Hello,
On Wed, Sep 25, 2013 at 5:48 PM, rajat desikan rajatdesi...@gmail.comwrote:
I have a dopc+50% cholesterol bilayer. I want to selectively choose the
upper and lower leaflets. I used g_select the following way
g_select -s DOPC_0.5chl.gro -select 'resname DOPC and resname Cholesterol
and
Hello,
On Tue, Sep 24, 2013 at 8:39 AM, Venkat Reddy venkat...@gmail.com wrote:
I have been using the new tool gmx gangle. My actual intention is to
calculate the orientation between any two same molecules (say cholesterol)
throughout the trajectory and there are 40 cholesterol molecules. But
Hi,
On Thu, Sep 19, 2013 at 7:19 PM, Venkat Reddy venkat...@gmail.com wrote:
@Teemu Murtola: Are there any modifications to the other gmx tools? (eg:
rdf calculation with dynamic selection...etc). I am trying to explore the
new version.
Unfortunately, there are currently very few tools
Hello,
Please keep correspondence on the list so that others may benefit from it,
and you don't need to wait for some particular person to respond.
On Tue, Sep 17, 2013 at 1:24 PM, Venkat Reddy venkat...@gmail.com wrote:
On Tue, Sep 17, 2013 at 12:38 AM, Teemu Murtola teemu.murt...@gmail.com
Hello,
On Sun, Sep 15, 2013 at 5:05 PM, Venkat Reddy venkat...@gmail.com wrote:
I found g_sgangle is the suitable tool
to calculate the angle between two cholesterol rings. But the problem is, I
want to do this analysis for my whole system, which has 40 cholesterol
molecules. Whereas I can
If that is really your selection, you are trying to select atoms that have
both name T3P and O, which is clearly impossible, so nothing gets selected.
Best regards,
Teemu
On Aug 21, 2013 5:13 PM, Albert mailmd2...@gmail.com wrote:
Hello:
I am trying to calculate the number of water molecules
Hi,
On Wed, May 15, 2013 at 7:13 PM, battis...@libero.it battis...@libero.itwrote:
do you know if it is possible make the bending angle calculation in the
following case?
I have got three groups (G1, G2, G3) into a system.
I have to define the center of mass of each one. I have to
Hi,
On Wed, May 8, 2013 at 4:44 PM, Albert mailmd2...@gmail.com wrote:
I am trying to run g_select with command:
g_select -f md.xtc -s md.pdb -os water.xvg -sf selection.dat
in the selection.dat I defined the following:
watero= name 0 and resname T3P;
close = water0 and within 0.6 of
Hi,
On Thu, Apr 4, 2013 at 10:01 PM, Oleksandr Sushko
o.sus...@eecs.qmul.ac.ukwrote:
I'm want to analyse stratified layers of water around protein,
so I provide next selection file to g_select:
[clip]
(shell2 is supposed to be a layer of whole water molecules from the layer
3 to 4 A)
but
Hi,
On Thu, Jan 10, 2013 at 11:08 AM, Albert mailmd2...@gmail.com wrote:
I am trying to use g_select to make an index file with command:
g_select_mpi -f md.xtc -s npt3.pdb -on density.ndx
but it failed with messages:
Assertion failed for g in file /home/albert/Desktop/gromacs-**
Hi,
On Wed, Jun 6, 2012 at 12:13 AM, Justin A. Lemkul jalem...@vt.edu wrote:
On 6/5/12 2:55 PM, Andrew DeYoung wrote:
I would like to use g_select_d to generate an index file containing the
atoms of BF4 residues whose centers of mass are in the range z12.24 nm.
I have tried the following:
On Tue, May 29, 2012 at 1:22 PM, Stephen Cox stephen.cox...@ucl.ac.uk wrote:
I'm running a number of energy minimizations on a clathrate supercell and I
get quite significantly different values for the total energy depending on
the number of mpi processes / number of threads I use.
You are
On Tue, May 1, 2012 at 9:55 PM, Justin A. Lemkul jalem...@vt.edu wrote:
On 5/1/12 2:40 PM, Lara Bunte wrote:
g_select -s molecule.pdb -select 'Close to ISO resname SOL and within
1.2 of resname ISO'
and
trjconv -n index.ndx -f molecule.pdb -s molecule.pdb -o output.pdb
I got only water in
On Thu, Apr 26, 2012 at 04:19, mu xiaojia muxiaojia2...@gmail.com wrote:
e.g, I want to make an HN group of both H and N from my 2nd residue,
There are multiple ways to achieve what you want with g_select.
Probably the easiest is
resnr 2 and name H N,
or if you need the atoms in a different
On Fri, Apr 13, 2012 at 18:30, Lara Bunte lara.bu...@yahoo.de wrote:
Is there no way only to use the .pdb file? How do I create from a .pdb a rtp
file. With pdb2gmx and than grompp?
You can also provide a .pdb file to the -s option of g_select. And you
don't need to provide a -f file in that
On Thu, Dec 1, 2011 at 16:46, Szilárd Páll szilard.p...@cbr.su.se wrote:
With the pgi compiler, I am most concerned about this floating point
overflow warning:
...
[ 19%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/trajana.c.o
[ 19%] Building C object
Hi,
On Fri, Feb 11, 2011 at 21:05, Justin A. Lemkul jalem...@vt.edu wrote:
I don't know of any Gromacs tool (other than pdb2gmx) that is smart enough
to determine terminal residues on its own. If you have multiple copies of
the same molecule, then you know how many atoms are in each, so you
Hi
On Thu, Jan 27, 2011 at 16:18, Manuel Nuno Melo m.n.m...@rug.nl wrote:
My idea is to count the number of water molecules within a certain z
distance of the bilayer center, and flag a pore above a certain threshold.
The problem is that the position of this z-slab cannot be hardcoded because
On Tue, Nov 30, 2010 at 16:58, leila karami karami.lei...@gmail.com wrote:
I enclosed the group name Protein-H and DNA-H in quotes ' ' and .
You should use double quotes, but that does not appear to be the
source of your problems.
but in both of states again:
selection parser: syntax error
On Thu, Oct 21, 2010 at 14:28, Justin A. Lemkul jalem...@vt.edu wrote:
My guess is that this is a matter of how the force field was #included in
the .top file. For instance:
#include my.ff/forcefield.itp
will match $GMXLIB first, but
#include ./my.ff/forcefield.itp
will match the
On Tue, Oct 19, 2010 at 4:14 PM, Sikandar Mashayak symasha...@gmail.com wrote:
Now I have upgraded to gromacs4.5.1 and when I check its template file ,
its completely different that the earlier version. Does that mean old
post-processing codes have to rewritten if I were to use new gromacs?
Hi,
ngjin zhongjin1...@yahoo.com.cn wrote:
I want to select waters in CNT using g_select.
g_select -f md.xtc -s md.tpr -sf selection.dat -os -oc -oi -om -selrpos
whole_mol_com -seltype whole_mol_com
selection.dat contains:resname SOL and ((x-1)^2+(y-1)^2= 1) and (z
=-0.7037 and z =
Hi again,
On Wed, Oct 13, 2010 at 11:36, Teemu Murtola teemu.murt...@cbr.su.se wrote:
Hi,
ngjin zhongjin1...@yahoo.com.cn wrote:
I want to select waters in CNT using g_select.
g_select -f md.xtc -s md.tpr -sf selection.dat -os -oc -oi -om -selrpos
whole_mol_com -seltype whole_mol_com
Hi,
On Mon, Feb 15, 2010 at 19:04, Saikat Banerjee banskt.sai...@gmail.com wrote:
I selected a sphere at a fixed center and noted the
number of water and DMSO molecules within that cut-off. I would like to know
if there are any methods to do the same within GROMACS.
The development (git)
On Tue, Dec 1, 2009 at 11:22, Henri Ervasti h.k.erva...@tudelft.nl wrote:
I just upgraded from Gromacs 4.0.2 to 4.0.5. I wanted to re-run some
jobs from the previous version to see if there would be any changes in
results. I have systems with Ryckaert-Bellemans (type 3) dihedrals and
Fourier
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