Re: [AMBER] equilirbration at constant volume

From: David A Case <>
Date: Fri, 30 Aug 2019 12:30:19 -0400

On Fri, Aug 30, 2019, Sadaf Rani wrote:
>I am doing multistep nvt of my system in which I want to increase the
>temperature in different steps. For first step I used following input:-
>Heating up the system equilibration stage 1
> &cntrl
> nstlim=5000, dt=0.0005, ntx=1, irest=0, ntpr=500, ntwr=500, ntwx=500,
> tempi =0.0, temp0=5.0, ntt=1, tautp=2.0, ig=1
> ntb=1, ntp=0,
> ntc=2, ntf=2,
>However the temperature of system doesnot remain in the limit of 0-5 K, but
>at start it is zero K and then in next step it is above 200K.

Your initial structure has lots of stored "potential energy", that is
being converted to kinetic energy in MD. What you describe is not all
that unusual.

Try setting ntt=3, gamma_ln to 5, and temp0 to 100K. It seems likely
that you will get a good low-temperature equilibration. If not, you may
need to examine the minimzation step to see if it got stuck, or you may
have problems with the initial setup of the system.


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Received on Fri Aug 30 2019 - 10:00:02 PDT
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