From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Mon Jan 08 2007 - 14:33:13 CST
Hi Rima,
have you tried visualizing this with the appropriate periodic boundary
conditions? It may be that your protein is in solvent, but doesn't
appear to be because its coordinates would not be wrapped unless the
whole chain crosses the boundary.
Peter
Rima Chaudhuri wrote:
> Hi All,
> I am trying to simulate a protein with a calcium ion and ligand
> attached using Amber forcefield in namd for 1ns, in two instances.
> Case1: Simulating the protein with Calcium attached in 10A water box
> Case2: Simulate the protein complex with inhibitor in a 10A water box
>
> In both the cases, right from frame 0, (I minimize for 1000 steps) the
> protein comes out of the water box and tethers to one edge, while the
> calcium ion and ligand comes out and tethers themselves to two other
> edges of the box. In other words they are partially immersed (just
> anchorched) to the water box on 3 different sides. Initially i thought
> it might be the parameters of Ca or ligand that is causing this, so I
> tried simulating the protein alone w/o Ca2+ even, it does the same
> thing, the protein comes out and even translates to another edge of
> the box after some 1000 frames randomly.
> The following is my .config file. Any guidance will be much appreciated.
>
> amber yes
> parmfile fxa_wat_ca.prmtop
> ambercoor fxa_wat_ca.inpcrd
>
>
>
> set temperature 310
> set outputname outFxa_ca
>
> firsttimestep 0
>
>
> #############################################################
> ## SIMULATION PARAMETERS ##
> #############################################################
>
> # Input
> paraTypeCharmm off
> temperature 0
> reassignFreq 1000
> reassignTemp 25
> reassignIncr 25
> reassignHold 310
>
>
> # Force-Field Parameters
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 12.
> switching on
> switchdist 8.
> pairlistdist 13.5
>
>
> # Integrator Parameters
> timestep 2.0 ; # 2fs/step
> rigidBonds all ;# needed for 2fs steps
> nonbondedFreq 1
> fullElectFrequency 2
> stepspercycle 10
> margin 5
>
> # Constant Temperature Control
> langevin on ;# do langevin dynamics
> langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
> langevinTemp 310
> langevinHydrogen off ;# don't couple langevin bath to hydrogens
>
>
> # Periodic Boundary Conditions
> cellBasisVector1 69.0 0. 0.
> cellBasisVector2 0. 76. 0.
> cellBasisVector3 0. 0. 66.1230010986
> cellOrigin - 0.0838125869632 0.121281333268
> -0.300958424807
>
> wrapAll on
>
>
> # PME (for full-system periodic electrostatics)
> PME yes
> PMEGridSizeX 70
> PMEGridSizeY 80
> PMEGridSizeZ 70
>
>
> # 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 310
>
> # Output
> outputName $outputname
>
> restartfreq 500 ;# 500steps = every 1ps
> dcdfreq 250
> xstFreq 250
> outputEnergies 150
> outputPressure 150
>
> #############################################################
> ## EXTRA PARAMETERS ##
> #############################################################
>
>
> #############################################################
> ## EXECUTION SCRIPT ##
> #############################################################
>
> # Minimization
> minimize 1000
> reinitvels 310
>
> run 500000 ;# 1000ps
>
>
>
>
>
>
> --
> -Rima
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