Dear all,
Due to the computational speed difference, I would like to use pmemd.MPI program rather than snader.MPI to carry out atom position restraint MD simulation. Using sander program, the input parameters for restraint are set like "ntr=1,restraintmask=':918',restraint_wt=2.0 " . Searching the archive in the website, the input parameters for pmemd calculation are set like this:
&cntrl
imin=0,irest=1,ntx=5,
nstlim=500000,dt=0.001,
ntc=2,ntf=2,
cut=12.0, ntb=2, ntp=1, taup=2.0,
ntpr=1000, ntwx=1000,
ntt=3, gamma_ln=2.0,
ntr=1,
temp0=310.0,
/
2.0
RES 918
END
END
But in the course of calculation, some error message occurred which is " rfree: Error decoding variable 1 3 from: RES". what is the problem with this. Would you like to give me some help? Thanks!
Best withes
Duan Baogen
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Received on Fri Dec 07 2012 - 03:00:02 PST
