[gmx-users] velacc & box of water

Jamie Seyed jamie.seyed at gmail.com
Sun Oct 11 19:23:36 CEST 2009 

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

On Sun, Oct 11, 2009 at 12:54 PM, Justin A. Lemkul <jalemkul at 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.seyed at gmail.com<mailto:
>> jamie.seyed at 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 <jalemkul at vt.edu
>>     <mailto:jalemkul at 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/> | (540) 231-9080
>>        http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>        ========================================
>>
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>>
>>
>>
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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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