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

Date: Thu, 20 Sep 2018 11:48:35 -0300 (UYT)

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 300ºK the RMS(T) is ~ 300 * 0.02773501 ~ 8ºK

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 Thu Sep 20 2018 - 08:00:04 PDT

Date: Thu, 20 Sep 2018 11:48:35 -0300 (UYT)

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 300ºK the RMS(T) is ~ 300 * 0.02773501 ~ 8ºK

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 Thu Sep 20 2018 - 08:00:04 PDT

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