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From: Rajesh Raju <rajesh.raju.mail.chem.tamu.edu>

Date: Wed, 06 Jul 2011 10:59:32 -0500

Dear Amber users,

I am working on DNA-protein interactions. I have followed the

following steps:

[1] Minimization of water box and counter ions keeping DNA and protein

fixed with a restrained force of 500kcal/mol

[2] Complete minimization of the whole system

[3] Heated the system from 0 to 100 K in 100ps, then from 100 to 200

in 100ps and in the last stage from 200 to 300 in 100ps. So overall

time is 300ps for the heating stage. Some of the simulations I used

1fs time steps, and some of them i used 1fs.

4] Equilibration in 3 steps

First step: Equilibrated the system at constant pressure for

100ps with a restraint force of 10 kcal mol-1 on the protein and DNA.

Second step: Equilibrated the system at constant pressure for

100ps with a restraint force of 1 kcal mol-1 on the protein and DNA.

third step: Free equilibration without any constraints. some of

the simulations I performed 1ns equilibration, some of them I

performed 2ns. Also I used time steps 1 fs and 2fs for some of the

simulations.

[5] production stage simulation for 4ns. Except for one simulation (C)

all other simulations are in NVT ensemble. For prodution stage

simulations I used only 2fs time steps.

I have performed 9 (A-I) different simulations with different

temperature coupling parameter (gamma_ln ) and pressure couling

parameters (taup).

For simulation A: gamma_ln=2, taup=2, dt=1 fs for heating

and equilbration, Equilibration stage3 1ns

For simulation B: gamma_ln=3, taup=3, dt=1 fs for heating

and equilbration, Equilibration stage3 1ns

For simulation C: gamma_ln=2, taup=2, dt=1 fs for heating

and equilbration, Equilibration stage3 1ns, production

ensemble NPT

For simulation D: gamma_ln=2, taup=5, dt=1 fs for heating

and equilbration, Equilibration stage3 1ns

For simulation E: gamma_ln=2, taup=1, dt=2 fs for heating

and equilbration, Equilibration stage3 1ns

For simulation F: gamma_ln=3, taup=3, dt=2 fs for heating

and equilbration, Equilibration stage3 1ns

For simulation G: gamma_ln=1, taup=1, dt=2 fs for heating

and equilbration, Equilibration stage3 1ns

For simulation H: gamma_ln=1, taup=1, dt=2 fs for heating

and equilbration, Equilibration stage3 2ns

For simulation I: gamma_ln=2, taup=2, dt=2 fs for heating

and equilbration, Equilibration stage3 2ns

Notes: B and F differs only in the time step(dt), G and H differs in

the equlibration stage3 length

I calculated the RMSD deviations withrest to the first frame (BLACK

lines in the RMSD plots) in the production stage and also with repect

to the minimized structure after minimzation step2 (RED lines).. I

have attached the RMSD plots. The RMSD plots shows a large variation

upon changing the simulation parameters..?

My questions:

If these trajectories differ by changing the simulations parameters,

how we can trust these results?

Is there any 'best parameters for gamma_ln and taup.

Is there any problems in the MD protocol which I followed?

What is the reason for the odd behaviour in the RMSD plots and what

should I do to get a stable MD trajectory?

This is the sample inputfile I used for the simulation A:

My inputs: I just changed the respective parameters (gamma, taup, dt,

simulation lenghth) in the input files

Min1:

Minimization solvent + ions Stage 1

&cntrl

imin = 1,

maxcyc = 10000,

ncyc = 5000,

ntb = 1,

ntr = 1,

cut = 12.0

/

Hold the Solute fixed

500.0

RES 1 437

END

END

Min2.in

Minimization whole system

&cntrl

imin = 1,

maxcyc = 10000,

ncyc = 5000,

ntb = 1,

ntr = 0,

cut = 12.0

/

Heat1:

Heating Stage 1

&cntrl

imin = 0,

irest = 0,

ntx = 1,

ntb = 1,

cut = 12.0,

ntr = 1,

ntc = 2,

ntf = 2,

tempi = 0.0,

temp0 = 100.0,

ntt = 3,

gamma_ln = 2.0,

nstlim = 100000, dt = 0.001

ntpr = 1000, ntwx = 1000, ntwr = 1000

/

weak restraints on solute

10.0

RES 1 437

END

END

Heat2:

Heating Stage 2

&cntrl

imin = 0,

irest = 0,

ntx = 1,

ntb = 1,

cut = 12.0,

ntr = 1,

ntc = 2,

ntf = 2,

tempi = 100.0,

temp0 = 200.0,

ntt = 3,

ig = -1,

gamma_ln = 2.0,

nstlim = 100000, dt = 0.001

ntpr = 1000, ntwx = 1000, ntwr = 1000

/

weak restraints on solute

10.0

RES 1 437

END

END

Heating Stage 3

&cntrl

imin = 0,

irest = 0,

ntx = 1,

ntb = 1,

cut = 12.0,

ntr = 1,

ntc = 2,

ntf = 2,

tempi = 200.0,

temp0 = 300.0,

ntt = 3,

ig = -1,

gamma_ln = 2.0,

nstlim = 100000, dt = 0.001

ntpr = 1000, ntwx = 1000, ntwr = 1000

/

weak restraints on solute

10.0

RES 1 437

END

END

Equilibration Stage 1

&cntrl

imin=0,irest=1,ntx=5,

ntc=2,ntf=2,

cut=12.0,

ntb=2, ntp=1, taup=2.0,

ntt=3, gamma_ln=2.0, ig=-1,

temp0=300.0,

tempi=300.0,

ntr=1,

nstlim=100000,dt=0.001,

ntpr=1000, ntwx=1000, ntwr=1000

/

weak restraints on solute

10.0

RES 1 437

END

END

Equilibration Stage 2

&cntrl

imin=0,irest=1,ntx=5,

ntc=2,ntf=2,

cut=12.0,

ntb=2, ntp=1, taup=2.0,

ntt=3, gamma_ln=2.0, ig=-1,

temp0=300.0,

tempi=300.0,

ntr=1,

nstlim=100000,dt=0.001,

ntpr=1000, ntwx=1000, ntwr=1000

/

weak restraints on solute

1.0

RES 1 437

END

END

Equilibration Stage 3

&cntrl

imin=0,irest=1,ntx=5,

ntc=2,ntf=2,

cut=12.0,

ntb=2, ntp=1, taup=2.0,

ntt=3, gamma_ln=2.0, ig=-1,

temp0=300.0,

tempi=300.0,

nstlim=1000000,dt=0.001,

ntpr=1000, ntwx=1000, ntwr=1000

/

MD Production Stage

&cntrl

imin = 0,

irest = 1,

ntx = 5,

ntb = 1,

cut = 12.0,

ntc = 2,

ntf = 2,

temp0 = 300.0,

tempi = 300.0,

ntt = 3,

ig = -1,

gamma_ln = 2.0,

nstlim = 2000000, dt = 0.002

ntpr = 1000, ntwx = 1000, ntwr = 1000

/

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Received on Wed Jul 06 2011 - 09:00:06 PDT

Date: Wed, 06 Jul 2011 10:59:32 -0500

Dear Amber users,

I am working on DNA-protein interactions. I have followed the

following steps:

[1] Minimization of water box and counter ions keeping DNA and protein

fixed with a restrained force of 500kcal/mol

[2] Complete minimization of the whole system

[3] Heated the system from 0 to 100 K in 100ps, then from 100 to 200

in 100ps and in the last stage from 200 to 300 in 100ps. So overall

time is 300ps for the heating stage. Some of the simulations I used

1fs time steps, and some of them i used 1fs.

4] Equilibration in 3 steps

First step: Equilibrated the system at constant pressure for

100ps with a restraint force of 10 kcal mol-1 on the protein and DNA.

Second step: Equilibrated the system at constant pressure for

100ps with a restraint force of 1 kcal mol-1 on the protein and DNA.

third step: Free equilibration without any constraints. some of

the simulations I performed 1ns equilibration, some of them I

performed 2ns. Also I used time steps 1 fs and 2fs for some of the

simulations.

[5] production stage simulation for 4ns. Except for one simulation (C)

all other simulations are in NVT ensemble. For prodution stage

simulations I used only 2fs time steps.

I have performed 9 (A-I) different simulations with different

temperature coupling parameter (gamma_ln ) and pressure couling

parameters (taup).

For simulation A: gamma_ln=2, taup=2, dt=1 fs for heating

and equilbration, Equilibration stage3 1ns

For simulation B: gamma_ln=3, taup=3, dt=1 fs for heating

and equilbration, Equilibration stage3 1ns

For simulation C: gamma_ln=2, taup=2, dt=1 fs for heating

and equilbration, Equilibration stage3 1ns, production

ensemble NPT

For simulation D: gamma_ln=2, taup=5, dt=1 fs for heating

and equilbration, Equilibration stage3 1ns

For simulation E: gamma_ln=2, taup=1, dt=2 fs for heating

and equilbration, Equilibration stage3 1ns

For simulation F: gamma_ln=3, taup=3, dt=2 fs for heating

and equilbration, Equilibration stage3 1ns

For simulation G: gamma_ln=1, taup=1, dt=2 fs for heating

and equilbration, Equilibration stage3 1ns

For simulation H: gamma_ln=1, taup=1, dt=2 fs for heating

and equilbration, Equilibration stage3 2ns

For simulation I: gamma_ln=2, taup=2, dt=2 fs for heating

and equilbration, Equilibration stage3 2ns

Notes: B and F differs only in the time step(dt), G and H differs in

the equlibration stage3 length

I calculated the RMSD deviations withrest to the first frame (BLACK

lines in the RMSD plots) in the production stage and also with repect

to the minimized structure after minimzation step2 (RED lines).. I

have attached the RMSD plots. The RMSD plots shows a large variation

upon changing the simulation parameters..?

My questions:

If these trajectories differ by changing the simulations parameters,

how we can trust these results?

Is there any 'best parameters for gamma_ln and taup.

Is there any problems in the MD protocol which I followed?

What is the reason for the odd behaviour in the RMSD plots and what

should I do to get a stable MD trajectory?

This is the sample inputfile I used for the simulation A:

My inputs: I just changed the respective parameters (gamma, taup, dt,

simulation lenghth) in the input files

Min1:

Minimization solvent + ions Stage 1

&cntrl

imin = 1,

maxcyc = 10000,

ncyc = 5000,

ntb = 1,

ntr = 1,

cut = 12.0

/

Hold the Solute fixed

500.0

RES 1 437

END

END

Min2.in

Minimization whole system

&cntrl

imin = 1,

maxcyc = 10000,

ncyc = 5000,

ntb = 1,

ntr = 0,

cut = 12.0

/

Heat1:

Heating Stage 1

&cntrl

imin = 0,

irest = 0,

ntx = 1,

ntb = 1,

cut = 12.0,

ntr = 1,

ntc = 2,

ntf = 2,

tempi = 0.0,

temp0 = 100.0,

ntt = 3,

gamma_ln = 2.0,

nstlim = 100000, dt = 0.001

ntpr = 1000, ntwx = 1000, ntwr = 1000

/

weak restraints on solute

10.0

RES 1 437

END

END

Heat2:

Heating Stage 2

&cntrl

imin = 0,

irest = 0,

ntx = 1,

ntb = 1,

cut = 12.0,

ntr = 1,

ntc = 2,

ntf = 2,

tempi = 100.0,

temp0 = 200.0,

ntt = 3,

ig = -1,

gamma_ln = 2.0,

nstlim = 100000, dt = 0.001

ntpr = 1000, ntwx = 1000, ntwr = 1000

/

weak restraints on solute

10.0

RES 1 437

END

END

Heating Stage 3

&cntrl

imin = 0,

irest = 0,

ntx = 1,

ntb = 1,

cut = 12.0,

ntr = 1,

ntc = 2,

ntf = 2,

tempi = 200.0,

temp0 = 300.0,

ntt = 3,

ig = -1,

gamma_ln = 2.0,

nstlim = 100000, dt = 0.001

ntpr = 1000, ntwx = 1000, ntwr = 1000

/

weak restraints on solute

10.0

RES 1 437

END

END

Equilibration Stage 1

&cntrl

imin=0,irest=1,ntx=5,

ntc=2,ntf=2,

cut=12.0,

ntb=2, ntp=1, taup=2.0,

ntt=3, gamma_ln=2.0, ig=-1,

temp0=300.0,

tempi=300.0,

ntr=1,

nstlim=100000,dt=0.001,

ntpr=1000, ntwx=1000, ntwr=1000

/

weak restraints on solute

10.0

RES 1 437

END

END

Equilibration Stage 2

&cntrl

imin=0,irest=1,ntx=5,

ntc=2,ntf=2,

cut=12.0,

ntb=2, ntp=1, taup=2.0,

ntt=3, gamma_ln=2.0, ig=-1,

temp0=300.0,

tempi=300.0,

ntr=1,

nstlim=100000,dt=0.001,

ntpr=1000, ntwx=1000, ntwr=1000

/

weak restraints on solute

1.0

RES 1 437

END

END

Equilibration Stage 3

&cntrl

imin=0,irest=1,ntx=5,

ntc=2,ntf=2,

cut=12.0,

ntb=2, ntp=1, taup=2.0,

ntt=3, gamma_ln=2.0, ig=-1,

temp0=300.0,

tempi=300.0,

nstlim=1000000,dt=0.001,

ntpr=1000, ntwx=1000, ntwr=1000

/

MD Production Stage

&cntrl

imin = 0,

irest = 1,

ntx = 5,

ntb = 1,

cut = 12.0,

ntc = 2,

ntf = 2,

temp0 = 300.0,

tempi = 300.0,

ntt = 3,

ig = -1,

gamma_ln = 2.0,

nstlim = 2000000, dt = 0.002

ntpr = 1000, ntwx = 1000, ntwr = 1000

/

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