Hi Seongeun
> Does the box shape matter?
> I tried "solvateoct NMA TIP3PBOX 8.0 iso" with the following md input.
It shouldn't matter sander should be able to handle all box shapes with
polarizable force fields. I don't think you need the iso option here. In
fact I didn't even know it existed as an option to solvateoct so I don't
know what it is doing here. Maybe it is benign, maybe not...
> --------------------------------------------
> &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,
You should probably run at least 10 to 20ps at constant volume before
changing to constant pressure. Also you are writing a restart file here
every 50 steps (very very often) and not writing a trajectory file at all
(ntwx=0). Are you sure this is what you want? I would typically write a
restart file no more often than 5,000 steps or so.
> cut = 8.0, nsnb = 10,
nsnb is not not used by default anymore - it is only used if you set
nbflag=0 so you don't need to specify it.
> nstlim = 10000, dt = 0.001,
> tempi = 300.0, temp0 = 300.0,
Hot starting at 300 K, rather than heating gradually can sometimes cause
you problems.
> ntt = 1, tautp = 1.0,
> ntp = 1, pres0 = 1.0, taup = 1.0,
> ipol = 1,
Did you use saveamberparmpol to save a prmtop with polarization info?
> ---------------------------------------------
> 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
This is strange - can you post the steps? I suspect your system has blown
up due to possibly being saved without using saveamberparmpol, being hot
started, being started with constant pressure and/or having a bad starting
structure. Try writing to the output every step (ntpr=1) and to mdcrd every
step (ntwx=1) then you can visualize the trajectory and see what is going
wrong.
> 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
This is strange - your input above looks good. Although perhaps you don't
have an initial space before the &dipoles and the /. Here is input I have
used before that works:
&dipoles
Group1 - a single water molecule
RES 1
END
Group2 - A selection of 2000 H2O mols from bulk
RES 2 2000
END
END
/
Note the leading space before & and /
Good luck
Ross
/\
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|\oss Walker
| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
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Received on Sun Oct 28 2007 - 06:07:40 PDT
