Re: [AMBER] Default temperature regulation during production run: Missed to declare ntt option

From: David A Case <>
Date: Wed, 15 Jul 2020 08:08:42 -0400

On Wed, Jul 15, 2020, Jorden Cabal wrote:

>Yes sir. It is not there in the manual as far as I have searched.
>So lets us assume the system took ntt=0 by default and in that case, the
>simulation will be NVE simulation, and the temperature and pressure should
>vary. In my input file, I have used ntp=1 as well as ntb=2. From the
>manual, I have figured out that in case ntp>0 and ntb=2, one can not
>perform NVE simulation. Please correct me if I am wrong. Furthermore, the
>out file shows clearly that the RMS in the pressure of the system is 0.0
>and there are adjustments in volume. Please correct me if I am wrong.
>In my opinion, I think the system has considered ntt=1 or 2 by default in
>my case. Although, I am not sure. So, I was wondering that how can we find
>the exact input parameters considered during simulation including ntt.

The default for ntt is zero for both sander and pmemd. If nothing is printed
out about temperature, that means that ntt was set to 0 internally.

Don't look only at the RMS fluctuations in temperature; rather, look at the
profile of temperature vs. time. Depending on the size of your system, the
length of the simulation, the value of dt you used, etc., running NVE may be
fine -- for any sizeable system that one is likely to use Amber for,
differences between the NVE and NVT ensemble should be very small.

Bottom line, if the temperature vs time course looks OK, you should be fine.


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Received on Wed Jul 15 2020 - 05:30:03 PDT
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