thank you!
On Wed, May 21, 2014 at 4:10 PM, Justin Lemkul jalem...@vt.edu wrote:
On 5/21/14, 9:06 AM, Nicola Staffolani wrote:
just to improve my knowledge in programming: and I can override it by
typing:
GMXLIB=address_of_the_new_topology_in_my_computer
right?
The details depend
Dear Dr. Warrem, Dear Tsjerk,
Thank you for your emails.
Following the suggestion of Dr. Warren I created several dir in which I applied
different protocols on my system
-- DIR1 --
1) trjconv_mpi -s npt.tpr -f test.xtc -o test-nojump.xtc -pbc nojump (output
System)
2) trjconv_mpi -s
Hi Vito,
Does npt.tpr correspond to the first frame of the trajectory and is the
structure in npt.tpr correctly assembled? (editconf -f npt.tpr -o
npt.tpr.pdb, and check). The only way that -pbc nojump can give a final
frame in which the complex is separated is if the reference structure has
them
Dear Tsjerk,
I exactly executed: editconf -f npt.tpr -o npt.pdb and I obtained a nicely
assembled system (npt.pdb).
Well, my system start to cross the boundaries after 20 ns of production phase
so the npt.tpr is not
the first frame of the trajectories that I trying to fix.
After your email
Hey Vito,
Don't use -skip. And add -pbc nojump to that first run of trjconv:
trjconv_mpi -f md_0_1.part0001.xtc -o test.xtc -s md_0_1.tpr -pbc nojump
Then have a look at the last frame to see if it's good. If md_0_1.tpr is
assembled properly, then the last frame should be too, provided the
Hello,
I want to do a reverse transformation of my system containing: bi-layer,
protein and water.
The Martini website (
http://md.chem.rug.nl/cgmartini/index.php/reverse-transformation) says to
install gromacs version 3.3.1
I am currently using 4.6.1 gromacs version.
ques A: Is this version
Hello,
I would like to know if it is possible to plot the RDF of water
molecules belonging to the solvation shell of a solute. I mean, I want to
know the effect of the solute on the water arrangement in the solvation
shell. Is there a way to do this?
Regards,
Sujith.
--
Gromacs Users
Did you check the .err file as well? What does it say?
How many cores do each node in the HPC have? There might be some issues
with the supercomputer that you may be using? One of the nodes might have
some issues which is probably causing the problem?
I have used 300 cores for replica exchange
Parameters for metals are readily available in various forcefields in
Gromacs. If your nanoparticles are gold spheres suspended freely in the
system, then you can just get the parameters from from the forcefield files
and specify the number of gold atoms in the topology file.
On Wed, May 21,
You should provide with more information. The error message clearly states
that there are multiple definitions for the moleculetype CU1. You should
check carefully for redundancies in the top file
On Wed, May 21, 2014 at 2:57 AM, Meenakshi Rajput
ashi.rajpu...@gmail.comwrote:
dear gromacs
Hi sxn,
I would argue that that method for reverse transformation is largely
obsolete. Please have a look at
http://www.cgmartini.nl/cgmartini/index.php/back
Cheers,
Tsjerk
On Thu, May 22, 2014 at 4:26 PM, shivangi nangia
shivangi.nan...@gmail.comwrote:
Hello,
I want to do a reverse
Dear Tsjerk,
I'm glad to write to you because it works fine!
The system is now perfectly assemble. -pbc nojump using the md_0_1.tpr is enough
to rebuild the system. The only problem is the water that diffuses leaving the
protein.
I think that with the -center flag i can bring back H20 inside
Hey,
Yes, everything runs fine if I work on one node with one or more GPU's. The
crash occurs, similar to the previous mailing list post:
http://comments.gmane.org/gmane.science.biology.gromacs.user/63911
It crashes when we attempt to work across multiple GPU enabled nodes. This
happens when
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Hi Sujith,
g_rdf is the tool you need.
Chandan
On Thu, May 22, 2014 at 8:18 PM, sujithkakkat . sujithk...@gmail.comwrote:
Hello,
I would like to know if it is possible to plot the RDF of water
molecules belonging to the solvation shell of a solute. I mean, I want to
know the effect
On Thu, May 22, 2014 at 5:31 PM, Thomas C. O'Connor tocon...@jhu.eduwrote:
Hey,
Yes, everything runs fine if I work on one node with one or more GPU's. The
crash occurs, similar to the previous mailing list post:
http://comments.gmane.org/gmane.science.biology.gromacs.user/63911
It
Hi Tsjerk,
Do the scripts available in the backward.zip file
http://www.cgmartini.nl/cgmartini/images/tools/backward/backward.zip help
me to backmap a coarse-grained polymer?
Chandan
On Thu, May 22, 2014 at 8:31 PM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi sxn,
I would argue that that
Hi Chandan,
You may have to write a mapping file, as explained in one of the tutorials
in the supplementary information of the paper. If that poses problems, you
can contact me. I may be interested in adding new mappings :)
Cheers,
Tsjerk
On May 22, 2014 6:42 PM, Chandan Choudhury
Thanks a lot Tsjerk.
Thanks,
Shivangi Nangia, Ph. D
Postdoctoral Research Associate
Department of Molecular and Cell Biology
University of Connecticut
On Thu, May 22, 2014 at 11:01 AM, Tsjerk Wassenaar tsje...@gmail.comwrote:
Hi sxn,
I would argue that that method for reverse
Hello Tsjerk,
Is there any example/tutorial on how to use the backward apart from the
notes in the initram.sh
Thanks,
sxn
On Thu, May 22, 2014 at 1:41 PM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi Chandan,
You may have to write a mapping file, as explained in one of the tutorials
in
I ran a 8 ns simulation on a small protein in a water box using PBC. I then
calculated the RMS using g_rms command. When I plotted the outcome my rms graph
looked like a Histogram instead of a rms plot. I then took a region of the
trajectories and view them in VMD. The protein starts out ok,
Hi sxn,
The paper describing the method has a tutorial as supplementary material.
It's also available from our site at the University of Erlangen, but I'l
have to look up the address. In addition, Alex de Vries from Groningen
recently developed another tutorial for a hands-on session he arranged.
Hi,
The usual workflow to fix these kinds of pbc issues can be found here:
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
Mark
On Thu, May 22, 2014 at 9:48 PM, Steve Seibold steve...@ymail.com wrote:
I ran a 8 ns simulation on a small protein in a water box
I'm trying to use g_disre to analyze NOE-derived distance restraints in my
simulation as :
g_disre -s gromacs46-run20.tpr -f run-20-dt100-nojump.pdb
And I get the error (logfile attached) :
Program g_disre, VERSION 4.6.5
Source code file: /root/gromacs-4.6.5/src/tools/gmx_disre.c, line: 189
Hi,
I have done a simulation of an organic molecule (a cyclodextrin) using
GAFF/AMBER parameters, and I would like to compare the results using another
force-field (OPLS or CHARMM). Is there any direct way to go from the topology
for AMBER to the topology for OPLS or CHARMM?
Thanks a lot for
On 5/22/14, 5:19 PM, Rebeca García Fandiño wrote:
Hi,
I have done a simulation of an organic molecule (a cyclodextrin) using
GAFF/AMBER parameters, and I would like to compare the results using another
force-field (OPLS or CHARMM). Is there any direct way to go from the topology
for AMBER
Hi,
I would like to generate specifically mdrun with mpi support.
with configure/make it was possible to use
configure ...
make mdrun
make install mdrun
How would you do this with cmake?
best regards
Soren
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Documentation/Installation_Instructions#4.2._Using_CMake_command-line_options
With 4.5/6 we generate a target with CMake called install-mdrun, so
make install-mdrun
will work.
With 5.0 things will change a bit and you'll have to turn on an
mdrun-only build.
--
Szilárd
Thanks!
That means you compile everything with
cmake
make
#and only at the last step the build is limited to mdrun?
make-mdrun
Do you already know how you will turn on an 'mdrun-only build' ?
best
Soren
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Gromacs Users mailing list
* Please search the archive at
Ok,
actually, both solutions generated mdrun_mpi.
Would you recommend to set a suffix for the libraries as well?
@Justin: I've got
Manually-specified variables were not used by the project:
GMX_BUILD_MDRUN_ONLY
Does this mean the variable is not used at all, or just not here? Or should
On 5/22/14, 6:57 PM, Soren Wacker wrote:
Ok,
actually, both solutions generated mdrun_mpi.
Would you recommend to set a suffix for the libraries as well?
@Justin: I've got
Manually-specified variables were not used by the project:
GMX_BUILD_MDRUN_ONLY
Does this mean the variable is
...and apparently everything gets compiled.
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Thanks!
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Hi List,
My query is not really related to gromacs but I appreciate response from
people who might have tried using coarse grained simualtions using Martini
force field in gromacs.
I haven't come across tutorial or mailing list where people have added
counter ions to a coarse grained protein
Hi,
I'm trying to figure out how to construct a rhombic dodecahedron for a
membrane system.
The manual (Section 3.2.1) states:
There are two different orientations of a rhombic dodecahedron that
satisfy equations 3.1, 3.2 and 3.3. The program editconf produces the
orientation which has a square
Hello Chandan,
Thank you for the response.
I have used g_rdf, but I guess it gives the RDF for the whole system.
Say, if I choose water oxygen, it will plot RDF from water molecules in the
whole system. But, I want the RDF for the solvation shell water molecules
,leaving the bulk water . I
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