Re: Waterbox unexpectedly deformed after minimization.

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Feb 28 2008 - 11:08:09 CST

Hi Kamilla,
two suggestions/notes:
-try an NPT equilibration after the minimization, as you probably don't
have enough water for your box size
-20000 steps minimization is an awful lot; if you watch the rms
gradients in the log file, my guess is you get to pretty low values in
the first few thousand steps. After that you probably ought to start an
equilibration.

Best,
Peter

Kamilla Kopec wrote:
> Dear NAMD mailing list,
>
> I am having some problems with the minimization of my protein.
> When I view the DCD trajectory for the minimization I see that
> two of the faces of the waterbox become concave with others
> remaining straight, deforming the waterbox. With orthogonal view
> the box looks like: *)__(*
> The input file is shown below and has been used successfully to
> minimize another very similar protein (same enzyme different
> species). A waterbox of the same size minimized without the
> protein shows the same deformation and the problem occurs on two
> different clusters. I have double checked the cell origin and
> cell basis vectors several times!
> Any suggestions about why this might be occurring would be
> seriously appreciated.
>
> Thanks
>
> Kamilla
>
> # Basic dynamics
>
> exclude scaled1-4
> 1-4scaling 1
> COMmotion no
> dielectric 1.0
> rigidBonds off ;# turn on for dynamics
>
> # Simulation space partitioning
>
> switching on
> switchdist 12
> cutoff 14 ;# leave this
> pairlistdist 16
>
> # Multiple timestepping
>
> firsttimestep 0
> timestep 1
> stepspercycle 20 ;# not<20
> nonbondedFreq 2 ;# non bonded calculated 2fs
> fullElectFrequency 4
>
> # Temperature control
>
> set temperature 300
> temperature $temperature; # initial temperature
>
> # PBC
>
> cellBasisVector1 73.82 0 0 ;#set correct basis vectors and origin;
> size of periodic
> cellBasisVector2 0 82.44 0
> cellBasisVector3 0 0 83.77
> cellOrigin 3.716 2.048 4.029
> wrapWater on
> wrapAll on
> wrapNearest off
> dcdUnitCell yes
>
> #PME
>
> PME yes
> PMEGridSizeX 75 ;#set correct pme grid size (multiples of 2 3 or 5)
> xyz eq basis vector 2,3,4
> PMEGridSizeY 84
> PMEGridSizeZ 84
>
> #simulation run
>
> minimize 20000 ;# steps just about to a local minimum. conjugate gradient
>
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