[gmx-users] velacc & box of water
Justin A. Lemkul
jalemkul at vt.edu
Sun Oct 11 19:52:15 CEST 2009
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 <jalemkul at vt.edu
> <mailto:jalemkul at 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
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto: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>
> <mailto:jamie.seyed at gmail.com <mailto:jamie.seyed at gmail.com>>
> <mailto:jamie.seyed at gmail.com
> <mailto:jamie.seyed at gmail.com> <mailto: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>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto: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/>
> <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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