Re: [AMBER] questions about the input file of MD process

From: Francesco Oteri <>
Date: Sun, 13 Mar 2011 15:41:04 +0100

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 - 08:00:04 PDT
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