[AMBER] TIP5P water simulation

From: °­Çö¾Æ <hakang.postech.ac.kr>
Date: Wed, 6 Mar 2013 20:31:48 +0900

Hello,

 

Now I am doing TIP5P water simulation.

 

Unlike TIP3P and TIP4P water simulation,
in TIP5P water simulation, make some troubles.

 

I have followed below procedure.

 

1) In xleap

 

source leaprc.ff99SB

loadAmberParams frcmod.tip5p

solvateBox TP5 TP5 12 0.75

saveAmberParm TP5 tip5p.prmtop tip5p.inpcrd

 

©£ Obtain tip5p.prmtop and tip5p.inpcrd files

 

2) Energy minimization

 

mdin file

 

&cntrl

  igb = 0,

 dielc = 1.0,

  ntx = 1,

  irest = 0,

  ntb = 1,

  ntp = 0,

  temp0 = 300.0,

  ntf = 1,

  ntc = 1,

  tol = 0.0005,

  cut = 8.0,

  ibelly = 0,

  dt = 0.002,

  maxcyc = 25000,

  imin = 1,

  ntmin = 2,

  ntpr = 1,

  ntwx = 0,

  ntt = 1,

  ntr = 0,

/Hold the sugar fixed

5.0

RES 1

&END

&end

 

&ewald

  nfft1 = 48, nfft2 = 48, nfft3 = 36,

  order = 4, ischrgd = 0, verbose = 0, ew_type = 0,

  dsum_tol = 0.00001, netfrc = 1, skinnb = 1.0,

&end

 

After energy minimization with above mdin file, generated mdinfo file is
very strange.

 

NSTEP ENERGY RMS GMAX NAME NUMBER

  25000 -7.9681E+06 4.5491E+10 2.2031E+12 O 1

 

BOND = 230.2710 ANGLE = 0.0000 DIHED = 0.0000

VDWAALS = -171.2044 EEL = -7968132.9306 HBOND = 0.0000

1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000

 

RMS and GMAX values seem to diverge.

 

I cannot find what is the problem with above procedure.

Please help me.

 

Thanks in advance.

 

 

Best regards,

Hyeona Kang

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Received on Wed Mar 06 2013 - 04:00:03 PST
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