Hi,
from the double output it looks like two identical mdruns,
each with 1 PP process and 10 OpenMP threads, are started.
Maybe there is something wrong with your MPI setup (did
you by mistake compile with thread-MPI instead of MPI?)
Carsten
On 09 Sep 2014, at 09:06, Albert
thank you for reply.
I compiled it with command:
env CC=mpicc CXX=mpicxx F77=mpif90 FC=mpif90 LDF90=mpif90
CMAKE_PREFIX_PATH=/home/albert/install/intel-2013/mkl/include/fftw:/home/albert/install/intel-mpi/bin64
cmake .. -DBUILD_SHARED_LIB=OFF -DBUILD_TESTING=OFF
thank you for reply.
I compiled it with command:
env CC=mpicc CXX=mpicxx F77=mpif90 FC=mpif90 LDF90=mpif90
CMAKE_PREFIX_PATH=/home/albert/install/intel-2013/mkl/include/fftw:/home/albert/install/intel-mpi/bin64
cmake .. -DBUILD_SHARED_LIB=OFF -DBUILD_TESTING=OFF
I recompiled Gromacs-5.0.1, finally it works now
Probably I made some mistakes in previous compiling
thanks a lot guys
regards
Albert
On 09/09/2014 09:16 AM, Carsten Kutzner wrote:
Hi,
from the double output it looks like two identical mdruns,
each with 1 PP process and 10 OpenMP
Dear all
I would like to simulate coarse grained thin polymer films supported on a
wall or a substrate (I don't really mind) but with the one interface to be
free. I would like to do this under NPT conditions.
I would expect that this can only be done by putting pbc=xy, as in the to
the
Dear gromacs user:
I plan to do a coarse grain simulation for a whole virus coat. It only contains
virus surface protein, so I'm afraid it will collapse due to lack of inner
member lipids. I plan to add a Spherical Position Restrain from the center of
the Box, to prevent the surface protein
On 9/9/14 12:51 AM, Christina Florina wrote:
Hi,
I have included the link to my dropbox where I have attached my
gromacs topology files. Though I have included the cyclohexane itp file in
the .top file still I am the same error NO SUCH MOLECULETYPE CHX. SO,
Kindly need help in this
A postdoctoral position in computational physics of Carbon Nano Tubes (CNTs) is
available at Khalifa University, Abu Dhabi, UAE.The successful candidate will
work in a highly collaborative environment with experimental and theoretical
scientist.
The candidate should have a good knowledge of
Hi,
Thanks for your suggestions.
If the .itp file has error, is there any other way to generate .itp
files for the solvents or do i need to write them manually? Because the
.itp files I have attached are generated using PRODRG. If I edit the
chx.itp file based on the corrections you have
Dear all,
I am currently trying to “mutate a protein by changing its backbone directly,
i.e. I am not interested in changing a specific amino acid against another
(I’ve found out that you can use VMD or Pymol for this purpose), but I am
rather interested in changing certain atoms in the
On 9/9/14 8:51 AM, Tim Stauch wrote:
Dear all,
I am currently trying to “mutate a protein by changing its backbone directly,
i.e. I am not interested in changing a specific amino acid against another (I’ve
found out that you can use VMD or Pymol for this purpose), but I am rather
Hello all
I would like to plot mean square displacement of hydrogen atoms of protein
versus temperature (in order to get dynamical transition temperature). I am
using g_msd for this purpose (g_msd -f *_nopbc.xtc -s *.tpr -n index.ndx -o
*.xvg) . I am getting following curves as uploded in :
Thank you very much to all of you. That should explain the difference in
performance.
I'll also discuss it with a more gromacs-knowledgeable colleague of mine.
Best Regards.
2014-09-06 8:58 GMT+02:00 Abhi Acharya abhi117acha...@gmail.com:
Thank you Mark and Szilard for your replies. It gave
Hi,
Thank you for the suggestions. I did the modifications in the .itp
file and the grompp step generated the .tpr file successfully.
But now, I am facing problem in the genion step, while adding the NA
ions the group 13 (usually SOL for water solvent) is not present there. If
I select
Hello all
I would like to plot mean square displacement of hydrogen atoms of protein
versus temperature (in order to get dynamical transition temperature). I am
using g_msd for this purpose (g_msd -f *_nopbc.xtc -s *.tpr -n index.ndx -o
*.xvg) . I am getting following curves as uploded in :
Dear gromacs users
I did MD simulation of my system containing DPPC lipids + water molecule
and 4 drug molecules.
I saw trajectory file using VMD.
Unfortunately, drug molecules jump across the box.
How to resolve this PBC problem?
which of -pbc options (none, mol, res, atom, nojump, cluster
Hi,
Try -pbc nojump
Best,
Mike
On 09/09/2014 15:11, shahab shariati shahab.shari...@gmail.com wrote:
Dear gromacs users
I did MD simulation of my system containing DPPC lipids + water molecule
and 4 drug molecules.
I saw trajectory file using VMD.
Unfortunately, drug molecules jump across
Also if you want to fix the position on the centre of mass (no rotating or
translating) try
-pbc nojump
Followed by -fit rot+trans
Remember to use you new .xtc from your no jump command for the -fit
command. Then view in vmd and your molecules will not jump, rotate, or
translate around the box.
On 9/9/14 9:41 AM, Christina Florina wrote:
Hi,
Thank you for the suggestions. I did the modifications in the .itp
file and the grompp step generated the .tpr file successfully.
But now, I am facing problem in the genion step, while adding the NA
ions the group 13 (usually SOL for
Thank you very much!
Sincerely
nil
On Thu, Sep 4, 2014 at 2:51 PM,
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Hi,
Is this rather large box a system that can actually be simulated with
a useful speed on a single Fermi GPU? Even with 5 fs time-step you
won't get much more than 1-1.5 ns/day on a fast Fermi GPU like a GTX
580.
Given that you are quite a bit above the limit, unless you are using a
quite
Dear Users
I am trying to find the net charge at the physiological pH value for a
protein molecule (Thrombin) in my case and am wondering if it is possible
to use GROMACS for doing it.
I am very new to GROMACS and at present I have been going through the
tutorials by Dr. Lemkul. I have seen that
Hi,
Can someone please explain if it is necessary to use the -t flag during
NPT equilibration?
The following command is mentioned in the lysozyme tutorial:
$ grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr
whereas , I have found the command without the -t flag in another
Hi Ansuman,
That is optional.
Regards,
Vijayan.R
On Tue, Sep 9, 2014 at 4:38 PM, Ansuman Biswas
ansu...@physics.iisc.ernet.in wrote:
Hi,
Can someone please explain if it is necessary to use the -t flag during
NPT equilibration?
The following command is mentioned in the lysozyme
On 9/9/14 5:09 PM, R.S.K.Vijayan wrote:
Hi Ansuman,
That is optional.
Generally speaking, no, it's not. The real truth lies in what the .mdp settings
are and what the intent of NPT is. If you don't pass the .cpt file to grompp
-t, you stand to lose much (or all) of the previous state
On 9/9/14 3:51 PM, Agnivo Gosai wrote:
Dear Users
I am trying to find the net charge at the physiological pH value for a
protein molecule (Thrombin) in my case and am wondering if it is possible
to use GROMACS for doing it.
I am very new to GROMACS and at present I have been going through
Quick answer is no.
In fact, that's really not what (standard) molecular dynamics is for. You
need a constant-pH MD method for that. Read this to get a bit more
acquainted with the subject (might be overkill for you, because I doubt
this is what you want/need):
Dear users,
I did some simulations of organic molecules in solution to study how
they interact, but I'm facing some problems and your help would be greatly
appreciated.
Consider the following case: I simulated two copies of molecule AcO
starting from a structure in which they are
On 9/9/14 9:09 PM, Leandro Bortot wrote:
Dear users,
I did some simulations of organic molecules in solution to study how
they interact, but I'm facing some problems and your help would be greatly
appreciated.
Consider the following case: I simulated two copies of molecule AcO
Thank you for your quick answer, Justin.
I'll make new .edr files using only CPUs.
Best regards,
Leandro
On Tue, Sep 9, 2014 at 10:11 PM, Justin Lemkul jalem...@vt.edu wrote:
On 9/9/14 9:09 PM, Leandro Bortot wrote:
Dear users,
I did some simulations of organic molecules in
did you center everything, or are you just looking at it in VMD?
Gesendet:Montag, 08. September 2014 um 18:30 Uhr
Von:Mahboobeh Eslami mahboobeh.esl...@yahoo.com
An:gmx-us...@gromacs.org gmx-us...@gromacs.org
Betreff:[gmx-users] protein-ligand complex by gromacs
hi GMX users
i have simulated
you should go down the list and use all the tools, and use some from seperate software. In my experience, the trjconv gets rid of say 4-5 crazy single points in a graph based on a single point where one of the atoms or residues involved moves between planes, which averidge out in a gaussian
Dear all,I would like to know what are the methods I could use to measure/plot the contact angle of a water nanodroplet on flat graphene.Is there a script or tool in GROMACS that can perform the contact angle calculation? I am aware that the commonly used Young's equation does not apply here,
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