AMBER Archive (2007)

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

From: Seongeun Yang (seongeun_at_korea.ac.kr)
Date: Thu Oct 25 2007 - 08:11:48 CDT

Hi all,

I'm doing test runs using ff02 force field and have some questions.

Does the box shape matter?
I tried "solvateoct NMA TIP3PBOX 8.0 iso" with the following md input.
--------------------------------------------
 &cntrl
  imin = 0, ntx = 1,
  irest = 0, iwrap = 1,
  ntpr = 2, ntwe = 50,
  ntwr = 50, ntwx = 0,
  ntave = 1000,
  ntf = 2, ntc = 2, ntb = 2,
  cut = 8.0, nsnb = 10,
  nstlim = 10000, dt = 0.001,
  tempi = 300.0, temp0 = 300.0,
  ntt = 1, tautp = 1.0,
  ntp = 1, pres0 = 1.0, taup = 1.0,
  ipol = 1,
 /
 &ewald
  indmeth = 1,
 /
---------------------------------------------
Then the run crashed after some steps with the messages:
   SANDER BOMB in subroutine nonbond_list
    volume of ucell too big, too many subcells
    list grid memory needs to be reallocated, restart sander

Or does the box dimension matter with solvateoct?
But when I used a cubic box made by "solvatebox NMA TIP3PBOX 8.0 iso", there was no problem.

Secondly, I want to print dipole values in output and added the following lines right below the above input.
--------------------------
&dipoles
GROUP1
RES 1 2
END
END
/
--------------------------
But I got an error message in mdout such as
         rfree: End of file on unit 5

Please let me know what's wrong or missing with this.
Thanks for your reply in advance.

Seongeun
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