Thank you so much,
I have one more question
My density seems to be very low around 0.08. The density of ethanol is
around 078. That means do I have reduce the starting box size? Otherwise it
will take longer time to equilibrate isn't it?
Chinthaka
On Tue, Jul 23, 2013 at 4:37 PM, M. L. Dodson <mldodson.comcast.net> wrote:
>
> On Jul 23, 2013, at 3:49 PM, Chinthaka Ratnaweera wrote:
>
> > Thanks
> > I tried to equilibrate what ever the box I have now. ( May be I can try
> the
> > truncated octahedral later.) But it won't allow me to do that and request
> > velocity info.
> > ERROR: I could not find enough velocities in
> > ethbox.inpcrd
> > Does that mean I must at least minimize few steps?
> >
> > Chinthaka
> >
>
> Your starting struct. file has no velocities. If it has a box that is no
> good. Hmmmm….. Try this: Write a simple shell script (you can just cut and
> paste
> commands you are using to run sander on multiple lines if you do not know
> shell
> scripting.) Run a single step minimization and write a restart file. Use
> that
> restart file as starting structure for a single step dynamics run and
> write a
> restart file. Copy and paste this two run sequence 15-20 times or so,
> sequentially, in your shell script, using the restart file for the
> previous run
> as the starting structure for the next. (You will have to come up with a
> file
> naming convention that keeps the files organized.) In my experience,
> this, MOST
> OF THE TIME, will eventually result in an output without NaN or ****
> entries.
> Use that restart file to do a regular minimization/NPT equilibration
> sequence. Be sure to plot the densities during the NPT equilibration to
> know
> when it has plateaued. Then I would run a fairly long final MD
> equilibration to
> be sure the box is relaxed to the force field.
>
> Good luck
>
> PS, it might be a good idea to set the temperature to 100K or so during the
> minimization/dynamics alternating sequence. You want enough temp to allow
> the
> atoms to move but not so much that you get vlimit violations. Remember,
> the
> only atoms that need to move to get an adequate starting structure are
> those on
> the box boundary that intrude into the next image.
>
> PPS, I think there are some tools mentioned in the crystal dynamics
> tutorial(s)
> that will allow this to work better than Packmol, but I never tried to use
> them.
> Maybe some enterprising graduate student might write single species and
> mixture
> periodic box preparation tutorials? :-)
>
>
> >
> > On Tue, Jul 23, 2013 at 3:26 PM, M. L. Dodson <mldodson.comcast.net>
> wrote:
> >
> >>
> >> On Jul 23, 2013, at 3:10 PM, Chinthaka Ratnaweera wrote:
> >>
> >>> Ok
> >>> I used 'setbox ETHBOX vdw {5,5,5}'
> >>> It make a box bigger than previous.
> >>>
> >>> The box dimensions now read as
> >>>> setbox ETHBOX vdw {5,5,5}
> >>> Box dimensions: 65.435279 64.286901 64.791138
> >>>
> >>> my Packmol box should be 50*50*50. Is this size enough now?
> >>>
> >>> but this gives the same problem in minimization. Are you mean I have to
> >> do
> >>> the equilibration at constant pressure without minimization? I try that
> >>>
> >>
> >> I've been away from this stuff for a couple of years, so all I can
> comment
> >> is
> >> that the boxes set with LEaP and Packmol were not oriented the same (if
> I
> >> remember correctly.) I figured this out a couple of years ago, but the
> >> details
> >> are hazy. IIRC, the most foolproof way I found was to create (counter
> >> intuitively) an origin-centered sphere with the correct number of
> >> molecules.
> >>
> >> Then enclose the sphere with with a truncated octahedron substantially
> >> bigger
> >> than the sphere. If your packmol structure is not tightly packed, you
> can
> >> probably get away with no (or minimal) minimization. Of course the
> larger
> >> the truncated octahedron "box," the longer the constant pressure run to
> >> equilibrate the density.
> >>
> >> I MAY have had to make sure the trunc. oct. and the sphere were
> >> co-centered,
> >> I can't remember.
> >>
> >> After you get an equilibrated restart file, you can cut out an
> >> appropriately
> >> sized cube with ptraj (IIRC, although can't remember the exact
> commands.)
> >>
> >> Good luck,
> >> Bud Dodson
> >>
> >> PS, another way to do this is to use a PDB with only a single molecule,
> >> then
> >> "solvate" that molecule with more of the same molecule. This is probably
> >> less trouble than using Packmol for single species boxes. Packmol is
> >> needed
> >> for mixtures, though, I believe.
> >>
> >>> On Tue, Jul 23, 2013 at 2:52 PM, M. L. Dodson <mldodson.comcast.net>
> >> wrote:
> >>>
> >>>>
> >>>> On Jul 23, 2013, at 2:45 PM, M. L. Dodson wrote:
> >>>>
> >>>>>
> >>>>> On Jul 23, 2013, at 2:19 PM, Chinthaka Ratnaweera wrote:
> >>>>>
> >>>>>> I followed the procedure in tutorial 15.
> >>>>>>
> >>>>>> This is my packmol input file
> >>>>>>
> >>>>>> tolerance 2.0
> >>>>>> output ethbox.pdb
> >>>>>> filetype pdb
> >>>>>> structure ethanol.pdb
> >>>>>> number 1000 # Number of molecules
> >>>>>> inside cube 0. 0. 0. 50. # x, y, z coordinates of box, and length of
> >>>> box in
> >>>>>> Angstroms
> >>>>>> end structure
> >>>>>>
> >>>>>> Then use leap to generate initial coordinates and topologies.
> >>>>>> source leaprc.gaff
> >>>>>> ETH = loadmol2 ethanol.mol2
> >>>>>> ETHBOX = loadpdb ethbox.pdb
> >>>>>> setbox ETHBOX centers
> >>>>>> saveAmberParm ETHBOX ethbox.prmtop ethbox.inpcrd
> >>>>>>
> >>>>>> But when running minimization under NVT it gave me this error
> >>>>>> forrtl: severe (174): SIGSEGV, segmentation fault occurred
> >>>>>>
> >>>>>> my minimization input is
> >>>>>> test run 1
> >>>>>> &cntrl
> >>>>>> imin = 1, ntpr = 100, ntwx=100, maxcyc = 10000, ntb=1
> >>>>>> &end
> >>>>>>
> >>>>>> This starts the first step of minimization
> >>>>>> TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
> >>>>>> | CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
> >>>>>> | CHECK d/dx switch(x): max rel err = 0.8314E-11 at 2.736960
> >>>>>> ---------------------------------------------------
> >>>>>> | Local SIZE OF NONBOND LIST = 1264139
> >>>>>> | TOTAL SIZE OF NONBOND LIST = 1264139
> >>>>>>
> >>>>>>
> >>>>>> NSTEP ENERGY RMS GMAX NAME
> NUMBER
> >>>>>> 1 2.1423E+09 4.7538E+08 4.7855E+10 H4 2698
> >>>>>>
> >>>>>> BOND = 547891.8779 ANGLE = 201752.1037 DIHED =
> >>>>>> 2455.8141
> >>>>>> VDWAALS = ************* EEL = 12317.8836 HBOND =
> >>>>>> 0.0000
> >>>>>> 1-4 VDW = 72044523.0714 1-4 EEL = -22796.8084 RESTRAINT =
> >>>>>> 0.0000
> >>>>>>
> >>>>>>
> >>>>>> Is this because of my box size?
> >>>>>>
> >>>>>>
> >>>>>
> >>>>> Probably not. Boxes created with packmol are not equilibrated with
> >>>> periodic boundaries.
> >>>>> Packmol just puts packs spheres (connected spheres in the case of
> >>>> ethanol.) At the
> >>>>> box boundaries, parts of molecules extend beyond the box. When the
> >> boxes
> >>>> are tiled,
> >>>>> some of the atoms overlap with the next image so you get VDW clashes.
> >>>> You need a box
> >>>>> bigger than the packmol box when you tile the boxes, then equilibrate
> >> at
> >>>> constant
> >>>>> pressure to shrink the box, equilibrate the density, and arrange the
> >> box
> >>>> edges to be
> >>>>> consistent with periodic boundaries.
> >>>>>
> >>>>
> >>>> Let me make this less ambiguous.
> >>>>
> >>>> Your Packmol box is not the problem, the box assigned by LEaP is too
> >> small
> >>>> if it is
> >>>> the same as the Packmol box. Boxes created with packmol are not
> >>>> equilibrated with
> >>>> periodic boundaries. Packmol just puts packs spheres (connected
> spheres
> >> in
> >>>> the case
> >>>> of ethanol.) At the Packmol box boundaries, parts of molecules extend
> >>>> beyond the box.
> >>>> When the boxes are tiled with LEaP, some of the atoms overlap with the
> >>>> next image so
> >>>> you get VDW clashes. You need a LEaP box bigger than the packmol box
> >> when
> >>>> you tile
> >>>> the boxes, then equilibrate at constant pressure to shrink the PBC
> box,
> >>>> equilibrate
> >>>> the density, and arrange the PBC box edges to be consistent with
> >> periodic
> >>>> boundaries.
> >>>>
> >>>>> Good luck,
> >>>>> Bud Dodson
> >>>>>
> >>>>>> On Tue, Jul 23, 2013 at 10:02 AM, David A. Case <
> >>>> case.biomaps.rutgers.edu>wrote:
> >>>>>>
> >>>>>>> On Mon, Jul 22, 2013, Chinthaka Ratnaweera wrote:
> >>>>>>>>
> >>>>>>>> Once the saveoff command make a box 'unit' ( I guess I have to
> save
> >>>> it
> >>>>>>> as
> >>>>>>>> a lib file), inorder to use that unit to solvate the protein, do I
> >>>> have
> >>>>>>> to
> >>>>>>>> use loadoff command to open it and give this unit name as second
> >>>> argument
> >>>>>>>> in solvatebox command?
> >>>>>>>
> >>>>>>> Yes.
> >>>>>>>
> >>>>>>>>
> >>>>>>>> Does size of the solvate box matters when setup the initial box
> >> using
> >>>>>>>> packmol?
> >>>>>>>
> >>>>>>> It's not a big deal which size you choose. Most of the "standard"
> >>>> boxes
> >>>>>>> are really smaller than they should be (some were made back in the
> >>>> 1980s
> >>>>>>> when
> >>>>>>> computers were much slower.) The solvateBox and solvateOct
> routines
> >>>> will
> >>>>>>> replicate and truncate boxes as needed. Something on the order of
> >> 1000
> >>>>>>> ethanol molecules should be fine.
> >>>>>>>
> >>>>>>> ...good luck....dac
> >>>>>>>
> >>>>>>>
> >>>>>>> _______________________________________________
> >>>>>>> AMBER mailing list
> >>>>>>> AMBER.ambermd.org
> >>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> --
> >>>>>> Chinthaka Nadun Ratnaweera
> >>>>>> Hand Lab Rm 1126
> >>>>>> Mississippi State University
> >>>>>> 310 Presidents Circle
> >>>>>> Starkville, MS 39762
> >>>>>> _______________________________________________
> >>>>>> AMBER mailing list
> >>>>>> AMBER.ambermd.org
> >>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>
> >>>>> --
> >>>>> M. L. Dodson
> >>>>> Business email: activesitedynamics-at-gmail-dot-com
> >>>>> Personal email: mldodson-at-comcast-dot-net
> >>>>> Gmail: mlesterdodson-at-gmail-dot-com
> >>>>> Phone: eight_three_two-five_63-386_one
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>> _______________________________________________
> >>>>> AMBER mailing list
> >>>>> AMBER.ambermd.org
> >>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>
> >>>> --
> >>>> M. L. Dodson
> >>>> Business email: activesitedynamics-at-gmail-dot-com
> >>>> Personal email: mldodson-at-comcast-dot-net
> >>>> Gmail: mlesterdodson-at-gmail-dot-com
> >>>> Phone: eight_three_two-five_63-386_one
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> AMBER mailing list
> >>>> AMBER.ambermd.org
> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>
> >>>
> >>>
> >>>
> >>> --
> >>> Chinthaka Nadun Ratnaweera
> >>> Hand Lab Rm 1126
> >>> Mississippi State University
> >>> 310 Presidents Circle
> >>> Starkville, MS 39762
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >> --
> >> M. L. Dodson
> >> Business email: activesitedynamics-at-gmail-dot-com
> >> Personal email: mldodson-at-comcast-dot-net
> >> Gmail: mlesterdodson-at-gmail-dot-com
> >> Phone: eight_three_two-five_63-386_one
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > Chinthaka Nadun Ratnaweera
> > Hand Lab Rm 1126
> > Mississippi State University
> > 310 Presidents Circle
> > Starkville, MS 39762
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> M. L. Dodson
> Business email: activesitedynamics-at-gmail-dot-com
> Personal email: mldodson-at-comcast-dot-net
> Gmail: mlesterdodson-at-gmail-dot-com
> Phone: eight_three_two-five_63-386_one
>
>
>
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Chinthaka Nadun Ratnaweera
Hand Lab Rm 1126
Mississippi State University
310 Presidents Circle
Starkville, MS 39762
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Received on Tue Jul 23 2013 - 16:00:03 PDT
