Dear Justin
Very thanks for your reply.
You said "I suspect your Gromacs version is somewhat outdated, as recent
versions account for periodicity when
making this check". I used 4.5.5 version of gromacs. What version of
gromacs is more appropriate for my case.
Based on your suggestion, I used -m
Dear GMX users,
I have a question about the combination of the installation parameters. I
compiled the fftw lib with --enable-sse2 and configured the gromacs with "cmake
.. -DGMX_CPU_ACCELERATION=SSE4.1". I'd like to know if it is ok to use such a
combination?
Many thanks.
Mingjun--
gmx
Hi,
On Sep 16, 2013, at 11:23 AM, mjyang wrote:
> Dear GMX users,
>
>
> I have a question about the combination of the installation parameters. I
> compiled the fftw lib with --enable-sse2 and configured the gromacs with
> "cmake .. -DGMX_CPU_ACCELERATION=SSE4.1". I'd like to know if it
Dear Justin
About following warning in grompp using
WARNING 1 [file em.mdp]:
The sum of the two largest charge group radii (6.940482) is larger than
rlist (1.20)
You said "You probably have molecules split across PBC in the input
coordinate file. here's nothing wrong in that case"
I mention
Dear all
I would like to calculate the standard deviation (as the error bar) for
dV/dlanda.xvg file. I used g_analyze command as the following:
g_analyze -ffree_bi_0.9.xvg -av average_0.9
I got:
set average *standard deviation* *std. dev. /
sqrt(n-1)*…
On 9/16/13 7:37 AM, shahab shariati wrote:
Dear Justin
About following warning in grompp using
WARNING 1 [file em.mdp]:
The sum of the two largest charge group radii (6.940482) is larger than
rlist (1.20)
You said "You probably have molecules split across PBC in the input
coordinate file
On 9/16/13 3:06 AM, shahab shariati wrote:
Dear Justin
Very thanks for your reply.
You said "I suspect your Gromacs version is somewhat outdated, as recent
versions account for periodicity when
making this check". I used 4.5.5 version of gromacs. What version of
gromacs is more appropriate fo
On 9/16/13 9:47 AM, shahab shariati wrote:
Dear Justin
My input coordinate file is a gro file (sys.gro). When I visualize that by VMD,
all things is ok and true.
After minimization, I obtained a gro file (em.gro). When I visualize that by
VMD, About 5 DOPC molecules leave bilayer structure an
Dear Justin
Very very thanks for your quick reply.
> The sys.gro file is positioned within a box that is too large, a fact that is
> easily observable in VMD. I suspect that the void space results in
> instability.
If I positioned system in a smaller box, my problem (instability) solved ???
On 9/16/13 10:52 AM, shahab shariati wrote:
Dear Justin
Very very thanks for your quick reply.
The sys.gro file is positioned within a box that is too large, a fact that is
easily observable in VMD. I suspect that the void space results in instability.
If I positioned system in a smaller
Dear Justin
Very very thanks for your quick reply.
> The sys.gro file is positioned within a box that is too large, a fact that is
> easily observable in VMD. I suspect that the void space results in
> instability.
If I positioned system in a smaller box, my problem (instability) solved ???
Hi,
I'm attempting to build GROMACS 4.6.3 to run entirely within a single Xeon
Phi (i.e. native) with either/both Intel MPI/OpenMP for parallelisation
within the single Xeon Phi.
I followed these instructions from Intel for cross compiling for Xeon Phi
with cmake:
http://software.intel.com/en-u
Hello. I was calculating the viscosity of hexane through the Gromacs
command g_energy. Three files are generated: visco.xvg, evisco.xvg and
eviscoi.xvg. The file visco.xvg presents the shear viscosity and bulk, but
the value does not match the experimental. I used 8 ns simulation at
equilibrium. Ho
I am sorry for the late follow-up on this subject.
My results using PME electrostatics do not show any differences between
versions 4.5.4 and 4.6.3 (I also checked with 4.6.1 and it gave the same
results):
https://www.dropbox.com/s/o2kswrw5eq8fcsp/plot_batch-1_pme.png
I hope that you, Niels, hav
Hello,
On Sun, Sep 15, 2013 at 5:05 PM, Venkat Reddy wrote:
> I found g_sgangle is the suitable tool
> to calculate the angle between two cholesterol rings. But the problem is, I
> want to do this analysis for my whole system, which has 40 cholesterol
> molecules. Whereas I can input either two
On Mon, Sep 16, 2013 at 7:04 PM, PaulC wrote:
> Hi,
>
>
> I'm attempting to build GROMACS 4.6.3 to run entirely within a single Xeon
> Phi (i.e. native) with either/both Intel MPI/OpenMP for parallelisation
> within the single Xeon Phi.
>
> I followed these instructions from Intel for cross compil
This is the command I used
pdb2gmx -f protein.pdb -o processed.gro -water spce -ignh
And I used OPLS-AA/L all-atom force field..
--
View this message in context:
http://gromacs.5086.x6.nabble.com/Seeking-solution-for-the-error-Atom-OXT-in-residue-TRP-323-was-not-found-in-rtp-entry-TRP-with-24
Hi Santhosh,
Try renaming the atom (mind the space):
sed 's/OXT/O2 /' pdbfile > fixed.pdb
And then run pdb2gmx on that.
Cheers,
Tsjerk
On Tue, Sep 17, 2013 at 6:05 AM, Santhosh Kumar Nagarajan <
santhoshraja...@gmail.com> wrote:
>
> This is the command I used
> pdb2gmx -f protein.pdb -o pro
Thank you sir for the nice tip. I will try it out and let you know if I
have any problem.
On Tue, Sep 17, 2013 at 12:38 AM, Teemu Murtola wrote:
> Hello,
>
> On Sun, Sep 15, 2013 at 5:05 PM, Venkat Reddy wrote:
>
> > I found g_sgangle is the suitable tool
> > to calculate the angle between two
hi my friends
please help me
i did 20 ns simulation by gromacs 4.5.5 but the power was shut down near the
end of the simulation
How to restart the crashed run?
in the gromacs.org following comment has been proposed
mdrun -s topol.tpr -cpi state.cpt
but i don't have state.cpt in my folder.
Hi all,
I'm trying to install and test gromacs 4.6.3 on our new cluster, and am
having difficulty with MPI. Gromacs has been compiled against openMPI
1.6.5. The symptom is, running a very simple MPI process for any of the
DHFR test systems:
orterun -np 2 mdrun_mpi -s topol.tpr
produces this open
http://www.gromacs.org/Documentation/How-tos/Doing_Restarts suggests
the 3.x-era restart strategy when checkpoint files are unavailable.
But if you simply have no output files, then you have no ability to
restart.
Mark
On Tue, Sep 17, 2013 at 1:59 AM, Mahboobeh Eslami
wrote:
> hi my friends
>
>
On Tue, Sep 17, 2013 at 2:04 AM, Kate Stafford wrote:
> Hi all,
>
> I'm trying to install and test gromacs 4.6.3 on our new cluster, and am
> having difficulty with MPI. Gromacs has been compiled against openMPI
> 1.6.5. The symptom is, running a very simple MPI process for any of the
> DHFR test
I have tried it Tsjerk.. But the same error is shown again..
-
Santhosh Kumar Nagarajan
MTech Bioinformatics
SRM University
Chennai
India
--
View this message in context:
http://gromacs.5086.x6.nabble.com/Seeking-solution-for-the-error-Atom-OXT-in-residue-TRP-323-was-not-found-in-rtp-entry-TR
Standard error and standard deviation measure different things. Please
consult a general work on reporting scientific results.
Mark
On Mon, Sep 16, 2013 at 7:40 AM, afsaneh maleki
wrote:
> Dear all
>
>
>
> I would like to calculate the standard deviation (as the error bar) for
> dV/dlanda.xvg fi
Please answer all of Justin's questions. What is in the PDB file -
what should the C terminus be!
Mark
On Tue, Sep 17, 2013 at 2:27 AM, Santhosh Kumar Nagarajan
wrote:
> I have tried it Tsjerk.. But the same error is shown again..
>
> -
> Santhosh Kumar Nagarajan
> MTech Bioinformatics
> SRM
Hi,
Please keep discussion on the mailing list.
If you have a .cpt file that is not called state.cpt, then you must
have asked for the checkpoint file to be named md.cpt in your original
mdrun command (e.g. with mdrun -cpo md). state.cpt is simply the
default filename (and mostly there is no reas
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