AMBER Archive (2007)

Subject: Re: AMBER: &dipole input and some questions on using polarizable force fields

From: Seongeun Yang (seongeun_at_korea.ac.kr)
Date: Tue Oct 30 2007 - 00:14:13 CST


Hi Ross,
Thanks for your reply.
I did again the test job with the following steps in amber9, loaded mdcrd in VMD,
but I don't see any strange thing happen at all.

> Can you try setting ntpr=1 and ntwx=1. Then take a look at the mdcrd file
> that is created in something like VMD and see if you can see anything
> strange happening to the structure. If you could also post the mdout file
> it will be easier to try and work out what is going on.

The topology file is made by:
     source leaprc.ff02pol.r1
     nma = sequence {ACE NME}
     solvateoct nma TIP3PBOX 8.0
     saveamberparmpol nma nma.top nma.crd

With mdin:
*************************************
 Heating to 100 K
 &cntrl
  imin = 0, ntx = 1,
  irest = 0, iwrap = 1,
  ntpr = 1, ntwe = 10,
  ntwr = 10, ntwx = 1,
  ntave = 500,
  ntf = 2, ntc = 2, ntb = 2,
  cut = 8.0, nsnb = 10,
  nstlim = 500, dt = 0.002,
  tempi = 5.0, temp0 = 100.0,
  ntt = 1, tautp = 1.0,
  ntp = 1, pres0 = 1.0, taup = 1.0,
  ipol = 1,
 /
 &ewald
  indmeth = 1,
 /

*************************************

Then, the last part of mdout says like this.
------------------------------------------------------------------------------
 NSTEP = 229 TIME(PS) = 0.458 TEMP(K) = 43.66 PRESS = -3130.7
 Etot = -3468.7970 EKtot = 81.5617 EPtot = -3550.3588
 BOND = 0.3924 ANGLE = 0.6519 DIHED = 2.8995
 1-4 NB = 0.9568 1-4 EEL = -58.8164 VDWAALS = 608.8347
 EELEC = -4103.3945 EHBOND = 0.0000 RESTRAINT = 0.0000
 EKCMT = 67.6928 VIRIAL = 832.7742 VOLUME = 11318.5174
 EPOLZ = -1.8831
 Dipole convergence: rms = 0.194E-04 iters = 2.00
                                                    Density = 0.8275
 ------------------------------------------------------------------------------

 Cutoff list exceeds largest sphere in unit cell!!
 Big problems with imaging!!
 a,b,c = 24.4937980338375 24.4937980338375
   24.4937980338375
 alpha,beta,gamma = 109.471219000000 109.471219000000
   109.471219000000
 cutlist,sphere = 10.0000000000000 9.99955167855377

*****

If you have any idea to fix the problem, please let me know.
Otherwise, I have no choice but to use "solvatebox".

Thanks.

Seongeun
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