I mean 0.78 g/ml
On Tue, Jul 23, 2013 at 5:43 PM, Chinthaka Ratnaweera <cnr88.msstate.edu>wrote:
> 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
>>
>>
>>
>>
>>
>>
>>
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>> 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
>
--
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 - 16:00:04 PDT
