On 9/09/2011 3:29 PM, aiswarya pawar wrote:
Thanks Lina and Justin.
Is this data good for finding the distance of protein and water as
function of time.
If the protein and water are in contact, what do you hope to learn?
Mark
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Hi all,
I understand this problem has been discussed before, but it seems no
conclusion has been drawn.
GLYCAM force field assigns negative force constants to some dihedrals, and
when amb2gmx.pl was used to convert prmtop file to gromacs top file, these
negative values seem to be ignored. Some
On 9/09/2011 4:21 PM, Yun Shi wrote:
Hi all,
I understand this problem has been discussed before, but it seems no
conclusion has been drawn.
Someone needs to do some work and report back :-)
GLYCAM force field assigns negative force constants to some dihedrals,
and when amb2gmx.pl
On 9/09/2011 1:46 AM, Marcin Zielinski wrote:
Hi there,
I've been having hard times the past days trying to build SP and DP
binaries
of GROMACS 4.5.4 on our Power6 system, here at SARA, using IBM XL
compilers,
LAPACK, BLAS, GSL and FFTW3.
At the end, I think I've succeeded and had to use
Dear Gromacs Users,
I am calculating SAS using g_sas of ligands in my system: protein, 30
ligands in water. The hydrophobic SAS of ligands decrease and reach stable
value. Hydrophilic remains stable over the simulation time. I am wondering
whether it (the decrease o hydrophobic) is because of
Hi all,
am facing an error while installing gridcount-
make[1]: *** [g_ri3Dc.o] Error 1
make[1]: Leaving directory `/home/proj11/aiswarya/Grid-count/src'
make: *** [all] Error 2
This error is while giving the make command.
Thanks
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On 9/09/2011 5:27 PM, aiswarya pawar wrote:
Hi all,
am facing an error while installing gridcount-
make[1]: *** [g_ri3Dc.o] Error 1
make[1]: Leaving directory `/home/proj11/aiswarya/Grid-count/src'
make: *** [all] Error 2
This error is while giving the make command.
This is not the right
Hi Mark,
Yes, GMX_ACCELERATION should do the trick, however it requires You to
turn off the THREADS.
Altho ppl tend to run the tools in serial anyway, I somehow sticked to that.
As for the FindLAPACK.cmake fix, I'm pretty sure I has been posted here
some time ago. I googled it
anyhow.
On 9/09/2011 5:50 PM, Marcin Zielinski wrote:
Hi Mark,
Yes, GMX_ACCELERATION should do the trick, however it requires You to
turn off the THREADS.
Altho ppl tend to run the tools in serial anyway, I somehow sticked to
that.
Only mdrun takes advantage of parallelism in GROMACS up to now. So
Or why not trying acpype?
Cheers,
Alan
On 9 September 2011 07:37, Mark Abraham mark.abra...@anu.edu.au wrote:
On 9/09/2011 4:21 PM, Yun Shi wrote:
Hi all,
I understand this problem has been discussed before, but it seems no
conclusion has been drawn.
Someone needs to do some work and
Hi Mark
Thanks for the rtp definitions. I added the rtp defs to aminoacids.rtp and
renamed residue and atom names in pdb file.
But pdb2gmx is still complaining about the terminal groups. It seems to have
picked up ACE, but not CT3.
pdb2gmx error message and modified pdb file are listed below.
Dear friends
I am trying to gromacs simulation with the metal (Zn) binding protein. But
here, i am not able to make itp file for the metal..I am preety new to this
field...anyone please suggest me, what i should do?
--
Om Prakash Sharma
Ph.D Scholar DIT JRF
Centre for Bioinformatics
On 09/09/11, Sandeep Somani ssom...@gmail.com wrote:
Hi Mark
Thanks for the rtp definitions. I added the rtp defs to aminoacids.rtp and
renamed residue and atom names in pdb file.
But pdb2gmx is still complaining about the terminal groups. It seems to have
picked up ACE, but
On 09/09/11, om prakash ombioi...@gmail.com wrote:
Dear friends
I am trying to gromacs simulation with the metal (Zn) binding protein. But
here, i am not able to make itp file for the metal..I am preety new to this
field...anyone please suggest me, what i should do?
You should
Ok, giving -DGMX_ACCELERATE=Power6 results with:
src/config.h
/* Define to a macro mangling the given C identifier (in lower and upper
case), which must not contain underscores, for linking with Fortran. */
#define F77_FUNC(name,NAME) name ##
/* As F77_FUNC, but for C identifiers
Hi,
are there someone love to share one md.mdp file for GPU version?
Thanks ahead,
--
Best Regards,
lina
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Please search the archive at
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lina wrote:
Hi,
are there someone love to share one md.mdp file for GPU version?
All the details are here:
http://www.gromacs.org/Downloads/Installation_Instructions/GPUs?highlight=gpu
The benchmark archive has example .mdp files that you can tweak.
-Justin
--
You still haven't provided all of the relevant information. For
example: what ff are you using? But please don't just sent that
information now... better for you to read about how to develop a good
post and next time be suer to include enough information that we could
reproduce the problem
Was my question not clear or noone can help me? I am wondering whether
calculations of ligand hydrophobic SAS (decrease during the simualtion) can
be result of binding to protein?
On Fri, Sep 9, 2011 at 8:23 AM, Steven Neumann s.neuman...@gmail.comwrote:
Dear Gromacs Users,
I am calculating
Steven Neumann wrote:
Was my question not clear or noone can help me? I am wondering whether
calculations of ligand hydrophobic SAS (decrease during the
simualtion) can be result of binding to protein?
Presumably it's due to both aggregation and binding to the protein, if, in fact
both
Dear all,
I want to calculate the density of my system and visualize it during
the simulation time. I've tried with g_density and with g_energy but
in all the cases the density calculated is the average density all
along the simulation and not the density of all the system in each
step
vferra...@units.it wrote:
Dear all,
I want to calculate the density of my system and visualize it during the
simulation time. I've tried with g_density and with g_energy but in all
the cases the density calculated is the average density all along the
simulation and not the density of all
On Fri, Sep 9, 2011 at 8:48 PM, Justin A. Lemkul jalem...@vt.edu wrote:
lina wrote:
Hi,
are there someone love to share one md.mdp file for GPU version?
All the details are here:
http://www.gromacs.org/**Downloads/Installation_**
On 9/09/2011 10:01 PM, Marcin Zielinski wrote:
Ok, giving -DGMX_ACCELERATE=Power6 results with:
src/config.h
/* Define to a macro mangling the given C identifier (in lower and upper
case), which must not contain underscores, for linking with
Fortran. */
#define F77_FUNC(name,NAME)
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I am trying to pull apart two dimers of tubulin protein joined together, to
form two separate dimers by steered molecular dynamics using Pull code. The
objective is to separate the dimers by pulling along one axis only (Y axis). I
ran the simulation for 25 ps and it accomplished well but while
Shilpi Chaurasia wrote:
I am trying to pull apart two dimers of tubulin protein joined
together, to form two separate dimers by steered molecular dynamics
using Pull code. The objective is to separate the dimers by pulling
along one axis only (Y axis). I ran the simulation for 25 ps and it
Dear users,
I have created radial distribution function plot for Carbon atoms in a
system containing polymer chains. I see some little jumps between first and
second peak.
I need your help to comment on how this behavior can be justified (or if the
plot is wrong).
g_rdf -f *.trr -s *.tpr -o
Moeed wrote:
Dear users,
I have created radial distribution function plot for Carbon atoms in a
system containing polymer chains. I see some little jumps between first
and second peak.
I need your help to comment on how this behavior can be justified (or if
the plot is wrong).
g_rdf -f
Thank you Justin for your reply. Simulation is 5 ns long ( before this a 500
ps NVT was done as equilibration) and total energy has been equilibrated
after around 3 ns.
-b is set to 4000 that is the last 1 ns has been used for rdf.
Best,
moeed
On Fri, Sep 9, 2011 at 3:37 PM, Justin A. Lemkul
Dear Gromacs Users:
I've been working with small unsaturated hydrocarbons using OPLS-AA with NVT
calculations using box dimensions according to : x=y z=3x centered in
1/2x,1/2y,1/2z in order to obtain surface tension. My system expands at the
begging of the mdrun calculation until it occupies the
Dear gromacs users,
I loaded my .psf and then loaded .pdb file into psf in VMD then used the
command “ topo writegmxtop myfile.top” in tk console. I finally generated a
gromacs .top file successfully. I want to use gromacs 4.5 tools for trajectory
analysis with namd dcd and pdb files. But
Moeed wrote:
Thank you Justin for your reply. Simulation is 5 ns long ( before this a
500 ps NVT was done as equilibration) and total energy has been
equilibrated after around 3 ns.
-b is set to 4000 that is the last 1 ns has been used for rdf.
For all but the simplest systems this
Hasan haska wrote:
Dear gromacs users,
I loaded my .psf and then loaded .pdb file into psf in VMD then used
the command “ topo writegmxtop myfile.top” in tk console. I finally
generated a gromacs .top file successfully. I want to use gromacs 4.5
tools for trajectory analysis with namd dcd
Hi. I've look through the manual and didn't find an answer on my question:
i've got a trajectory and i want to convert it in *.pdb with such parameters
of index file [all atoms within a sphere with a chosen radius around
selected atom]. What can i do? Thank you
--
*С уважением!
***
*
Nemo me
Алексей Раевский wrote:
Hi. I've look through the manual and didn't find an answer on my
question: i've got a trajectory and i want to convert it in *.pdb with
such parameters of index file [all atoms within a sphere with a chosen
radius around selected atom]. What can i do? Thank you
Hi Mark
It worked ! pdb2gmx is now properly processing the pdb, and moreover the
potential energy from gmx is within 1.27 kJ/mol of that from Charmm. More on
energy comparison shortly.
However, further tinkering of the rtp and pdb file was required to generate
the topology:
1.
The original rtp
On Fri, Sep 9, 2011 at 4:18 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Moeed wrote:
Thank you Justin for your reply. Simulation is 5 ns long ( before this a
500 ps NVT was done as equilibration) and total energy has been equilibrated
after around 3 ns.
-b is set to 4000 that is the
Moeed wrote:
On Fri, Sep 9, 2011 at 4:18 PM, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu wrote:
Moeed wrote:
Thank you Justin for your reply. Simulation is 5 ns long (
before this a 500 ps NVT was done as equilibration) and total
energy has been
On Sat, Sep 10, 2011 at 3:35 AM, Moeed lecie...@googlemail.com wrote:
Dear users,
I have created radial distribution function plot for Carbon atoms in a
system containing polymer chains. I see some little jumps between first and
second peak.
I need your help to comment on how this behavior
lina wrote:
On Sat, Sep 10, 2011 at 3:35 AM, Moeed lecie...@googlemail.com
mailto:lecie...@googlemail.com wrote:
Dear users,
I have created radial distribution function plot for Carbon atoms in
a system containing polymer chains. I see some little jumps between
first and
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