Re: [gmx-users] solvation

[Justin A. Lemkul]

Jamie Seyed wrote:
Hi Justin,
My aim is to add water inside the pore (I do not care about outside), so 
as you told me I used the first line of spc216.gro and I do not know why 
after the calculations that I posted before it says segmentation fault?? 
Thanks in advance/Jamie


Is it giving a seg fault when using a proper .gro file?  I don't understand what 
you're asking about.

The previous seg fault was from an either improperly-formatted or incomplete 
.gro file.  Having an intact file should not generate a seg fault, unless the 
algorithm is failing (which I have seen when molecules simply will not fit in 
the space you're trying to squeeze them).

-Justin

On Thu, Aug 13, 2009 at 2:41 PM, Justin A. Lemkul <jalem...@vt.edu 
<mailto:jalem...@vt.edu>> wrote:



    Jamie Seyed wrote:

        Hi Justin,

        Does it mean each time I can add one until I get the number that
        I want...?? Many Thanks/Jamie


    No need to do it manually.  That's what -nmol is for.

    -Justin

        On Thu, Aug 13, 2009 at 2:13 PM, Justin A. Lemkul
        <jalem...@vt.edu <mailto:jalem...@vt.edu>
        <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote:



           Jamie Seyed wrote:

               Hi Justin,

               I made an insert.gro file for 2 water molecules,  and when I
               used genbox I got a fatal error: more than one residue in
        insert
               molecules, program terminated.


           Right, like I said before, the insert.gro file should contain
           coordinates for *one* molecule.


               I wanted to look at insert.gro, it does not show
        anything. And
               when I convert it to pdb I got a warning [file
        aminoacids.dat,
               line 1]: Bad box file insert.gro


           Well, how did you make this file?  A .gro file has a specific
        format:

           http://manual.gromacs.org/current/online/gro.html


               When I looked at the insert.pdb file I found only 1.5 water
               molecule! Which means 1 water plus a OH. Do you have any idea
               what should I do or if I am missing some thing? Many
        Thanks in
               Advance/Jamie


           I have no idea how you created this broken file, so I can't
        really
           comment :) The easiest thing to do (I would think) would be
        to take
           the first molecule of spc216.gro, keep the header lines, set
        number
           of atoms = 3 and preserve the box information at the bottom.
         I've
           used that before in a few cases.

           -Justin

               On Thu, Aug 13, 2009 at 1:20 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,
                      Thanks for your answer,
                      On Thu, Aug 13, 2009 at 11:42 AM, 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 all,
                             I want to know how can I use genbox to fill
        inside
               of the
                      pore
                             as well as a layer outside. From the "man
        genbox"
               page I
                      try to
                             use -shell with a negative value (?) but it
        put waters
                      far from
                             the outside of the pore and I think it does
        not care
                      about the
                             sign. It seems strange to me because when I
        had 10
               10 10
                      in the
                             last line of my f.gro, by a shell 0.5 or
        0.2, I got a
                      layer of
                             few molecule around the pore, but when I
        change it
               to 1.
                      1. 1.,
                             the water molecules generated far away. I
               appreciate if
                      someone
                             tell me (1) how I can add water inside the pore
               and (2) why


                         (1) The -vdwd option may help, or even -ci
        -nmol.  If
               you have a
                         pore, wouldn't water diffuse in over time
        anyway during
                         equilibration (assuming an otherwise correct
        setup and
               realistic
                         physical model)?

                       Long time ago I did an experiment on water in
        confined
               geometry
                      and I want to see if the results can obtain from the
                       simulation... So for using -nmol -ci (at random
               position), it
                      says I must use a file like insert.gro would you
        please
               explain
                      me how I can make insert.gro?


                  The "insert.gro" file contains the coordinates of one
               molecule that
                  you want to insert, i.e. one water molecule.

                  -Justin

                         (2) If you haven't re-positioned your system within
               the box, it
                         probably doesn't make any sense.  The Gromacs
               convention is
                      to place
                         the corner of the box at the coordinate origin, and
                      everything else
                         is relative to that.  Is a 1-nm cubic box large
        enough to
                      encompass
                         your system?  If not, genbox is doing what it's
        told -
               filling a
                         1-nm box near the origin, and leaving
        everything else out.



                         -Justin

                             changing the box size will give a opposite
        result.
               Please
                             advise..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/> | (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)
               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/> | (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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