Re: protein shifts out of the water box

From: Joshua Adelman (jadelman_at_berkeley.edu)
Date: Wed Apr 29 2009 - 19:07:05 CDT

Hi Eric,

Unless you have a bubble in your system, it is impossible for the
protein to be "outside" of the water box/not solvated, if you are
using PBC (which you are). The display issue is caused by the way you
have chosen to wrap the coordinates in your system, rather than
something physical that's going on. I'd take a look at the manual,
search the namd-l archive, and google PBC, to get a sense of what you
should be expecting to see.

Josh

On Apr 29, 2009, at 4:52 PM, Eric Userlist wrote:

> Hi
> I am running a md simulation with the following input file. After I
> examine the trajectory, part of the protein is outside the water
> grid. I solvate the protein with 9 angstrom from the edge of the
> grid. Should I use a bigger water box or restrain the protein
> somehow. Thank you.
>
> Eric
>
> ###### Input Files and Parameters #######
>
> set temperature 310
> set outputname protein_md2
> set restartfreq 500
>
> structure ../common/protein_ionized.psf
> coordinates ../md/protein_md.pdb
> bincoordinates ../md/protein_md.restart.coor
> binvelocities ../md/protein_md.restart.vel
> extendedSystem ../md/protein_md.xsc
>
> ######################
> # Force-Field Parameters
> paratypecharmm on
> parameters ../common/par_all27_prot_lipid.inp
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 9.
> switching on
> switchdist 8.
> pairlistdist 11
>
> # Integrator Parameters
> timestep 1.0 ;# 2fs/step
> rigidBonds all ;# needed for 2fs steps
> rigidTolerance 0.00000001
> margin 2.5
> nonbondedFreq 2
> fullElectFrequency 4
> stepspercycle 20
>
> # Temperature Control
> langevin on
> langevinTemp 310
> langevinDamping 1
> #temperature $temperature
> #reassignFreq 100
> #reassignTemp 25
> #reassignIncr 25
> #reassignHold 300
>
> # Periodic Boundary Conditions
> cellBasisVector1 66.3 0 0
> cellBasisVector2 0 71.5 0
> cellBasisVector3 0 0 78.9
> cellOrigin 23.77 24.54 11.70
> wrapAll on
> wrapNearest on
>
> # PME (for full-system periodic electrostatics)
> PME yes
> PMEGridSizeX 72
> PMEGridSizeY 72
> PMEGridSizeZ 80
>
> # Constant Pressure Control (variable volume)
> useGroupPressure yes
> useFlexibleCell no
> LangevinPiston on
> LangevinPistonTarget 1
> LangevinPistonPeriod 200
> LangevinPistonDecay 500
> LangevinPistonTemp 310
>
> # Output
> outputname $outputname
> outputEnergies 10
> restartfreq $restartfreq
> DCDfreq 500
> binaryoutput no
> binaryrestart yes
> outputTiming 100
>
>
> ########## Extra Parameters ################
>
> # Constraints
> #constraints on
> #consref ../min/protein_min.pdb
> #conskfile ../min/protein_min_constraint.pdb
> #conskcol B
>
> ########## Execution ##############
>
> #minimize 1000
>
> run 10000000
>
>
>

------------------------------------------------------------------------------------------------------
Joshua L. Adelman
Biophysics Graduate Group Lab: 510.643.2159
218 Wellman Hall Fax: 510.642.7428
University of California, Berkeley http://nature.berkeley.edu/~jadelman
Berkeley, CA 94720 USA jadelman_at_berkeley.edu
------------------------------------------------------------------------------------------------------

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