Re: [AMBER] Temperature RMS, ntslim limit

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

Dear Nick,

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
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Received on Thu Sep 20 2018 - 08:00:04 PDT
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