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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Received on Sun Oct 28 2007 - 06:07:22 PDT
