Re: protein shifts out of the water box

From: Rabab Toubar (rtoubar_at_yahoo.com)
Date: Wed Apr 29 2009 - 20:59:41 CDT

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://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
=======================================================================
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