[gmx-users] velacc & box of water
Jamie Seyed
jamie.seyed at gmail.com
Sun Oct 11 19:58:39 CEST 2009
Oh, I just changed the [-cs spc216.gro] to [-cp spc216.gro] and this is
working normally...??!! Do you have any idea?
On Sun, Oct 11, 2009 at 1:52 PM, Justin A. Lemkul <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>> 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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> Please search the archive at http://www.gromacs.org/search before posting!
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