Re: molecule leaves water box during md

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Jul 19 2007 - 16:00:31 CDT

Hi Irene,
please see earlier discussions on this subject, eg,
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/3919.html
Your molecule should be expected to diffuse during simulation; it will
not be wrapped about a periodic boundary condition unless:
a. you have wrapall on, and
b. the entire chain leaves the box

Peter

Irene Newhouse wrote:
> I minimized my molecule. No problems. I did an equilibration at constant P. No problems. I tried to do MD at constant V, using the volume that pertained at the end of the P-equilibration. The molecule did not stay centered in the cell, and by 3ns, it had moved completely outside the waters, which still formed a nice coherent box.
>
> Can someone please tell me what I'm doing wrong?
>
> This is the control/config file for the md:
>
> # input system......
> structure lstawi.psf
> coordinates lstawir_p.coor
>
> #..force field........................
> paratypecharmm on
> parameters par_kitsink.prm
> exclude scaled1-4
> 1-4scaling 1.0
> dielectric 1.0
>
> switching on
> switchdist 8.0
> cutoff 12.0
> pairlistdist 13.5
> margin 0.0
> stepspercycle 20
> rigidBonds all
> rigidTolerance 0.00001
> rigidIterations 100
>
> # Ewald EL..........................
> PME on
> PMETolerance 0.000001
> PMEGridSizeX 27
> PMEGridSizeY 40
> PMEGridSizeZ 27
>
>
> #integrator ............
> timestep 1.0
> fullElectFrequency 4
>
>
> #output....................
> outputenergies 10000
> outputtiming 10000
> binaryoutput no
> outputname lstawi_md
> restartname lstawir_md
> restartfreq 10000
> binaryrestart no
> DCDfile lstawi_md.dcd
> dcdfreq 10000
>
> #MD protocol..............
> seed 3010
> numsteps 20000000
> temperature 310
>
> # periodic boundary conditions......
> cellBasisVector1 29.9 0.0 0.0
> cellBasisVector2 0.0 41.758 0.0
> cellBasisVector3 0.0 0.0 29.313
> cellOrigin -2.3 8.5 -1.565
>
> wrapWater on
>
> Thanks ever so much!
> Irene Newhouse
> _________________________________________________________________
> Local listings, incredible imagery, and driving directions - all in one place! Find it!
> http://maps.live.com/?wip=69&FORM=MGAC01
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:44:59 CST