Re: Explicit Water System Condensing

From: Jeffrey J. Potoff (jpotoff_at_chem1.eng.wayne.edu)
Date: Thu Feb 25 2010 - 10:13:43 CST

Hi Keith,
    A quick calculation using your numbers gives a water density of
2.19g/cm^3
40000 [molecules] * 18 [g/mol]/6.023x10^23 [molecules/mole]/(94*83*70
[A^3]*1x10^-24][cm^3/A^3]) = 2.19 g/cm^3

Normally, if you are seeing a vacuum form in simulations where you have
a large solvated object, such as a peptide/protein, it means you don't
have enough water/solvent, although based on the numbers you've given,
you have way too much water. Something doesn't add up.

After loading your data into VMD, if you issue the following commands in
the TK Console, what do you get?
>set sel [atomselect top all]
>measure minmax $sel

Regards,
    Jeff

Keith Battle wrote:
> Hi NAMD world,
>
> My group has assembled a system for MD consisting of a short peptide
> solvated in a TIP3P waterbox atop a fixed crystal surface. The
> waterbox contains ~40,000 waters and has a dimension of 94 X 83 X 70
> angstroms. We designed the box to give a water density close to 1. We
> ran a short 1000 step minimization and MD run at NVE conditions for
> 10,000 steps just to get a feel for how the system will equilibrate.
> After about 5,000 steps into MD we noticed the corners of the waterbox
> condensing and forming a vacuum (we used IMD to watch the simulation).
> Any insight on how to stop this process would be greatly appreciated.
> My input file is given below.
>
> # input
> amber yes
> coordinates C:/Users/Alan/Desktop/a1_solvated/A_1_system_new.pdb
> extendedSystem C:/Users/Alan/Desktop/a1_solvated/test.xsc
> parmfile C:/Users/Alan/Desktop/a1_solvated/A_1_system.prmtop
>
> # output
> set output C:/Users/Alan/Desktop/a1_solvated/A_1_system_new
> outputname $output
> dcdfile ${output}.dcd
> xstFile ${output}.xst
> dcdfreq 50
> xstFreq 50
>
> binaryoutput no
> binaryrestart no
> outputEnergies 100
> restartfreq 1000
>
> # mobile atom selection:
> # protein or waters
> fixedAtoms on
> fixedAtomsFile
> C:/Users/Alan/Desktop/a1_solvated/A_1_system_new_fixed.pdb
> fixedAtomsCol O
>
> # Basic dynamics
> exclude scaled1-4
> 1-4scaling 1
> COMmotion no
> dielectric 1.0
> rigidBonds water
>
> # Simulation space partitioning
> switching on
> switchdist 9
> cutoff 10
> pairlistdist 12
>
> # Multiple timestepping
> firsttimestep 0
> timestep 1
> stepspercycle 20
> nonbondedFreq 2
> fullElectFrequency 4
>
> # Temperature control
>
> set temperature 310
> temperature $temperature; # initial temperature
>
> # PBC
> wrapAll on
> dcdUnitCell yes
>
> #IMD
> IMDon on ;#
> IMDport 3000 ;# port number (enter it in VMD)
> IMDfreq 1 ;# send every 1 frame
> IMDwait yes ;# wait for VMD to connect before running?
>
> # Scripting
>
> minimize 1000
> reinitvels $temperature
> run 10000
>
>
>
> Best,
>
> Keith Battle
> University of South Alabama
>

-- 
======================================================================
Jeffrey J. Potoff                         jpotoff_at_chem1.eng.wayne.edu
Associate Professor                       Wayne State University		
Department of Chemical Engineering and Materials Science
5050 Anthony Wayne Dr                     Phone:(313)577-9357		
Detroit, MI 48202                         Fax:  (313)578-5815
http://potoff1.eng.wayne.edu
======================================================================

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