AMBER Archive (2009)

Subject: Re: Re: [AMBER] exchange attempt in REMD

From: zgong.hust (zgong.hust_at_gmail.com)
Date: Wed Dec 30 2009 - 22:22:54 CST

I have done some unfolding simualtions and choose the high temperature, then ,divided the temperature range between 300 to 440 with 8 parts


2009-12-31



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



发件人： Carlos Simmerling
发送时间： 2009-12-31 11:09:19
收件人： AMBER Mailing List
抄送：
主题： Re: [AMBER] exchange attempt in REMD
 
How did you choose your temperatures?
On Dec 30, 2009, at 9:34 PM, "zgong.hust" <zgong.hust_at_gmail.com> wrote:
> 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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> AMBER_at_ambermd.org
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