Re: [gmx-users] velacc & box of water

[Justin A. Lemkul]

Jamie Seyed wrote:
Hi Justin,
But this seems that did not change the number of molecule in the output 
(only the volume and density are changing) and it seems that -maxsol has 
not been used... my full command
"genbox -cp spc216.gro -maxsol 500 -o out.gro -p topol.top -box 4 4 4"
if I change 500 to any thing else the result is the same and changing 4 
4 4 to any thing else will change the volume and density...

When simultaneously specifying -maxsol and -box, the two must work in harmony. 
A smaller box may not fit 500 molecules, and trying a larger number of molecules 
may not fit in a fixed 4x4x4 nm box.  The command I used that worked was:

genbox -cs spc216.gro -maxsol 500 -o out.gro -box 5 5 5

Note that this gives a weird output configuration, probably because the box is 
not appropriate, but at least its a template of a command that should, in 
theory, work.

Alternatively, you can use the editconf/genbox combination to define a box and 
center the solute (which is water) with editconf -c, then fill the box with 
genbox, where -cp indeed specifies the solute (water) and provides solvent 
(water again!) with -cs.

-Justin

I got confused... I appreciate any hint on that/Thanks/Jamie

On Sun, Oct 11, 2009 at 2:07 PM, Jamie Seyed <jamie.se...@gmail.com 
<mailto:jamie.se...@gmail.com>> wrote:

    Thanks Justin,
    As I understood -cp is for solute and -cs is for solvent... in this
    case I thought that small created volume of water are plying as
    solute... and then genbox should fill the box...
    Anyways thank you :-)

    On Sun, Oct 11, 2009 at 2:01 PM, Justin A. Lemkul <jalem...@vt.edu
    <mailto:jalem...@vt.edu>> wrote:



        Jamie Seyed wrote:

            Oh, I just changed the [-cs spc216.gro] to [-cp spc216.gro]
            and this is working normally...??!! Do you have any idea?


        Oops, I hadn't seen that before.  That is what you should do.
         The -cp flag is the coordinate file that should have solvent
        added to it, and that's what you're after, isn't it?

        -Justin

            On Sun, Oct 11, 2009 at 1:52 PM, Justin A. Lemkul
            <jalem...@vt.edu <mailto:jalem...@vt.edu>
            <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote:



               Jamie Seyed wrote:

                   I converted  spc216.pdb to gro using editconf. SO
            they must be the


               I suppose that's fine, I just don't see all the need for
               interconverting file formats.  It just opens up the
            possibility of
               more errors if you don't keep track of what you're doing :)


                   same(?). The version is 4.0.5 ...it was fine
            before... yes ran
                   it just now for fws tuto... how long it takes time in
            your machine?


               I have the same version.  The commands you showed
            completed in just
               a fraction of a second, like most simple solvation
            procedures.

               -Justin


                   On Sun, Oct 11, 2009 at 1:33 PM, Justin A. Lemkul
                   <jalem...@vt.edu <mailto:jalem...@vt.edu>
            <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>
                   <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
            <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>> wrote:



                      Jamie Seyed wrote:

                          Hi Justin,
                          yes resize.gro is a created file from editconf
            which has box
                          size of  5.05918 on the last line
                          my command was "editconf -bt cubic -f
            spc216.pdb -o
                   resize.gro -d 1"


                      Do you actually have separate spc216.pdb and
            spc216.gro
                   files?  Just
                      trying to make sure this actually worked.


                          and for second command I changed 1 to 5 but it
            still stops in
                          the same point. I am trying to examine 2
            methods that you
                   & Mark
                          suggested me to


                      Very weird.  Both of your commands worked on my
            machine.  What
                      version of Gromacs are you using?  Does genbox
            work for other
                   systems?

                      -Justin

                          create a box of water.../Many Thanks/Jamie

                          On Sun, Oct 11, 2009 at 12:54 PM, Justin A. Lemkul
                          <jalem...@vt.edu <mailto:jalem...@vt.edu>
            <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>
                   <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
            <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>
                          <mailto:jalem...@vt.edu
            <mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu
            <mailto:jalem...@vt.edu>>
                   <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
            <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>>> wrote:



                             Jamie Seyed wrote:

                                 Dear Gmx users,
                                 Does any one know why genbox stops when
            I use this
                   command:
                                 "genbox -cp resize.gro -cs spc216.gro
            -o b4em.pdb -p
                          topol.top"
                                 or when I use this command:
                                 "genbox -cs spc216.gro -box 1 1 1
            -maxsol 500 -o
                   out.gro -p
                                 topol.top"
                                 It goes until
                                 Reading solvent configuration
                                 Solvent configuration contains 648
            atoms in 216
                   residues
                                 and then stops....
                                 Would you please let me know why it
            happens?? Many
                   Thanks in
                                 Advance/Jamie


                             Is "resize.gro" a new file?  Or something
            you have
                   created before
                             (i.e., an empty file with a box size defined)?

                             Defining -box 1 1 1 generates a 1-nm cubic
            box, which
                   is almost
                             certainly too small to contain 500 solvent
            molecules.
                    Define an
                             appropriate box size.

                             -Justin


                                  On Sun, Oct 11, 2009 at 12:04 PM,
            Jamie Seyed
                                 <jamie.se...@gmail.com
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            <mailto:jamie.se...@gmail.com>>>>
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            <mailto:jamie.se...@gmail.com>>>>>>

                                 wrote:

                                    Thanks to Justin & Mark for
            answering my second
                          question...
                                    Could any one give me a hint on my first
                   question that
                          I copy
                                 it again?
                                    --about g_velacc and calculating the
            diffusion
                          constant from
                                 that.
                                    In mailing list people say that we
            need to
                   divide it
                          by mass
                                 squared
                                    and 1/3. Then I found another recent
            post that
                   said it
                          has been
                                    included in the code... Would you please
                   clarify this
                          that if
                                 I need
                                    the factors or not. Also I found 2
            numbers after
                          integration.

                                    Integral   1   0.01595
                                    set    average
                                    SS1   3.718082e-04
                                    Would you please inform me what are
            these
                   number and
                          what is the
                                    relation between them?
                                    Many Thanks in Advance/Jamie

                                    On Sat, Oct 10, 2009 at 8:39 PM,
            Justin A. Lemkul
                                 <jalem...@vt.edu
            <mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu
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            <mailto:jalem...@vt.edu>>
                   <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
            <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>>>> wrote:



                                        Jamie Seyed wrote:

                                            Dear Gmx Users,
                                            I have a 2 questions. First
            about
                   g_velacc and
                                 calculating
                                            the diffusion constant from
            that. In
                   mailing list
                                 people say
                                            that we need to divide it by
            mass
                   squared and
                          1/3. Then I
                                            found another recent post
            that said it
                   has been
                                 included in
                                            the code... Would you please
            clarify
                   this that
                          if I
                                 need the
                                            factors or not. Also I found
            2 numbers
                   after
                          integration.
                                            Integral   1   0.01595
                                            set    average
                                            SS1   3.718082e-04
                                            --1) Would you please inform
            me what
                   are these
                          number and
                                            what is the relation between
            them?
                                                                Can't
            comment on
                   the first part...maybe the code will
                                 point you
                                        in the right direction?


                                            --2) My second question is I
            want to make a
                          box of only
                                            water (spce) with let say
            500 water
                   molecules.
                          Would you
                                            please give me quick hints
            how to do it
                   (the
                          proper
                                 way) or
                                            refer me to good point? Up
            to now I can
                   only
                          have 216
                                 water
                                            molecules from tuto/water
            folder and I
                   tried a lot


                                        This task might be approached in
            a couple
                   of ways:

                                        1. genconf -nbox to define a
            suitable number of
                          replicate
                                 systems.
                                        2. genbox -box -maxsol 500 to
            define a
                          suitably-sized box and
                                        fill it with only the desired
            number of
                   molecules.

                                        -Justin

                                            to start from the beginning,
            but I
                   could not
                          make it... I
                                            appreciate if you help me to
            understand
                   the first
                                 issue and
                                            be able to overcome the
            second one.
                   Many Thanks in
                                 Advance/Jamie


                                                             
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                                        --              
            ========================================

                                        Justin A. Lemkul
                                        Ph.D. Candidate
                                        ICTAS Doctoral Scholar
                                        Department of Biochemistry
                                        Virginia Tech
                                        Blacksburg, VA
                                        jalemkul[at]vt.edu
            <http://vt.edu/> <http://vt.edu/>
                   <http://vt.edu/>
                          <http://vt.edu/> <http://vt.edu/> |

                                 (540) 231-9080

                                                   
            http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

                                       
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                             --    ========================================

                             Justin A. Lemkul
                             Ph.D. Candidate
                             ICTAS Doctoral Scholar
                             Department of Biochemistry
                             Virginia Tech
                             Blacksburg, VA
                             jalemkul[at]vt.edu <http://vt.edu/>
            <http://vt.edu/> <http://vt.edu/>
                   <http://vt.edu/> | (540)
                          231-9080
                           
             http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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                      --    ========================================

                      Justin A. Lemkul
                      Ph.D. Candidate
                      ICTAS Doctoral Scholar
                      Department of Biochemistry
                      Virginia Tech
                      Blacksburg, VA
                      jalemkul[at]vt.edu <http://vt.edu/>
            <http://vt.edu/> <http://vt.edu/> | (540)
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               --    ========================================

               Justin A. Lemkul
               Ph.D. Candidate
               ICTAS Doctoral Scholar
               Department of Biochemistry
               Virginia Tech
               Blacksburg, VA
               jalemkul[at]vt.edu <http://vt.edu/> <http://vt.edu/> |
            (540) 231-9080
               http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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        -- 
        ========================================

        Justin A. Lemkul
        Ph.D. Candidate
        ICTAS Doctoral Scholar
        Department of Biochemistry
        Virginia Tech
        Blacksburg, VA
        jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
        http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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