[gmx-users] velacc & box of water

[Justin A. Lemkul]

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

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

========================================