Re: change in box geometry for simulation of pure water

From: Chris Harrison (charris5_at_gmail.com)
Date: Wed Aug 27 2008 - 21:23:22 CDT

Maria,

Can you confirm for me that the box becomes thinner in the z-axis? And: was
the water box minimized and pre-equilibrated prior to turning-on
usecontantratio and useflexbilecell?

-Chris

On Wed, Aug 27, 2008 at 7:48 AM, maria goranovic
<mariagoranovic_at_gmail.com>wrote:

> Hello,
>
> I ran a simulation of a box of water with a standard config file using
> useconstantratio and useflexiblecell. However, the simulation box becomes
> thinner in one dimension, until the simulation crashes. Why does this
> happen?
>
> Thanks for the suggestions, config file below:
>
> !!!!!!!!!!!!!!!!!!!!!!!!!
> set MOL wat2
>
> set temp 310
>
> set xbox 39.97
> set ybox 39.94
> set zbox 39.94
>
> structure ${MOL}.psf
> coordinates ${MOL}.pdb
> temperature 0
> parameters par-combined.prm
> paraTypeCharmm on
>
> outputEnergies 5000
> outputTiming 5000
> xstFreq 5000
> dcdFreq 5000
> wrapAll on
> margin 5
>
> rigidbonds on
> timestep 2
> nonBondedFreq 1
> fullElectFrequency 1
> stepsPerCycle 20
>
> exclude scaled1-4
> 1-4scaling 1.0
> switching on
> switchDist 10
> cutoff 12
> pairlistdist 14
>
> cellBasisVector1 $xbox 00.00 00.00
> cellBasisVector2 00.00 $ybox 00.00
> cellBasisVector3 00.00 00.00 $zbox
>
> #########################################
> cellOrigin 0.05952 0.09806 -0.1598
>
> Pme on
> PmeGridsizeX 40
> PmeGridsizeY 40
> PmeGridsizeZ 40
>
> #########################################
> # PRESSURE AND TEMPERATURE CONTRON
> #########################################
>
> # temperature
> langevin on
> langevinDamping 5
> langevinTemp $temp
> langevinHydrogen no
>
> useflexiblecell yes
> useconstantratio yes
> langevinPiston on
> langevinPistonTarget 1.01325
> langevinPistonPeriod 100
> langevinPistonDecay 50
> langevinPistonTemp $temp
>
> binaryoutput on
> outputname ${MOL}-equil
>
> # INITIAL ENERGY
> minimize 0
>
> minimize 5000
> output ${MOL}-min1
>
> #########################################
> # HEAT
> #########################################
>
> set tem 310
> langevinTemp $tem
>
> for {set p 1 } { $p < 11 } { incr p } {
> run 1000000
> output ${MOL}-$p
> }
>
>
>
> --
> Maria G.
> Technical University of Denmark
> Copenhagen
>

-- 
Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
char_at_ks.uiuc.edu Voice: 217-244-1733
http://www.ks.uiuc.edu/~char Fax: 217-244-6078

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:21:16 CST