Dear all,I am a beginner here. I have prepared my ligand topology file using
prodrg, it gave me the following error,
PRODRG> Starting up PRODRG version AA100323.0717PRODRG> Parameter set
'pd/gromos96' (fftype=2).PRODRG> PDB mode detected.PRODRG> WARNING: deleted
hydrogen(s) from your input.PRODR
Hi,
I used the "gmx do_dssp" command to get the secondary structure of the protein
during the simulation but the resolution of the resulted .xpm file is very low.
how can I increase its resolution?
Thank you, Mohammad.
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Hi,
What is your system details?Do you have GPU ,if yes CUDA library is
installed?
if not please install CUDA library and MPI packages too!
hope it will fix
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On 2/12/16 8:47 AM, Alexander Alexander wrote:
Dear Gromacs user,
I am calculation the PMF of a single water molecule to pull it away from
top of metallic surface along vacuum in the Z direction ,following the
Justin umbrella tutorial. I am only interested in the behavior of PMF in
0.002 nm t
On 2/12/16 11:06 AM, Malihe Hasanzadeh wrote:
Dear Justin,
Thank you for your reply. I have parameters from some manuscript and add
all of them in force field. There is two parts of dihedral types in
ffbonded.itp that one of them has func=4 and another has func=9. Also I
have two types of param
Hi,
I configure libxml2 without python or threads or anything except zlib,
since we use none of that. You have enabled python, which is probably not
fatal, but has caused problems some other time.
More importantly is that you are trying to specify everything to cmake, and
not handling zlib correc
Hi,
I have compiled my own libxlm2-2.9.3 (this is not a devel from what I know)
Using:
./configure CC=mpixlcxx_r --prefix=/home/ikosh/programs/autotools-bin
--with-python-install-dir=/home/ikosh/programs/autotools-bin --with
-zlib=/soft/libraries/alcf/current/xl/ZLIB --enable-static --disable-shar
Hi,
What command did you use to use their libxml2? Things work for me, but that
doesn't mean there isn't a problem :-)
Mark
On Fri, 12 Feb 2016 20:41 Irina Kosheleva
wrote:
> Hello Mark,
> This is the response I'm getting
> Please send your problem to gmx user forum
> http://www.gromacs.org/Su
Hello Mark,
This is the response I'm getting
Please send your problem to gmx user forum
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List). Your problem
seems come from Gromacs cmake command parsing. The related source code is
pretty convoluted. Relevant Gromacs developer may answer
Hi All,
I'm trying to install GROMACS 5.1.2 on ubuntu 14.04 LTS. I used:
cmake .. -DGMX_GPU=on -DGMX_USE_OPENCL=on -DGMX_BUILD_OWN_FFTW=ON
-DREGRESSIONTEST_DOWNLOAD=ON
Everything went fine, but make ended with:
[100%] Building C object
src/gromacs/CMakeFiles/libgromacs.dir/__/external/thread_mpi/
Dear Justin,
Thank you for your reply. I have parameters from some manuscript and add
all of them in force field. There is two parts of dihedral types in
ffbonded.itp that one of them has func=4 and another has func=9. Also I
have two types of parameters for dihedral;* Proper* and* Improper *dihedr
Hello Adam
For me alcf scientist suggested to compile with:
Use xl compilers in your .soft environment.
cmake -DCMAKE_C_COMPILER=mpixlc_r -DCMAKE_CXX_COMPILER=mpixlcxx_r
-DCMAKE_TOOLCHAIN_FILE=BlueGeneQ-static-XL-C -DGMX_SIMD=IBM_QPX
-DFFTWF_INCLUDE_DIR=/soft/libraries/alcf/current/xl/FFTW3/incl
Sorry for the confusion, yes, find and replace Marenostrum with Juqeen for most
of that last mail. Just got some PRACE test accounts and I got myself confused.
The 2.6 version of cmake was from Marenostum before I’d loaded the proper
module.
Try again:
Fermi (failed build, xl compiler) - cmake
Hi,
As Adam says, you want to understand the reason why the forcefield
specifies the settings it does. For example, until at least AMBER 2003,
their force field papers did not specify PME parameters more precisely than
"x nm cutoff was used." If PME was used at all. ;-) So you can be guided
also b
Hi,
On Fri, Feb 12, 2016 at 1:42 PM Hardy, Adam wrote:
> Hi Mark,
>
> I was able to compile GROMACS on Marenostrum, the cmake version is
> "2.6-patch 2".
>
That seems wildly unlikely. GROMACS has required CMake 2.8+ for quite a few
versions now.
On Fermi it failed, the cmake version is "2.8.8"
Dear Gromacs user,
I am calculation the PMF of a single water molecule to pull it away from
top of metallic surface along vacuum in the Z direction ,following the
Justin umbrella tutorial. I am only interested in the behavior of PMF in
0.002 nm to 0.8 nm intervalon top of the surface, but I do no
Dear all,
I am using GROMACS-4.6.5 for studying gas hydrates and related
systems.
A useful order parameter which indicates water to hydrate transition is the
F4 order parameter where F4 is related to the H--O--O--H dihedral angle for
a pair of water molecules
Exact expression for F4 can be f
There are people more qualified than me to explain the fine details of this,
but in brief:
Verlet on it's own doesn't adjust rvdw or rcoloumb (rcoulomb may be adjusted if
you rae using PME for the coulomb interactions), but by default it will adjust
the neighbour list cut-off (rlist) to remain
I have trouble in correctly setting cut-offs with Verlet scheme to match
force-field specific settings.
It automatically adjusts cut-off and it looks like they change their
values from ones recommended for the force field.
Is there a way to correct it and set up them properly?
The paper on FF l
Hi Mark,
I was able to compile GROMACS on Marenostrum, the cmake version is "2.6-patch
2".
On Fermi it failed, the cmake version is "2.8.8".
This is not necassarily a fair comparison. I compiled using gnu on Marenostrum
as I couldn't find the xl compiler oddly and wasn't feeling compelled to
Hi,
Do the cmake versions differ?
Mark
On Fri, 12 Feb 2016 12:44 Hardy, Adam wrote:
> Dear all,
>
>
> I'm having some difficulty compiling GROMACS 5.1.1 on a Bluegene/Q
> machine. This is using the xl compiler.
>
>
> I recieve the error:
>
>
> ADD_LIBRARY for library mdrun_objlib is used with
Dear all,
I'm having some difficulty compiling GROMACS 5.1.1 on a Bluegene/Q machine.
This is using the xl compiler.
I recieve the error:
ADD_LIBRARY for library mdrun_objlib is used with the MODULE option, but the
target platform supports only STATIC libraries. Building it STATIC instead.
Dear Ming,
Still, that means that your simulation is ok, or at least not broken in the way
your visualisation software suggested.
Kind regards,
Erik
> On 12 Feb 2016, at 06:51, Ming Tang wrote:
>
> Dear Erik,
>
> Thanks for your advice. I think you are right. However, when using -pbc
> whol
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