Dear AMBER ,
I have posted this problem already ,
but this time I have a problem in writing the out put files .
I am trying to run the Targeted molecular dynamics in explicit water ,
The both Targeted and the Reference structure are having same number of molecules (both solute and solvent )
I have given a run in vaccum , The simulation runs ,
After adding water (TIP3P) , I have minimized and equillibriated the system and gave a MD run for 100Ps ,
after that I took both the structures and tried to perform Targeted Molecular dynamics ,
when I impose the periodic boundary condition ,
NTB = 2 ,
the sander is utillising 100% CPU and the out put files are empty ,
and the .mdcrd , vel , mdinfo , rst nothing is being created
But when I do the same with the
option NTB =0 , it prints the outputs , mdcrd , vel , eng , and all
I would like to know is there any technical problem i am facing
or PBC condition can not be applied for Targeted moleculardynamics
thanks in advance
balaji
UOM
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Received on Wed May 20 2009 - 11:33:43 PDT
