AMBER Archive (2009)

Subject: [AMBER] NPT md with PME method for a water box

From: Jeffrey (jeffry20072008_at_yahoo.cn)
Date: Wed Jan 14 2009 - 08:41:24 CST

Dear all,

     I am going to perform md simulation of a water box under NPT ensemble. First, I built the water box by packmol and then created the .prmtop, inpcrd files in xleap. In order to use the pme method for electrostatic interaction, the setBox command was used to add the periodic boundary conditions to the unit.

My questions are:

1. minimization:
input:
-------
 energy minimization for starting structures

 &cntrl
        imin=1, maxcyc=2000, ncyc=2000, ntpr=20,
        ntx=1,irest=0,
        ntb=1, cut=10.0
/
 &ewald
    eedmeth=5,
 /
----------

output:
-------
  NSTEP ENERGY RMS GMAX NAME NUMBER
     1020 -1.3947E+09 1.2216E+11 8.6032E+12 H1 677

 BOND = 30799.0575 ANGLE = 0.0000 DIHED = 0.0000
 VDWAALS = 13173.5998 EEL = ************* HBOND = 0.0000
 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000

   NSTEP ENERGY RMS GMAX NAME NUMBER
     1040 -5.1545E+12 2.7440E+16 1.9325E+18 O 3196

 BOND = 30799.3577 ANGLE = 0.0000 DIHED = 0.0000
 VDWAALS = 13173.8199 EEL = ************* HBOND = 0.0000
 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000
----------

Where the energy jumped from -1.3947E+09 to -5.1545E+12 for only 20 steps and the ele interaction was so not printed. Are these behaviors reasonable?

2. equilibration and production runs:
Which temperature method should I choose? NTT=1 or NTT=3? It is said in the amber mannual that "Unless you are sure you know what you are doing, please don't use ntt=1!", but in the benchmark (ambermd.org) input files, I notice that the temperature method is set to ntt=1. If ntt=3 is adopted, what the best values of gamma_ln at heating, equilibrating, production stages?

Thanks so much for the time.
Have a nice day. 

----
Jeffrey  

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