Hi Jason,
Thanks again. I had diffed the files as well, and based on that thought
energies should indeed be zero with exclusions2.prmtop.
My first guess as to why your input gives the expected result, whereas ours
didn't was right:
When you remove igb=6 from the input (effectively setting igb=0), then the
energies aren't zero and identical as with the original prmtop.
I hadn't realized that for this small test system, igb=0 and igb=6 wouldn't
be equivalent.
BTW, I tried setting "igb=0, eedmeth=4", which should be the true
equivalent of igb=6, but eedmeth wasn't understood:
Cannot match namelist object name eedmeth
namelist read: missplaced = sign
All the best,
Marc
On 7 December 2011 01:07, Jason Swails <jason.swails.gmail.com> wrote:
> On Tue, Dec 6, 2011 at 3:35 PM, Marc van der Kamp
> <marcvanderkamp.gmail.com>wrote:
>
> > Hi Jason,
> >
> > Yes, I think the student originally put them in one command, but played
> > around as it didn't seem to work.
> > I get the same prmtop (only timestamp differs) when I do use the combined
> > command, and the correct atoms (all 4 ions) are selected by the mask.
> >
>
> When I diffed the 2 topologies you gave me, I got this:
>
> $ diff -w 4ions.prmtop exclusions2.prmtop
> 1c1
> < %VERSION VERSION_STAMP = V0001.000 DATE = 12/06/11 15:38:03
>
> ---
> > %VERSION VERSION_STAMP = V0001.000 DATE = 12/06/11 13:59:27
> 8c8
> < 4 4 0 0 0 0 0 0 2
> 0
> ---
> > 13 4 0 0 0 0 0 0 2
> 0
> 25c25
> < 1 1 1 1
> ---
> > 6 4 2 1
> 91c91,92
> < 0 0 0 0
> ---
> > 2 2 3 3 4 4 3 3 4
> 4
> > 4 4 0
>
> Clearly the exclusion atom list is different here. (I've fixed parmed so
> it doesn't duplicate identical exclusions like above (2 2 3 3 4 4 3 3 4 4 4
> 4 0 should be 2 3 4 3 4 4 0) but the results from sander remain the same).
>
> >From the original prmtop I get the following in my mdout file:
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 1.0587E+07 4.5553E+07 1.1102E+08 Cl- 2
>
> BOND = 0.0000 ANGLE = 0.0000 DIHED =
> 0.0000
> VDWAALS = 10587886.4492 EEL = -469.5927 EGB =
> 0.0000
> 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT =
> 0.0000
>
>
> >From the exclusions2.prmtop I get:
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 0.0000E+00 0.0000E+00 0.0000E+00 Na+ 1
>
> BOND = 0.0000 ANGLE = 0.0000 DIHED =
> 0.0000
> VDWAALS = 0.0000 EEL = 0.0000 EGB =
> 0.0000
> 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT =
> 0.0000
>
>
> So I'm not quite sure why you were getting what you were getting. Here's
> my mdin file:
>
> input file
> &cntrl
> imin=1, maxcyc=1, ntb=0, igb=6, cut=9999,
> /
>
> Thanks in advance for your help!
> > Marc
> > PS I note that exclusions2.prmtop is a lot smaller than the original
> > 4ions.prmtop, but I don't think this is the problem
> >
>
> This is due to whitespace. leap prints every line in the prmtop file with
> 80 characters (filling the empty ones with spaces). parmed does not have
> those spaces, which is why the file size is smaller.
>
> All the best,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Wed Dec 07 2011 - 02:30:02 PST
