For technical reasons, parallel make with GMX_BUILD_OWN_FFTW can have
this problem. Run make a second time and it will work.
Mark
On Wed, Sep 11, 2013 at 6:22 AM, shahid nayeem msnay...@gmail.com wrote:
Thanks Wahab
I followed your instruction and added #define HAVE_SYS_TIME_H
at the very
No idea if it's causing your problem, but you need all the Ds in
-DBUILD_SHARED_LIBS=no
Mark
On Wed, Sep 11, 2013 at 6:15 AM, Qin Qiao qiaoqi...@gmail.com wrote:
Dear all,
I'm trying to install gromacs4.6.3 with mvapich2-1.9a on a local cluster
and got the following error in step 'make':
If the version of gcc is unsuitable, you can write the path to it in
gold leaf and it still won't help :-) Check gcc --version for the
exercise, and then find out how to install 4.7.x or 4.8.x.
Mark
On Wed, Sep 11, 2013 at 5:09 AM, Golshan Hejazi
golshan.hej...@yahoo.com wrote:
Hello,
i am
In reality, what we should do is make it a fatal error, because truly,
frozen groups should be used very sparingly and certainly never with NPT.
It just doesn't make sense. I understand what you're trying to accomplish,
but the underlying theory becomes flawed.
Agreed
Mark
--
gmx-users
See
http://www.gromacs.org/Documentation/Acceleration_and_parallelization#Pinning_threads_to_physical_cores
On Sat, Sep 7, 2013 at 2:06 PM, vidhya sankar scvsankar_...@yahoo.com wrote:
respected mark sir ,
Thank you fro your previous reply
When i run the production Mdrun
Hi,
There's simply no way you can expect compilers more than three years
old (icc 11, gcc 4.4) to work seamlessly and produce high performance
with brand-new hardware and code. That's like working on a Formula One
car with a flint axe. Installing a new compiler is not rocket science!
Mark
On
Thanks. But when I ran make again I am getting this error
[ 0%] Built target gmxfftw
make[2]: *** No rule to make target
`//cygdrive/c/packages/gromacs-4.6.3/build/src/contrib/fftw/gmxfftw-prefix/lib/libfftw3.a',
needed by `src/gmxlib/cyggmx_d-8.dll'. Stop.
CMakeFiles/Makefile2:1238: recipe for
Thanks Mark
$ make
[ 0%] Built target gmxfftw
make[2]: *** No rule to make target
`//cygdrive/c/packages/gromacs-4.6.3/build/src/contrib/fftw/gmxfftw-prefix/lib/libfftw3.a',
needed by `src/gmxlib/cyggmx_d-8.dll'. Stop.
CMakeFiles/Makefile2:1238: recipe for target
Dear all,
This is my first time here. I apologize if I am not aware any rules for posting
a new message.
I was testing Gromacs on two servers, one server has AMD Opteron processor
(Server 1), and the other has Intel Xeon processor (Server 2). The simulation
system that I tried is the lysozyme
Dear Justin,
I followed your advice and started a gas-phase simulation. I removed the
solvent and simulated only the polymer molecule but I ended up with this error:
One of the box vectors has become shorter than twice the cut-off length or
box_yy-|box_zy| or box_zz has become smaller than the
Don't know, sorry. None of the devs use Cygwin. I suggest you follow
the normal instructions to install FFTW manually, and then direct
CMake to use it.
Mark
On Wed, Sep 11, 2013 at 9:38 AM, shahid nayeem msnay...@gmail.com wrote:
Thanks Mark
$ make
[ 0%] Built target gmxfftw
make[2]: ***
Pressure coupling with a single molecule (i.e. in the gas phase)
doesn't sound workable to me.
Mark
On Wed, Sep 11, 2013 at 11:28 AM, Jernej Zidar jernej.zi...@gmail.com wrote:
Dear Justin,
I followed your advice and started a gas-phase simulation. I removed the
solvent and simulated only
It's not clear whether you are reporting single points or
post-equilibration time averages, but either way you must expect
differences. MD simulations are chaotic. However, the long-time
ensemble averages should agree well - that's the point of the
simulation.
Mark
On Wed, Sep 11, 2013 at 10:35
On 11.09.2013 09:38, shahid nayeem wrote:
I checked in folder
/cygdrive/c/packages/gromacs-4.6.3/build/src/contrib/fftw/gmxfftw-prefix/lib/libfftw3.a
, this file exists but perhaps `src/gmxlib/cyggmx_d-8.dll' is not able to
locate it.
Did you 'cmake' with -DGMX_PREFER_STATIC_LIBS=ON ?
BTW,
On Wed, Sep 11, 2013 at 12:04 PM, Mirco Wahab
mirco.wa...@chemie.tu-freiberg.de wrote:
On 11.09.2013 09:38, shahid nayeem wrote:
I checked in folder
/cygdrive/c/packages/gromacs-4.6.3/build/src/contrib/fftw/gmxfftw-prefix/lib/libfftw3.a
, this file exists but perhaps
On 9/11/13 12:12 AM, Dwey Kauffman wrote:
True, but thermostats allow temperatures to oscillate on the order of a few
K,
and that doesn't happen on the macroscopic level either. Hence the small
disconnect between a system that has thousands of atoms and one that has
millions or trillions.
Hi there,
I have installed a couple of days ago the latest (4.6.3) version of
Gromacs, in a 12-core Xeon machine using the latest version (14.0) of
the non-comercial Intel C++ compiler for linux.
The installation seems to have succeeded, but I ran the latest set of
tests available (4.6.1)
On 9/11/13 5:28 AM, Jernej Zidar wrote:
Dear Justin,
I followed your advice and started a gas-phase simulation. I removed the
solvent and simulated only the polymer molecule but I ended up with this error:
One of the box vectors has become shorter than twice the cut-off length or
On Wed, Sep 11, 2013 at 3:08 PM, Mark Abraham mark.j.abra...@gmail.comwrote:
No idea if it's causing your problem, but you need all the Ds in
-DBUILD_SHARED_LIBS=no
Mark
On Wed, Sep 11, 2013 at 6:15 AM, Qin Qiao qiaoqi...@gmail.com wrote:
Dear all,
I'm trying to install gromacs4.6.3
Various things changed after 4.6.1, such that the 4.6.1 tests cannot
be used to verify correctness of more recent versions. Unfortunately,
the install guide got out of sync there. I've changed the link so that
it directs you to the 4.6.3 test set. Please try that, and I expect
you'll have no
I am trying to simulate a peptide inside a nanotube and using isotropic
pressure coupling for the system. The nanotube is immersed in a cuboidal
box of water and aligned along the z direction of the box.
The XX, YY components of the stress tensor are about ~570 bars and the ZZ
component is about
Hi Justin,
Should I use R-B dihedrals for DMPC lipids rather than periodic
dihedrals.
I'm getting an Error message like,
ERROR 18815 [file topol.top, line 54180]:
No default Ryckaert-Bell. types
ERROR 18816 [file topol.top, line 54181]:
No default Ryckaert-Bell. types
--Rama
On
On 9/11/13 9:01 AM, HANNIBAL LECTER wrote:
I am trying to simulate a peptide inside a nanotube and using isotropic
pressure coupling for the system. The nanotube is immersed in a cuboidal
box of water and aligned along the z direction of the box.
The XX, YY components of the stress tensor are
Thanks for the comments, Mark.
Sorry that I did not explain my question clear enough.
I am actually talking about post-equilibration time average. I understand that
some instantaneous deviations are expected, but the simulations should be
correct as long as the ensemble averages are the same
500ps simulations. Yes everything is immersed in a bath of water. Can you
please elaborate a little more as to why do you doubt semiisotropic
coupling may not be necessary?
On Wed, Sep 11, 2013 at 9:05 AM, Justin Lemkul jalem...@vt.edu wrote:
On 9/11/13 9:01 AM, HANNIBAL LECTER wrote:
I am
Hmm, that looks like a problem. Which GROMACS version, and which
compiler version? (See mdrun -version)
On Wed, Sep 11, 2013 at 3:06 PM, Xu, Jianqing x...@medimmune.com wrote:
Thanks for the comments, Mark.
Sorry that I did not explain my question clear enough.
I am actually talking about
On 9/11/13 9:05 AM, Rama Krishna Koppisetti wrote:
Hi Justin,
Should I use R-B dihedrals for DMPC lipids rather than periodic
dihedrals.
You should use whatever the force field tells you.
I'm getting an Error message like,
ERROR 18815 [file topol.top, line 54180]:
No default
On 9/11/13 9:09 AM, HANNIBAL LECTER wrote:
500ps simulations. Yes everything is immersed in a bath of water. Can you
please elaborate a little more as to why do you doubt semiisotropic
coupling may not be necessary?
Water should compress isotropically. I understand where you're coming
Yes
On Wed, Sep 11, 2013 at 9:18 AM, Justin Lemkul jalem...@vt.edu wrote:
On 9/11/13 9:09 AM, HANNIBAL LECTER wrote:
500ps simulations. Yes everything is immersed in a bath of water. Can you
please elaborate a little more as to why do you doubt semiisotropic
coupling may not be
Would there be artifacts because of that?
On Wed, Sep 11, 2013 at 9:20 AM, HANNIBAL LECTER hanniballecte...@gmail.com
wrote:
Yes
On Wed, Sep 11, 2013 at 9:18 AM, Justin Lemkul jalem...@vt.edu wrote:
On 9/11/13 9:09 AM, HANNIBAL LECTER wrote:
500ps simulations. Yes everything is
On 9/11/13 9:20 AM, HANNIBAL LECTER wrote:
Yes
Then I would call your outcome an artifact of a physically unreasonable setup.
-Justin
On Wed, Sep 11, 2013 at 9:18 AM, Justin Lemkul jalem...@vt.edu wrote:
On 9/11/13 9:09 AM, HANNIBAL LECTER wrote:
500ps simulations. Yes everything
Thanks again for the message!
I am using the Gromacs 4.6.3.
Hmm, indeed a lot of information from mdrun -version.
Both servers used gcc, and they are in different versions.
Server 1 (AMD) has gcc 4.1.2
Server 2 (Intel) has gcc 4.4.7
I know the compilers are a bit old, but can this cause
Yep. There are lots of known bugs in old compilers. It's not an
accident that the GROMACS installation instructions tell you to get up
to date compilers - both for correctness and performance of the
resulting code. 4.4.7 might be correct (if you can run the 4.6.3
regression tests on it, it might
Hi Justin,
These type of dihedrals I'm using now, Is it correct format.
[ dihedral
s
]
; GROMOS improper dihedrals
; ai aj ak al funct angle fc
LH1 LOS LC2 LC22 35.26 334.72
LC LOS LO LP22 0.00 167.36
LC LOS LO LP22 0.00
On 9/11/13 9:57 AM, Rama Krishna Koppisetti wrote:
Hi Justin,
These type of dihedrals I'm using now, Is it correct format.
[ dihedral
s
]
; GROMOS improper dihedrals
; ai aj ak al funct angle fc
LH1 LOS LC2 LC22 35.26 334.72
LC LOS LO LP22
Now all tests PASSED. Thanks!
But the folder that appeared after decompression of the tarball was
actually the regressiontests-4.6.2.
Regarding the benchmark, I tryied to compile with gcc 4.7, but without
success. Then I gave icc a try. But can't recall right now the reason
for the
Those lines are related to DMPC lipid dihedrals.
-_Rama
On Wed, Sep 11, 2013 at 8:17 AM, Justin Lemkul jalem...@vt.edu wrote:
On 9/11/13 9:05 AM, Rama Krishna Koppisetti wrote:
Hi Justin,
Should I use R-B dihedrals for DMPC lipids rather than periodic
dihedrals.
You should use
On 9/11/13 10:06 AM, Rama Krishna Koppisetti wrote:
Those lines are related to DMPC lipid dihedrals.
I know that much. I am trying to extract some actual detail here so I can help
you reach a conclusion. The error indicates line numbers in the topology. On
those line numbers are a
Sorry.., Justin
Yes.. It is a sequence of atom numbers from DMPC atoms. The errors are
coming from all DMPC atoms dihedrals only not by protein dihedrals.
--Rama
On Wed, Sep 11, 2013 at 9:08 AM, Justin Lemkul jalem...@vt.edu wrote:
On 9/11/13 10:06 AM, Rama Krishna Koppisetti wrote:
Hi,
I have a piece of code in C that is supposed to write atom coordinates
in xtc format. I want to use the xtcio functions from the gromacs
library. I use open_xtc() and close_xtc() at the beginning and end of my
code. Between them I have multiple calls to write_xtc(), one for each
frame. I
On Wed, Sep 11, 2013 at 4:03 PM, Herbert Georg hcge...@ufg.br wrote:
Now all tests PASSED. Thanks!
But the folder that appeared after decompression of the tarball was actually
the regressiontests-4.6.2.
Sure - no content changed between those two, so I just copied the
tarball. Content changed
I appreciate your comments/suggestions, Mark. But trust me ... everything
may become rocket science when you work for a company with ~10,000
employees.
Cheers,
On Wed, Sep 11, 2013 at 3:23 AM, Mark Abraham mark.j.abra...@gmail.comwrote:
Hi,
There's simply no way you can expect compilers
OK, it's your funeral - but you only need the compiler on the machine
that builds GROMACS, and that compiler doesn't have to be installed in
root file space.
Mark
On Wed, Sep 11, 2013 at 10:32 PM, Guanglei Cui
amber.mail.arch...@gmail.com wrote:
I appreciate your comments/suggestions, Mark. But
Hi,
I wrote an entry in the rtp file of the force field OPLS-AA + Berger lipid
parameters
[ DMPC ]
[ atoms ]
;ai Ber_type charge resnr mass
CN1LC30.4000115.0350
CN2LC30.40001 15.0350
CN3LC30.4000115.0350
NTMLNL
On 9/11/13 6:19 PM, Rama Krishna Koppisetti wrote:
Hi,
I wrote an entry in the rtp file of the force field OPLS-AA + Berger lipid
parameters
[ DMPC ]
[ atoms ]
;ai Ber_type charge resnr mass
CN1LC30.4000115.0350
CN2LC30.40001 15.0350
On 9/11/13 6:07 PM, Rafael I. Silverman y de la Vega wrote:
Hi all,
in another thread it was recommended that instead of changing the atom
types by analogy to ones with the desired parameter already assigned, that
instead one should assign bonded parameters by analogy. I was just
wondering
Justin Lemkul wrote
On 9/11/13 12:12 AM, Dwey Kauffman wrote:
True, but thermostats allow temperatures to oscillate on the order of a
few
K,
and that doesn't happen on the macroscopic level either. Hence the
small
disconnect between a system that has thousands of atoms and one that has
i want to analyze the change of secondary structure of the mainchian frome
residue 20 to residue 60. so i want to make a index file that only contain the
maninchian+H from residue 20 to residue 60. i have inputed the command
make_ndx -f em.pdb -o index.ndx, but i don't kown how to do next .
I carried out independent NPT processes with different tau_p values =
1.5,
1.0 and 0.5
## tau_p 1.5
Energy Average Err.Est. RMSD Tot-Drift
---
Pressure
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