[gmx-users] velacc & box of water
Justin A. Lemkul
jalemkul at vt.edu
Sun Oct 11 20:39:55 CEST 2009
Jamie Seyed wrote:
> Hi Justin,
> But this seems that did not change the number of molecule in the output
> (only the volume and density are changing) and it seems that -maxsol has
> not been used... my full command
> "genbox -cp spc216.gro -maxsol 500 -o out.gro -p topol.top -box 4 4 4"
> if I change 500 to any thing else the result is the same and changing 4
> 4 4 to any thing else will change the volume and density...
When simultaneously specifying -maxsol and -box, the two must work in harmony.
A smaller box may not fit 500 molecules, and trying a larger number of molecules
may not fit in a fixed 4x4x4 nm box. The command I used that worked was:
genbox -cs spc216.gro -maxsol 500 -o out.gro -box 5 5 5
Note that this gives a weird output configuration, probably because the box is
not appropriate, but at least its a template of a command that should, in
theory, work.
Alternatively, you can use the editconf/genbox combination to define a box and
center the solute (which is water) with editconf -c, then fill the box with
genbox, where -cp indeed specifies the solute (water) and provides solvent
(water again!) with -cs.
-Justin
> I got confused... I appreciate any hint on that/Thanks/Jamie
>
> On Sun, Oct 11, 2009 at 2:07 PM, Jamie Seyed <jamie.seyed at gmail.com
> <mailto:jamie.seyed at gmail.com>> wrote:
>
> Thanks Justin,
> As I understood -cp is for solute and -cs is for solvent... in this
> case I thought that small created volume of water are plying as
> solute... and then genbox should fill the box...
> Anyways thank you :-)
>
> On Sun, Oct 11, 2009 at 2:01 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> Jamie Seyed wrote:
>
> Oh, I just changed the [-cs spc216.gro] to [-cp spc216.gro]
> and this is working normally...??!! Do you have any idea?
>
>
> Oops, I hadn't seen that before. That is what you should do.
> The -cp flag is the coordinate file that should have solvent
> added to it, and that's what you're after, isn't it?
>
> -Justin
>
> On Sun, Oct 11, 2009 at 1:52 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:
>
> 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>
> <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:
>
> 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>>
> <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
> <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,
> 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>>>
> <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
> <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>
> <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
> <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>>>
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> <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>
> <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
> <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/>
> <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/>
> <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 <http://vt.edu/>
> <http://vt.edu/> <http://vt.edu/> | (540)
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> 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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