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 <jalem...@vt.edu
<mailto:jalem...@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
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@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
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@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.se...@gmail.com
<mailto:jamie.se...@gmail.com> <mailto:jamie.se...@gmail.com
<mailto:jamie.se...@gmail.com>>
<mailto:jamie.se...@gmail.com
<mailto:jamie.se...@gmail.com> <mailto:jamie.se...@gmail.com
<mailto:jamie.se...@gmail.com>>>
<mailto:jamie.se...@gmail.com
<mailto:jamie.se...@gmail.com>
<mailto:jamie.se...@gmail.com
<mailto:jamie.se...@gmail.com>> <mailto:jamie.se...@gmail.com
<mailto:jamie.se...@gmail.com>
<mailto:jamie.se...@gmail.com
<mailto:jamie.se...@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
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>
<mailto:jalem...@vt.edu
<mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu
<mailto:jalem...@vt.edu>>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@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/> |
(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/> | (540)
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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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Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
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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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