Hi all,
I perform a MD to investigate an obvious conformational change of a protein. The protein have 500 residues and it is a dimer. But the canon MD can get the right conformation change. Thus I try to use the simulated annealing (SA) method to accelerate the conformational sampling. I have several questions for this.
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?
2) If I want to perform a 200ns MD, should I perform SA many times or just once? For example, 200ns 10 times SA, 20 ns per SA? the last state of one SA is the initial state of next SA. Or 200ns just 1 SA, 40 ns for heating from 300K to 400K, 100ns MD at 400K and 60 ns for cooling?
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
3) Can I combine SA with aMD or GaMD? If this is allowed, should I insert the SA into the GaMD.in file? Just like the following
&cntrl
imin=0, irest=0, ntx=1,
ioutfm=1, nstlim=100000000, dt=0.002,
ntt=3, gamma_ln=5.0, ig=-1,
tempi=310.0, temp0=310.0, ntp=0, ntb=1, ntc=2, ntf=2,
cut=10, ntwr=10000, ntpr=10000, ntwx=10000,
ntwe=10000, iwrap=1, ntr=0,
igamd=3, iE=1, irest_gamd=1,
ntcmd=0, nteb=0, ntave=200000,
ntcmdprep=0, ntebprep=0,
sigma0P=6.0, sigma0D=6.0
&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
Thank you!
Qiao Xue
xmgign.126.com
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Received on Tue Jul 03 2018 - 02:00:03 PDT
