AMBER Archive (2009)

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

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu Dec 31 2009 - 09:50:24 CST

it's much more complex than that. It is difficult to give advice when
I don't know how much you've read about REMD and don't know anything
about your simulation system or goals, but it's an advanced method and
you'll need to do a lot of reading before you can be successful. I
suggest finding articles in the literature that used REMD to solve
problems very much like yours, and follow their procedures. Keep in
mind that temperature spacing is system size dependent. If nobody has
used REMD on a system like yours, be prepared for a lot of trial and
error and you'll probably only get it to work if you have extensive
experience with REMD and with RNA simulations. Keep in mind that RNA
force fields are less well developed than those for proteins, so it
may not be possible to get acceptable results even if you get the REMD
part to work well.

2009/12/30 zgong.hust <zgong.hust_at_gmail.com>:
> 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
>> _______________________________________________
>> AMBER mailing list
>> AMBER_at_ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
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