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From: Matias Machado <mmachado.pasteur.edu.uy>

Date: Fri, 21 Sep 2018 09:06:16 -0300 (UYT)

Dear Nick,

I'm not an AMBER code developer but my guess is that this nstlim length is about the limit for any integer number (of 32-bit)...

Check this out: [https://en.wikipedia.org/wiki/2,147,483,647]

So it may be a computational limitation rather than a code one...

Best,

Matias

------------------------------------

PhD.

Researcher at Biomolecular Simulations Lab.

Institut Pasteur de Montevideo | Uruguay

[http://pasteur.uy/en/laboratorios-eng/lsbm]

[http://www.sirahff.com]

----- Mensaje original -----

De: "Nikolay N. Kuzmich" <nnkuzmich.gmail.com>

Para: amber.ambermd.org

Enviados: Viernes, 21 de Septiembre 2018 6:34:30

Asunto: Re: [AMBER] AMBER ntslim limit

Dear Matias and Amber users,

2) several days ago I tried to start a 5 microseconds production run

simulation of a small protein

in implicit solvent (igb=8) but a runtime error occured:

At line 717 of file mdin_ctrl_dat.F90 (unit = 5, file =

'abk_gb_ProdRun5us.in')

Fortran runtime error: Integer overflow while reading item 4

Error termination. Backtrace:

nick.user039l:~/amber18/ABK_protein_MD> #0 0x2b67f0db05cd in ???

#1 0x2b67f0db1115 in ???

#2 0x2b67f0db187a in ???

#3 0x2b67f0f14d79 in ???

#4 0x2b67f0f1523b in ???

#5 0x2b67f0f18be3 in ???

#6 0x2b67f0f1a65f in ???

#7 0x2b67f0f2254f in ???

#8 0x2b67f0f22808 in ???

#9 0x4282cf in ???

#10 0x4cad6d in ???

#11 0x4b1a59 in ???

#12 0x40612c in ???

#13 0x2b67f1cb1f49 in ???

#14 0x419219 in ???

at ../sysdeps/x86_64/start.S:120

#15 0xffffffffffffffff in ???

So the item 4 was actually ntslim; neither 2500000000 nor 3000000000 worked,

only run with ntslim=2000000000 could be started.

I have found reports of similar issues in the Amber mail reflector

but just wanted to make it clear.

P.S. Matias, thank you for the answer on the 1st question

Kind regards,

Nick

______________________________________________________________________

Dear Nick,

1. A similar issue was already addressed in [

https://www.researchgate.net/post/How_can_I_reduce_temperature_oscillation_in_NVT_ensemble_simulation_of_FPMD

]

According to thermodynamics, the temperature fluctuation in a closed system

containing N atoms is proportional to 1/sqrt(N), that is essentially what

you expect from a normal distribution as is the case in a proper canonical

ensemble (I mean "proper" if you are not using the Berendsen thermostat).

Hence, the larger the system the smaller the temperature fluctuations...

That is the reason why in implicit simulations you expect larger

fluctuations comparing to explicit ones...

Just to give you an example: for a system of 1300 particles you would

expect a fluctuation of 1/sqrt(1300) = 0.02773501 (or 2.7%), so running at

300?K the RMS(T) is ~ 300 * 0.02773501 ~ 8?K

2. I don't understand this question... are you not able to set more nstlim

steps? Then you can just continue the simulation up to the desire time...

Best,

Matias

------------------------------------

PhD.

Researcher at Biomolecular Simulations Lab.

Institut Pasteur de Montevideo | Uruguay

[http://pasteur.uy/en/laboratorios-eng/lsbm]

[http://www.sirahff.com]

----- Mensaje original -----

De: "Nikolay N. Kuzmich" <nnkuzmich.gmail.com>

Para: amber.ambermd.org

Enviados: Jueves, 20 de Septiembre 2018 9:29:24

Asunto: [AMBER] Temperature RMS, ntslim limit

Dear Amber users and developers,

1. is the temperature RMS=10.0K within the limits for a good quality

simulation conducted in implicit solvent? This is the mdin file:

Stage 2 equlibration 0-5ns

&cntrl

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

ntc=2, ntf=2, ig=-1, ntt=3,

tautp=0.5, tempi=300.0, temp0=300.0,

ntpr=500, ntwx=500, saltcon=0.15, ntb=0,

igb=8, gamma_ln=1.0, cut=999., rgbmax=999.

/

I just noticed that RMS(T) of explicit solvent simulation was remarkably

lower...

2. Is ntslim=2 000 000 000 really a limit for the input?

Kind regards,

Nick

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

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

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

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

Received on Fri Sep 21 2018 - 05:30:04 PDT

Date: Fri, 21 Sep 2018 09:06:16 -0300 (UYT)

Dear Nick,

I'm not an AMBER code developer but my guess is that this nstlim length is about the limit for any integer number (of 32-bit)...

Check this out: [https://en.wikipedia.org/wiki/2,147,483,647]

So it may be a computational limitation rather than a code one...

Best,

Matias

------------------------------------

PhD.

Researcher at Biomolecular Simulations Lab.

Institut Pasteur de Montevideo | Uruguay

[http://pasteur.uy/en/laboratorios-eng/lsbm]

[http://www.sirahff.com]

----- Mensaje original -----

De: "Nikolay N. Kuzmich" <nnkuzmich.gmail.com>

Para: amber.ambermd.org

Enviados: Viernes, 21 de Septiembre 2018 6:34:30

Asunto: Re: [AMBER] AMBER ntslim limit

Dear Matias and Amber users,

2) several days ago I tried to start a 5 microseconds production run

simulation of a small protein

in implicit solvent (igb=8) but a runtime error occured:

At line 717 of file mdin_ctrl_dat.F90 (unit = 5, file =

'abk_gb_ProdRun5us.in')

Fortran runtime error: Integer overflow while reading item 4

Error termination. Backtrace:

nick.user039l:~/amber18/ABK_protein_MD> #0 0x2b67f0db05cd in ???

#1 0x2b67f0db1115 in ???

#2 0x2b67f0db187a in ???

#3 0x2b67f0f14d79 in ???

#4 0x2b67f0f1523b in ???

#5 0x2b67f0f18be3 in ???

#6 0x2b67f0f1a65f in ???

#7 0x2b67f0f2254f in ???

#8 0x2b67f0f22808 in ???

#9 0x4282cf in ???

#10 0x4cad6d in ???

#11 0x4b1a59 in ???

#12 0x40612c in ???

#13 0x2b67f1cb1f49 in ???

#14 0x419219 in ???

at ../sysdeps/x86_64/start.S:120

#15 0xffffffffffffffff in ???

So the item 4 was actually ntslim; neither 2500000000 nor 3000000000 worked,

only run with ntslim=2000000000 could be started.

I have found reports of similar issues in the Amber mail reflector

but just wanted to make it clear.

P.S. Matias, thank you for the answer on the 1st question

Kind regards,

Nick

______________________________________________________________________

Dear Nick,

1. A similar issue was already addressed in [

https://www.researchgate.net/post/How_can_I_reduce_temperature_oscillation_in_NVT_ensemble_simulation_of_FPMD

]

According to thermodynamics, the temperature fluctuation in a closed system

containing N atoms is proportional to 1/sqrt(N), that is essentially what

you expect from a normal distribution as is the case in a proper canonical

ensemble (I mean "proper" if you are not using the Berendsen thermostat).

Hence, the larger the system the smaller the temperature fluctuations...

That is the reason why in implicit simulations you expect larger

fluctuations comparing to explicit ones...

Just to give you an example: for a system of 1300 particles you would

expect a fluctuation of 1/sqrt(1300) = 0.02773501 (or 2.7%), so running at

300?K the RMS(T) is ~ 300 * 0.02773501 ~ 8?K

2. I don't understand this question... are you not able to set more nstlim

steps? Then you can just continue the simulation up to the desire time...

Best,

Matias

------------------------------------

PhD.

Researcher at Biomolecular Simulations Lab.

Institut Pasteur de Montevideo | Uruguay

[http://pasteur.uy/en/laboratorios-eng/lsbm]

[http://www.sirahff.com]

----- Mensaje original -----

De: "Nikolay N. Kuzmich" <nnkuzmich.gmail.com>

Para: amber.ambermd.org

Enviados: Jueves, 20 de Septiembre 2018 9:29:24

Asunto: [AMBER] Temperature RMS, ntslim limit

Dear Amber users and developers,

1. is the temperature RMS=10.0K within the limits for a good quality

simulation conducted in implicit solvent? This is the mdin file:

Stage 2 equlibration 0-5ns

&cntrl

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

ntc=2, ntf=2, ig=-1, ntt=3,

tautp=0.5, tempi=300.0, temp0=300.0,

ntpr=500, ntwx=500, saltcon=0.15, ntb=0,

igb=8, gamma_ln=1.0, cut=999., rgbmax=999.

/

I just noticed that RMS(T) of explicit solvent simulation was remarkably

lower...

2. Is ntslim=2 000 000 000 really a limit for the input?

Kind regards,

Nick

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

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

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

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

Received on Fri Sep 21 2018 - 05:30:04 PDT

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