Hi Charles,
Thanks for your help and sorry for bothering you once more.
There still is something missing from my Torsion dynamics setup and I am
running
out of ideas. I added potential terms (although there seems to be a problem
with
the RAMA potential terms, see below). The system simulates and prints out
energies but, eventually, nothing seems to move:
protocol.initTopology(('protein'))
protocol.initParams(('protein'))
protocol.loadPDB("03_min.pdb")
xplor.simulation.deleteAtoms("not known")
protocol.massSetup()
dyn = ivm.IVM()
dyn.group( AtomSel( 'resid 1:107' ) )
dyn.group( AtomSel( 'resid 122:338') )
protocol.torsionTopology( dyn )
from potList import PotList
pot = PotList()
pot.append( XplorPot('CDIH') )
protocol.initRamaDatabase()
>>> This may be a trouble maker, it displays 4 lines like:
>>> VECTOR: zero atoms selected
...
pot.append( XplorPot('RAMA') )
pot.append( XplorPot('VDW') )
pot.append( XplorPot("BOND") )
pot.append( XplorPot("ANGL") )
pot.append( XplorPot("IMPR") )
protocol.initDynamics( ivm=dyn,
potList=pot,
bathTemp=500,
finalTime=1,
numSteps=500,
printInterval=10,
)
dyn.run()
I also tried the higher level AnnealIVM but can't quite figure out what a
minimal rampedParams record would look like. The examples I found so far are
all
dealing with refinement data...
Best regards,
Raik
Charles at Schwieters.org wrote:
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> Hello Raik--
>
>> The very last bit does NOT work -- I try to set up a IVM MD with the
>> two domains fixed and the linker remaining flexible but the MD doesn't
>> do anything. So there is something crucial missing... Anyway, here
>> comes the script as it looks so far -- any comments are most welcome!
>>
>
>> from potList import PotList
>>
>> protocol.initDynamics( ivm=I,
>> bathTemp=500,
>> finalTime=1,
>> numSteps=5000,
>> printInterval=10,
>> )
>> xplor.command( """flags include * end""")
>
> You have not specified a potList to initDynamics- the ivm runs with no
> potential energy term. Please see e.g. eginput/gb1_rdc/anneal.py for how
> to use XPLOR energy terms with the IVM in the python interface.
>
> best regards--
> Charles
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--
________________________________
Dr. Raik Gruenberg
http://www.raiks.de/contact.html
________________________________
