Hello everyone,
I want to consult you some questions. I have a REMD process using AMBER12. In my input files ( one of the input file is shown blow ), I use Langevin dynamics by setting ntt=3 , and use implicit water models by setting igb =2.
The input file for one replica in REMD:
&cntrl
irest=0, ntx=1,
nstlim=2000, dt=0.002,
irest=0, ntt=3, gamma_ln=1.0,
temp0=260, ig=-7039,
ntc=2, ntf=2, nscm=1000,
ntb=0, igb=2,
cut=999.0, rgbmax=999.0,
ntpr=1000, ntwx=1000, ntwr=1000,
numexchg=1000,
/
&wt TYPE='END'
/
(1) Can the Langevin dynamics and implicit water models be used in the same REMD process?
(2) When I am using Langevin dynamics, how to choose the ig value?
(3) Is it necessary to change the ig value when the simulations be restarted?
(4) Can the Langevin dynamics be repeated totally? Or can’t?
As for my progress, the jobs must be frequently restarted ( one of the restart input files is shown below).
The restart input file for one replica in REMD:
&cntrl
irest=1, ntx=5,
nstlim=2000, dt=0.002,
irest=1, ntt=3, gamma_ln=1.0,
temp0=260, ig=4000,
ntc=2, ntf=2, nscm=1000,
ntb=0, igb=2,
cut=999.0, rgbmax=999.0,
ntpr=1000, ntwx=1000, ntwr=500000,
numexchg=2000,
/
&wt TYPE='END'
/
(5) Which parameter should be modified to make sure restart normaly?
I modify the irest =1, ntx=5, but the restart trajectories are wrote in the wrong way.
(6)Should I modify the temp0 and ig at every restart time? And how?
Please give me a hand, thank you very much!
--
Wangmoye
University of Chinese Academy of Sciences
Beijing, China
2015/4/29
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Received on Wed Apr 29 2015 - 01:00:03 PDT
