AMBER Archive (2006)

Subject: AMBER: how to choose the parameter for the production/sampling run after the equilibration run

From: hbluo (hbluo_at_hkbu.edu.hk)
Date: Fri Nov 03 2006 - 19:57:01 CST

Dear Amber Users,

We would like to conduct a molcular dynamics of 16 ns (8 ns for the equilibration run and 8 ns for the production/sampling run) in NPT ensemble. But I'm not quite sure if the following parameter is appropriate for the production/sampling run in AMBER 8.0. The main difference in my setting between the two runs is in the GAMMA_LN (Temperature) and TAUP (pressure).

--------------------------------------------------------------------------------------------
Equilibration run:

     ntb = 2, ntp = 1, TAUP = 2.0,
     temp0 = 300.0, ntt = 3, tautp = 2.0, vlimit = 20.0, GAMMA_LN = 1.0,

Production/sampling run:
     ntb = 2, ntp = 1, TAUP = 1.0
     temp0 = 300.0, ntt = 3, tautp = 2.0, vlimit = 20.0, GAMMA_LN = 5.0,
--------------------------------------------------------------------------------------------

Any information will be appreciated.

Thank you in advance!
กกกก
Haibin Luo
hbluo_at_hkbu.edu.hk
---------------------------------------------
Chemistry Department, Hong Kong Baptist University
Kowloon Tong, Hong Kong
Voice: +(852) 3411-5815
Fax: +(852) 3411-7348
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