Thank for the clarification,
in each case to be valid this pressure coupling must be enabled with ntp>0
Il 13/03/2011 16:07, asakiayumikio.gmail.com ha scritto:
> Francesco Oteri！
>
>
> thank you, i just look at the output file, if i did not setup the pres0, it went to 1 as a default!
>
> and at last, thank you for sharing your experience of how to do with the steps!
> 2011-03-13
>
> asakiayumikio.gmail.com
>
>
>
>
>
> 发件人：Francesco Oteri
> 发送日期：2011-03-13 22:41
> 收件人：amber.ambermd.org
> 抄送：
> 主题： Re: [AMBER] questions about the input file of MD process
> No problem :)
>
> The equilibrium protocolo is an art.
>
> Usually I run equlibration using the following steps:
> 1.minimization of water using a constrain force of 500kcal on protein.
> 2.minimization of the whole system (i.e. without constrain)
> 3.100ps of NVT MD at 100 Kelvin, timestep 1fs
> 4.100ps of NVT MD at 200 Kelvin, timestep 1fs
> 5.100ps of NVT MD at 300 Kelvin, timestep 1fs
> 6.100ps of NPT MD at 300 Kelvin, 1bar, timestep 1fs
>
> Production run: NPT MD at 300 Kelvin, 1bar, timestep 2fs
>
>
>
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Received on Sun Mar 13 2011 - 08:30:04 PDT
