepout
> fepOutFreq 10
>
>
> # LOOP OVER LAMBDA-STATES
>
> fepEquilSteps 5000
> set nSteps 110000
>
> set dLambda 0.04
>
> set init {0.0 0.00001 0.0001 0.001 0.01 0.02}
> set end {0.98 0.99 0.999 0.9999 0.99999 1.0}
>
> runFEPlist $init $nSteps
> runFEP 0.02 0.98 $dLambda $nSteps
> runFEPlist $end $nSteps
>
>
>
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