Re: [AMBER] How should I perform a long-time Simulated Annealing MD?

From: <>
Date: Wed, 4 Jul 2018 10:06:14 +0800

Hi dac,

Many thanks.

I saw a tutorial which set gamma_ln 1000. Does it have special meaning?
The tutorial web:

And I have tried aMD and GaMD for several times and I can not get the right protein conformation. The protein has significant conformational change which has identified by X-ray. Does Amber has other enhenced sampling method can simulate the protein allosteric effect?

Thank you!
Qiao Xue

On Tue, Jul 03, 2018, wrote:
> 1) When I use the SA in a production MD simulation. should I set ntt=3
> or ntt=1? If ntt=3, is gamma_ln=2 a good value?
ntt=3 and values of gamma_ln from 2 to 5 should work well.
> 2) If I want to perform a 200ns MD, should I perform SA many times or
> just once?
I don't know, and the answer is probably system specific.
> I write a .in file, is it right?
> &cntrl
> imin=0,irest=1,ntx=5,
> nstlim=100000000,dt=0.002, ioutfm=1
> ntc=2, ntf=2, ig=-1,
> cut=10.0, ntb=2, ntp=1, taup=2.0,
> ntpr=1000, ntwx=1000,
> ntt=3, gamma_ln=2.0,
> temp0=310,
> &end
> &wt type='TEMP0', istep1=0, istep2=10000000, value1=300.0, value2=400, &end
> &wt type='TEMP0', istep1=10000001, istep2=50000000, value1=400, value2=400, &end
> &wt type='TEMP0', istep1=50000001, istep2=70000000, value1=400, value2=350, &end
> &wt type='TEMP0', istep1=70000001, istep2=90000000, value1=350, value2=310, &end
> &wt type='TEMP0', istep1=90000001, istep2=100000000, value1=310, value2=310, &end
> &wt type='END' &end
I don't see anything wrong with the above; note that going to high
temperatures with constant pressure could lead to problems, since the system
volume might increase by so much that you would not get back to the original
density upon cooling. You may have to experiment some here. (I'm not sure
why you start at 300K but end at 310K....)
> 3) Can I combine SA with aMD or GaMD? If this is allowed, should I
> insert the SA into the file? Just like the following
You won't be able to "re-weight" your snapshots if the temperature is
changing; but you may not want to do that anyway. If I were doing this, I'd
try aMD at constant temperature first. But feel free to experiment: I don't
have any direct experience here.
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Received on Tue Jul 03 2018 - 19:30:02 PDT
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