AMBER Archive (2009)

Subject: [AMBER] exchange attempt in REMD

From: zgong.hust (zgong.hust_at_gmail.com)
Date: Wed Dec 30 2009 - 20:34:21 CST

Hi all :
        I'm using AMBER 9 to perform the REMD simulations of RNA. However, I found that the exchange was not successful, the velocity scaling factor was -1.0, and all the successful rate are 0.0

Here is the rem.log file

# Replica #, Velocity Scaling, T, Eptot, Temp0, NewTemp0, Success rate (i,i+1)
# exchange 1
 1 -1.00 0.00-141136.98 300.50 300.50 0.00
 2 -1.00 0.00-138374.96 320.20 320.20 0.00
 3 -1.00 0.00-134936.24 340.40 340.40 0.00
 4 -1.00 0.00-132143.00 360.20 360.20 0.00
 5 -1.00 0.00-129004.34 380.80 380.80 0.00
 6 -1.00 0.00-125925.38 400.50 400.50 0.00
 7 -1.00 0.00-122600.65 420.60 420.60 0.00
 8 -1.00 0.00-119381.25 440.00 440.00 0.00
# exchange 2
 1 -1.00 301.02-141324.61 300.50 300.50 0.00
 2 -1.00 319.84-138070.09 320.20 320.20 0.00
 3 -1.00 341.43-134893.06 340.40 340.40 0.00
 4 -1.00 357.82-131767.92 360.20 360.20 0.00
 5 -1.00 378.64-129054.21 380.80 380.80 0.00
 6 -1.00 401.51-125653.98 400.50 400.50 0.00
 7 -1.00 416.16-122579.43 420.60 420.60 0.00
 8 -1.00 440.44-119685.69 440.00 440.00 0.00
# exchange 3
 1 -1.00 302.90-141103.66 300.50 300.50 0.00
 2 -1.00 319.86-138178.43 320.20 320.20 0.00
 3 -1.00 338.56-135038.45 340.40 340.40 0.00
 4 -1.00 361.47-132086.03 360.20 360.20 0.00
 5 -1.00 379.33-128997.99 380.80 380.80 0.00
 6 -1.00 400.13-125885.92 400.50 400.50 0.00
 7 -1.00 419.82-122649.25 420.60 420.60 0.00
 8 -1.00 439.00-119556.06 440.00 440.00 0.00
# exchange 4
 1 -1.00 299.07-141126.55 300.50 300.50 0.00
 2 -1.00 316.91-138327.78 320.20 320.20 0.00
 3 -1.00 343.08-135129.07 340.40 340.40 0.00
 4 -1.00 360.19-131906.88 360.20 360.20 0.00
 5 -1.00 378.95-129000.50 380.80 380.80 0.00
 6 -1.00 398.61-125970.45 400.50 400.50 0.00
 7 -1.00 417.66-122794.69 420.60 420.60 0.00
 8 -1.00 438.90-119366.36 440.00 440.00 0.00
# exchange 5
 1 -1.00 297.45-141273.10 300.50 300.50 0.00
 2 -1.00 318.77-138085.22 320.20 320.20 0.00
 3 -1.00 342.69-135422.12 340.40 340.40 0.00
 4 -1.00 359.83-131942.59 360.20 360.20 0.00
 5 -1.00 376.77-129293.08 380.80 380.80 0.00
 6 -1.00 399.03-125808.27 400.50 400.50 0.00
 7 -1.00 421.07-122355.32 420.60 420.60 0.00
 8 -1.00 442.53-119554.84 440.00 440.00 0.00

Here is my input file

 &cntrl
   irest=1, ntx=5,
   nstlim=5000, dt=0.002,
   ntt=3, gamma_ln=1.0,
   temp0=300.5,
   nscm=1000,
   ntb=2,pres0 = 1.0,ntp=1,
   taup = 2.0,
   cut=10.0,ntr=0,ntc=2,ntf=2,
   ntpr=2500, ntwx=2500, ntwr=100000,
   numexchg=1000,
 /
 &wt TYPE='END'
 /

Please help me out

Thank you very much
Happy New Year

2009-12-31

Zhou Gong
School of Physics
Huazhong University of Science and Technology
Wuhan
Hubei Province
China
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