Re: protein shifts out of the water box

From: Eric H. Lee (ericlee_at_ks.uiuc.edu)
Date: Fri May 08 2009 - 18:31:02 CDT

The results will be usable if the periodic images are not too close to
each other. You can check these by loading the trajectory and then
viewing the periodic images in VMD. Assuming you've set up
appropriate boundaries at the beginning, it should probably be ok, but
best to check.

-Eric

On May 8, 2009, at 6:22 PM, Eric Userlist wrote:

> 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://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/
>
>
>
>
>

Eric H. Lee
Medical Scholars Program
Theoretical and Computational Biophysics Group, UIUC
ericlee_at_ks.uiuc.edu

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