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 - 08:30:03 PDT
