Re: protein shifts out of the water box

From: Eric Userlist (eric.userlist_at_gmail.com)
Date: Fri May 08 2009 - 18:22:52 CDT

Hi
Thank you all for the discussion. Should I rerun the simulation by a bigger
water box or the results are still usable?

Eric

On Wed, Apr 29, 2009 at 9:51 PM, David Hardy <dhardy_at_ks.uiuc.edu> wrote:

> With the "wrapAll" directive, each molecule is wrapped back into the
> periodic cell based on its geometric center. So it makes sense that the end
> of Eric's protein appears to be sticking out of the box, but the geometric
> center of the protein is still inside of the box.
> -Dave
>
>
> On Apr 29, 2009, at 8:59 PM, Rabab Toubar wrote:
>
> Hi all,
>
> I was just wondering how would the protein move without the water box when
> Eric is using "wrapAll"
>
> Rabab
>
> --- On *Wed, 4/29/09, Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu>* wrote:
>
>
> From: Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu>
> Subject: Re: namd-l: protein shifts out of the water box
> To: "Eric Userlist" <eric.userlist_at_gmail.com>
> Cc: namd-l_at_ks.uiuc.edu
> Date: Wednesday, April 29, 2009, 8:14 PM
>
> On Wed, 2009-04-29 at 16:52 -0700, 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.
>
> eric,
>
> please consider that you have periodic boundary conditions.
> your water has a suspiciously large hole, right? ;)
>
> apart from that, it is probably a good idea to check the
> motion of the total center of mass and remove it. this kind
> of drift would be leading to having the system being colder
> than the kinetic energy idicates. think of an extremely
> fast icecube as an extreme example of that...
>
> cheers,
> axel.
>
>
> > 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
> >
> >
> >
>
> --
> =======================================================================
> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu<http://us.mc01g.mail.yahoo.com/mc/compose?to=akohlmey@cmm.chem.upenn.edu>
> http://www.cmm.upenn.edu
> Center for Molecular Modeling -- University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot.
>
>
>
>
>
> --
> David J. Hardy, Ph.D.
> Theoretical and Computational Biophysics
> Beckman Institute, University of Illinois
> dhardy_at_ks.uiuc.edu
> http://www.ks.uiuc.edu/~dhardy/ <http://www.ks.uiuc.edu/%7Edhardy/>
>
>
>
>
>

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