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From: Jason Swails <jason.swails.gmail.com>

Date: Wed, 7 Dec 2011 08:42:42 -0500

On Wed, Dec 7, 2011 at 5:15 AM, Marc van der Kamp

<marcvanderkamp.gmail.com>wrote:

*> 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:
*

*>
*

eedmeth is a variable in the &ewald namelist. However, setting that

variable gives the same (wrong?) behavior you described above. I'm not

sure why igb=0,eedmeth=4 gives different results in this case than igb=6.

It appears that igb=0,eedmeth=4 does not obey the exclusion list, but

igb=6 does. (When I add bonds, angles, and a dihedral to the system,

igb=0,eedmeth=4 does properly exclude each atom from the non-bonded

calculation list).

Note that these 2 approaches follow different code paths. The first

(igb=0,eedmeth=4) traverses the ewald code for the EEL/VDW calculations,

whereas igb=6 traverses the GB code path for the EEL/VDW calculations, so

it would appear that only GB calculations will respect the

arbitrarily-modified exclusion list.

You can see this when igb=1 (or any other GB model), you'll get the result

you're aiming for (note, however, that the EGB energies don't change based

on the exclusion list).

HTH,

Jason

*>
*

*> 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
*

*> > _______________________________________________
*

*> > AMBER mailing list
*

*> > AMBER.ambermd.org
*

*> > http://lists.ambermd.org/mailman/listinfo/amber
*

*> >
*

*> _______________________________________________
*

*> AMBER mailing list
*

*> AMBER.ambermd.org
*

*> http://lists.ambermd.org/mailman/listinfo/amber
*

*>
*

Date: Wed, 7 Dec 2011 08:42:42 -0500

On Wed, Dec 7, 2011 at 5:15 AM, Marc van der Kamp

<marcvanderkamp.gmail.com>wrote:

eedmeth is a variable in the &ewald namelist. However, setting that

variable gives the same (wrong?) behavior you described above. I'm not

sure why igb=0,eedmeth=4 gives different results in this case than igb=6.

It appears that igb=0,eedmeth=4 does not obey the exclusion list, but

igb=6 does. (When I add bonds, angles, and a dihedral to the system,

igb=0,eedmeth=4 does properly exclude each atom from the non-bonded

calculation list).

Note that these 2 approaches follow different code paths. The first

(igb=0,eedmeth=4) traverses the ewald code for the EEL/VDW calculations,

whereas igb=6 traverses the GB code path for the EEL/VDW calculations, so

it would appear that only GB calculations will respect the

arbitrarily-modified exclusion list.

You can see this when igb=1 (or any other GB model), you'll get the result

you're aiming for (note, however, that the EGB energies don't change based

on the exclusion list).

HTH,

Jason

-- Jason M. Swails Quantum Theory Project, University of Florida Ph.D. Candidate 352-392-4032 _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Wed Dec 07 2011 - 06:00:10 PST

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