[gmx-users] velacc & box of water
Justin A. Lemkul
jalemkul at vt.edu
Sun Oct 11 18:54:49 CEST 2009
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
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