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From: <xmgign.126.com>

Date: Tue, 3 Jul 2018 16:32:16 +0800

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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AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Tue Jul 03 2018 - 02:00:03 PDT

Date: Tue, 3 Jul 2018 16:32:16 +0800

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

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Tue Jul 03 2018 - 02:00:03 PDT

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