[gmx-users] velacc & box of water
Jamie Seyed
jamie.seyed at gmail.com
Sun Oct 11 19:50:26 CEST 2009
I converted spc216.pdb to gro using editconf. SO they must be the 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?
On Sun, Oct 11, 2009 at 1:33 PM, Justin A. Lemkul <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>> 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>>>
>> 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>>> 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/> |
>> (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
>>
>> ========================================
>> _______________________________________________
>> gmx-users mailing list gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>
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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
>
> ========================================
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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