AMBER Archive (2009)

Subject: [AMBER] help_me to know the reason

From: balaji nagarajan (balaji_sethu_at_hotmail.com)
Date: Fri Apr 17 2009 - 23:30:07 CDT

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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