From: Grzegorz Jezierski (jezierski_at_theochem.tu-muenchen.de)
Date: Fri Aug 05 2005 - 06:23:57 CDT
Yes, I tried this.
I also (in another run) transformed my system so that the center of
geometry was 0.0 0.0 0.0.
That is an equivalent trick. But - none of them worked. Same with
"WrapAll" and "WrapNearest" flags - I tried all the combinations.
Grzegorz
nordgren_at_sas.upenn.edu wrote:
>Hi Grzegorz,
>
>It certainly seems like something simple is messed up with your coord
>wrapping.
>
>Just to be clear... you have tried setting the "CellOrigin" parameter to
>the actual coords of the geometric center of your system, instead of (0 0 0),
>and you still see strange coords output?
>
>If you turn off the "WrapAll" and "WrapNearest" flags, does that fix things?
>
>- Erik
>
>C. Erik Nordgren, Ph.D.
>Department of Chemistry
>University of Pennsylvania
>
>
>Quoting surendra negi <negi009_at_yahoo.com>:
>
>
>
>>try following commands in VMD
>>
>>measure minmax $t
>># then calculate cellBasisVector1 =abs|x1+x2|/2
>># and box center by
>>measure center $t
>>
>>best, surendra
>>
>>--- Grzegorz Jezierski
>><jezierski_at_theochem.tu-muenchen.de> wrote:
>>
>>
>>
>>>Hi,
>>>I tried centering the system as well as many other
>>>tricks, but to no avail.
>>>I know there's a new version of NAMD coming, but I
>>>don't think they
>>>fixed this.
>>>Any hints?
>>>
>>>Charles Danko wrote:
>>>
>>>
>>>
>>>>Hello,
>>>>
>>>>It was my understanding that cellOrigin should be
>>>>
>>>>
>>>the center of the
>>>
>>>
>>>>periodic box, not 0 0 0. Try changing it to the
>>>>
>>>>
>>>geometric center of
>>>
>>>
>>>>the box. You should be able to calculate this
>>>>
>>>>
>>>easily for your system
>>>
>>>
>>>>in VMD. If you have trouble, search google, or
>>>>
>>>>
>>>post again.
>>>
>>>
>>>>Regards,
>>>>Charles Danko
>>>>
>>>>On 7/25/05, *Grzegorz Jezierski*
>>>>
>>>>
>>><jezierski_at_theochem.tu-muenchen.de
>>>
>>>
>>>><mailto:jezierski_at_theochem.tu-muenchen.de>> wrote:
>>>>
>>>> Dear NAMD users,
>>>> While running NAMD simulations on DNA immersed
>>>>
>>>>
>>>in water, and using
>>>
>>>
>>>> AMBER
>>>> forcefield, I encountered the following
>>>>
>>>>
>>>problem:
>>>
>>>
>>>> During the first step of calculation (MD or
>>>>
>>>>
>>>minimization), the initial
>>>
>>>
>>>> periodic box was split in 4 smaller boxes and
>>>>
>>>>
>>>displaced by a half
>>>
>>>
>>>> of box
>>>> dimension, plus the structure was reflected in
>>>>
>>>>
>>>mirror planes along
>>>
>>>
>>>> the
>>>> main axes. The DNA duplex was split into 2
>>>>
>>>>
>>>individual chains and also
>>>
>>>
>>>> displaced.
>>>> When a box is smaller than a cube with 25 A
>>>>
>>>>
>>>long side, no reflection
>>>
>>>
>>>> occurs, just displacement. Then, during
>>>>
>>>>
>>>subsequent steps of
>>>
>>>
>>>> simulation,
>>>> the system behaves correctly. This problem is
>>>>
>>>>
>>>seen only when Periodic
>>>
>>>
>>>> Boundary Conditions are on.
>>>> Having performed numerous tests and trials I
>>>>
>>>>
>>>think this might be a bug
>>>
>>>
>>>> in NAMD code, but before submitting a report I
>>>>
>>>>
>>>want to ask if someone
>>>
>>>
>>>> has had similar problems?
>>>> Thank you
>>>> G. Jezierski
>>>>
>>>>
>>>> PS. Below a configuration file:
>>>>
>>>>
>>>>
>>>================================================
>>>
>>>
>>>> # ==== NAMD 2.5 ==== EM TEST ==== DNA IN WATER
>>>>
>>>>
>>>====
>>>
>>>
>>>> bincoordinates em_test.coor
>>>> parameters
>>>>
>>>>
>>>/parameters/toppar/par_amber_98.inp
>>>
>>>
>>>> paraTypeCharmm off
>>>> Amber yes
>>>> parmfile T3.top
>>>> ambercoor T3.center.rst
>>>>
>>>> outputName em_test
>>>> outputEnergies 10
>>>> wrapAll on
>>>> wrapNearest on
>>>>
>>>> numsteps 10
>>>>
>>>> dielectric 1.0
>>>> switching off
>>>> switchDist 9.0
>>>> cutoff 10.0
>>>> pairlistdist 12.0
>>>> margin 1.0
>>>> exclude scaled1-4
>>>> 1-4scaling 0.833333
>>>> scnb 2
>>>>
>>>> cellBasisVector1 50.2 0.0 0.0
>>>> cellBasisVector2 0.0 47.9 0.0
>>>> cellBasisVector3 0.0 0.0 59.2
>>>> cellOrigin 0 0 0
>>>>
>>>> Pme on
>>>> PmeGridsizeX 50
>>>> PmeGridsizeY 50
>>>> PmeGridsizeZ 60
>>>>
>>>> minimization on
>>>>
>>>>
>>>>
>>>>
>>>================================================
>>>
>>>
>
>
>
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