# 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.

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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