Hello:
I've produced 3 round of 1 ns MD for MMPBSA calcualtion, each of then
contains 100 frames. Here is my setting:
production
&cntrl
imin=0,irest=1,ntx=5,
nstlim=500000,dt=0.002,
ntc=2,ntf=2,
cut=9.0, ntb=2, ntp=1, taup=2.0,
ntpr=5000, ntwx=5000,
ntt=3, gamma_ln=2.0,
temp0=300.0,
/
so if I use the following mmpbsa.in for mmpbsa.py:
&general
endframe=100, verbose=1,
/
&gb
igb=2, saltcon=0.150
/
&pb
istrng=0.150, fillratio=4.0
/
I am just wondering how many frames in all would be calculated? 100
frames or 300 frames? I am a little bit confused for that.
Here is my command line for mmpbsa.py:
mpirun -np 16 MMPBSA.py.MPI -O -i 06-mmpbsa.in -o
FINAL_RESULTS_MMPBSA.dat -sp sol.prmtop -cp com.prmtop -rp rec.prmtop
-lp lig.prmtop -y prod1.mdcrd prod2.mdcrd prod3.mdcrd > progress.log&
thx a lot
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Received on Fri Jul 17 2015 - 03:30:02 PDT
