Hello:
I am trying to compile Gromacs-4.6.2 for a GPU cluster with following
command:
CC=icc FC=ifort F77=ifort CXX=icpc
CMAKE_PREFIX_PATH=/export/intel/cmkl/include/fftw:/export/mpi/mvapich2.amd/1.4
cmake .. -DGMX_MPI=ON
-DCMAKE_INSTALL_PREFIX=/home/albert/install/gromacs -DGMX_GPU=ON
-
On 2013-07-04 08:32, Ishwor wrote:
I have really tried to calculate diffusion coefficient using both commands
but i cant find the comparable results.
i have my *.mdp file as
;PREPROCESSING parameters
tinit = 0
integrator = md
dt =.002
nsteps =
why not to pick up a QM technique to study the "interaction"?
Dr. Vitaly V. Chaban
On Thu, Jul 4, 2013 at 3:58 AM, Jong Wha Lee wrote:
> Thank you Mark and Vitaly.
>
>
>
> I understand that simulation of protons in the solution phase is
> unphysical.
> Though I haven't mentioned beforehand, I'm
It would be nice to see plotted velocity autocorrelation function, VACF,
which you integrate?
The resulting diffusion constant looks crazy large, so there must be
something rotten in the VACF.
Dr. Vitaly V. Chaban
On Thu, Jul 4, 2013 at 8:32 AM, Ishwor wrote:
> I have really tried to calcul
On Thu, Jul 4, 2013 at 9:09 AM, Albert wrote:
> Hello:
>
> I am trying to compile Gromacs-4.6.2 for a GPU cluster with following
> command:
>
>
> CC=icc FC=ifort F77=ifort CXX=icpc
> CMAKE_PREFIX_PATH=/export/intel/cmkl/include/fftw:/export/mpi/mvapich2.amd/1.4
> cmake .. -DGMX_MPI=ON -DCMAKE_INS
Yeah, ab initio MD sounds like the clearly best approach, and you will
not do that with GROMACS.
Mark
On Thu, Jul 4, 2013 at 9:50 AM, Dr. Vitaly Chaban wrote:
> why not to pick up a QM technique to study the "interaction"?
>
> Dr. Vitaly V. Chaban
>
>
> On Thu, Jul 4, 2013 at 3:58 AM, Jong Wha L
On Thu, Jul 4, 2013 at 5:38 AM, Ishwor wrote:
> Dear all
> I have calculated the diffusion coefficient using command g_msd and I want
> to calculate diffusion coefficient using command g_velacc. I am confused
> with some terms.
> 1>I have looked the manual page of g_velacc and i found the stateme
It seems that GROMACS is looking for a shared library, but you compiled
FFTW statically (--enable-static). Either recompile FFTW --enable-shared
or link GROMACS statically by passing -DBUILD_SHARED_LIBS=OFF to cmake.
On our cluster I had problems compiling the MPI version of GROMACS with
dynam
On Thu, Jul 4, 2013 at 10:43 AM, Oliver Schillinger
wrote:
> It seems that GROMACS is looking for a shared library, but you compiled FFTW
> statically (--enable-static). Either recompile FFTW --enable-shared or link
> GROMACS statically by passing -DBUILD_SHARED_LIBS=OFF to cmake.
The FindFFTW.cm
Dear users,
I'm trying to run MD with SWM4-DP model (data from
http://virtualchemistry.org), but I always have error:
"Can not invert matrix, determinant =".
I did energy minimization etc. but it don't help...
May be someone have complete stuff of files for
shell MD, including .mdp file ?
Serge
On Thu, Jul 4, 2013 at 10:31 AM, Mark Abraham wrote:
> On Thu, Jul 4, 2013 at 9:09 AM, Albert wrote:
>> Hello:
>>
>> I am trying to compile Gromacs-4.6.2 for a GPU cluster with following
>> command:
>>
>>
>> CC=icc FC=ifort F77=ifort CXX=icpc
>> CMAKE_PREFIX_PATH=/export/intel/cmkl/include/fftw
On 07/04/2013 10:43 AM, Oliver Schillinger wrote:
It seems that GROMACS is looking for a shared library, but you
compiled FFTW statically (--enable-static). Either recompile FFTW
--enable-shared or link GROMACS statically by passing
-DBUILD_SHARED_LIBS=OFF to cmake.
Hello guys:
thanks a l
Hi all,
I ran 20ns simulation on protein drug complex..now i want to check overall
stability of this complex
to acheive this i did following i supplied index file and choose
Protein_Lig option for both least square fit and RMSD calculation..i used
following command
g_rms -f em.tpr (intital struct
No idea. I do not think there is any need for you to use
BUILD_SHARED_LIBS=OFF, and it could well be the problem.
Mark
On Thu, Jul 4, 2013 at 11:07 AM, Albert wrote:
> On 07/04/2013 10:43 AM, Oliver Schillinger wrote:
>>
>> It seems that GROMACS is looking for a shared library, but you compiled
Hi Tsjerk,
Thanks for information i limited number of frames ..which worked perfectly
:)
Cheers,
Sainitin
On Thu, Jun 27, 2013 at 8:06 PM, Tsjerk Wassenaar wrote:
> Hi Sainitin,
>
> You can extract only the protein and ligand, using a suitable index file,
> or you can limit the number of fram
On 07/04/2013 11:18 AM, Mark Abraham wrote:
No idea. I do not think there is any need for you to use
BUILD_SHARED_LIBS=OFF, and it could well be the problem.
Mark
thank you all the same.
I found the problem, there is a subdirectory in cuda5.0:
/export/cuda5.0/cuda
the problem solved after I
My .mdp file is following:
title= spce
cpp = /lib/cpp
integrator = md
cutoff-scheme= verlet
nsteps = 5
nstlist = 10
dt = 0.001
pbc = xyz
coulombtype
Hello:
I am using the following configuration to compile gromacs-4.6.2 in a
GPU cluster:
CC=icc FC=ifort F77=ifort CXX=icpc
CMAKE_PREFIX_PATH=/export/intel/cmkl/include/fftw:/export/mpi/mvapich2-1.8-rhes6
cmake .. -DGMX_MPI=ON
-DCMAKE_INSTALL_PREFIX=/home/albert/install/gromacs -DGMX_GPU
Those are remarks, not errors. Find the error.
Mark
On Jul 4, 2013 11:43 AM, "Albert" wrote:
> Hello:
>
> I am using the following configuration to compile gromacs-4.6.2 in a GPU
> cluster:
>
>
>
> CC=icc FC=ifort F77=ifort CXX=icpc CMAKE_PREFIX_PATH=/export/**
> intel/cmkl/include/fftw:/**expo
Dear Gromacs users,
I want to convert a tpr file from different version of Gromacs, I have
looked in the archive, I found that I have to use regenerate but I didn't
understand exactly if it is a command or a special program that I have to
use. Could you please inform me about since I a new gromacs
You can't convert a .tpr file's version in either direction. We try to
make the .tpr format backwards compatible, inasmuch as an old .tpr
should generally still work with new code.
For learning about the process of building one, check out some
tutorial material online.
Mark
On Thu, Jul 4, 2013 a
Dear Mark ,
Thank you for your quick reply.
Could you please provide me a tutorial link example ? I will be grateful.
Thank you very much
On 4 July 2013 21:00, Mark Abraham wrote:
> You can't convert a .tpr file's version in either direction. We try to
> make the .tpr format backwards compatibl
Google knows them better than I :-)
Mark
On Thu, Jul 4, 2013 at 2:05 PM, Souilem Safa wrote:
> Dear Mark ,
> Thank you for your quick reply.
> Could you please provide me a tutorial link example ? I will be grateful.
> Thank you very much
>
>
> On 4 July 2013 21:00, Mark Abraham wrote:
>
>> You
On 7/4/13 5:17 AM, Sainitin Donakonda wrote:
Hi all,
I ran 20ns simulation on protein drug complex..now i want to check overall
stability of this complex
to acheive this i did following i supplied index file and choose
Protein_Lig option for both least square fit and RMSD calculation..i used
f
Hi Justin,
Thank your very much for reply i have done both ways i also have backbone
RMSD data so i will consider only this in my analysis.
Cheers,
Sainitin
On Thu, Jul 4, 2013 at 3:50 PM, Justin Lemkul wrote:
>
>
> On 7/4/13 5:17 AM, Sainitin Donakonda wrote:
>
>> Hi all,
>>
>> I ran 20ns si
FYI: 4.6.2 contains a bug related to thread affinity setting which
will lead to a considerable performance loss (I;ve seen 35%) as well
as often inconsistent performance - especially with GPUs (case in
which one would run many OpenMP threads/rank). My advice is that you
either use the code from git
Hi all, I am trying to simulate a protein complex of two protein with and a
ligand. I would like to learn from other's experience, how to prepare the
complex. do i prepare the protein components separately and then combine
the gro files?
thanks
ayesha
--
gmx-users mailing listgmx-users@gromacs
On 7/4/13 11:52 AM, Ayesha Fatima wrote:
Hi all, I am trying to simulate a protein complex of two protein with and a
ligand. I would like to learn from other's experience, how to prepare the
complex. do i prepare the protein components separately and then combine
the gro files?
No need. pdb2
As some may end up following these steps let me make a few comments.
On Sun, Jun 30, 2013 at 1:06 AM, Mare Libero wrote:
> Thanks guys! I think it's working now. Just in case others may run into the
> same difficulties, I am summarizing below what worked for me.
>
> I installed both gcc-4.4 and g
On Mon, Jun 24, 2013 at 4:43 PM, Szilárd Páll wrote:
> On Sat, Jun 22, 2013 at 5:55 PM, Mirco Wahab
> wrote:
>> On 22.06.2013 17:31, Mare Libero wrote:
>>>
>>> I am assembling a GPU workstation to run MD simulations, and I was
>>> wondering if anyone has any recommendation regarding the GPU/CPU
>
On 07/04/2013 05:52 PM, Szilárd Páll wrote:
FYI: 4.6.2 contains a bug related to thread affinity setting which
will lead to a considerable performance loss (I;ve seen 35%) as well
as often inconsistent performance - especially with GPUs (case in
which one would run many OpenMP threads/rank). My a
I plan to release 4.6.3 tomorrow, once I've gotten some more urgent
stuff off my plate :-).
Mark
On Thu, Jul 4, 2013 at 7:47 PM, Albert wrote:
> On 07/04/2013 05:52 PM, Szilárd Páll wrote:
>>
>> FYI: 4.6.2 contains a bug related to thread affinity setting which
>> will lead to a considerable per
Hello :
I've got a question about the the entropy. As we all know that in the
md.edr file it will give us the entropy value of the system along the
simulations.
However, my system is a protein/membrane system, and I am only would
like to make statics for the protein/water related entropy. I
On 07/04/2013 07:59 PM, Mark Abraham wrote:
I plan to release 4.6.3 tomorrow, once I've gotten some more urgent
stuff off my plate:-).
Mark
thanks a lot for kind messages, Mark.
It seems that Gromacs update more and more frequently
Albert
--
gmx-users mailing listgmx-users@gromacs.o
No.
This is a statistical mechanical issue, not a GROMACS issue. For
interacting systems, entropy is a quantity describing the system as a
whole, and cannot be defined for different parts of the system, at
least not in any way such that the individual components can be added
together.
I'm also n
Hi all,
I have set of 5 different drugs which are complexed with same protein
(homology model). So i wanted to run MD simulation using gromacs. I
followed one procedure as follows
1) I took homology model and minimized it
2) Then followed general procedure of simulation in gromacs.
4 drugs with
On 7/4/13 3:00 PM, Sainitin Donakonda wrote:
Hi all,
I have set of 5 different drugs which are complexed with same protein
(homology model). So i wanted to run MD simulation using gromacs. I
followed one procedure as follows
1) I took homology model and minimized it
2) Then followed general p
Hi Justin,
Thanks for reply.
using pdbgmx i generated charmm27 force field for protein
I prepared ligand topologies using swissparam online tool for all 5
ligands. But it worked for 4 and 5th one is creating problem at energy
minimization step.
Thanks
-sainitin
On Thu, Jul 4, 2013 at 9:02 PM,
On 7/4/13 3:16 PM, Sainitin Donakonda wrote:
Hi Justin,
Thanks for reply.
using pdbgmx i generated charmm27 force field for protein
I prepared ligand topologies using swissparam online tool for all 5
ligands. But it worked for 4 and 5th one is creating problem at energy
minimization step.
Dear Mark,
Thank you, I did it already :)
I tried to make a nick name because the actual contains personal
informations but always google knows every thing ;)
Some additional fun also with using Gromacs when there is a luck of
concentration ;)
On 4 July 2013 22:44, Mark Abraham wrote:
> Google
Dear Gmx users,
I want to simulate the liquid water vapour interface in presence of an
externally applied
electric field.I know there is provision to add external field in gromacs
but this being a
perturbation to the normal conditions how do we know during equilibration
that the system
is equilibr
Hello:
I've installed Gromacs-4.6.2 in GPU cluster with following configurations:
CC=icc FC=ifort F77=ifort CXX=icpc
CMAKE_PREFIX_PATH=/export/intel/cmkl/include/fftw:/export/mpi/mvapich2-1.8-rhes6
cmake .. -DGMX_MPI=ON
-DCMAKE_INSTALL_PREFIX=/home/albert/install/gromacs -DGMX_GPU=ON
-DBUIL
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