Hi all,
I can't seem to find the correct combination of EDI parameters impose a
harmonically-constrained simulation along an eigenvector in GROMACS 4.6.2, and
I'd like to confirm that the inputs I have are actually correct. Here is the
make_edi command I used to generate the .edi file fed to m
Hi Po-chia,
On Sep 10, 2013, at 9:53 AM, "Chen, Po-chia" wrote:
> Hi all,
> I can't seem to find the correct combination of EDI parameters impose a
> harmonically-constrained simulation along an eigenvector in GROMACS 4.6.2,
> and I'd like to confirm that the inputs I have are actually correct
Dear Users,
I am using the ATB web server to build topologies of my ligands.
I have tried to include the ligand UNITED ATOM STRUCTURE (generated by the
ATB) into my protein gro file generated by GROMACS by copying the
information in the lines starting with HETAM to the end of my protein gro
file an
Hi Gromacs mailing list supporters,
I had previously posted query on xpm2ps.
http://lists.gromacs.org/pipermail/gmx-users/2013-April/080729.html
There are 100 frames in the simulations. I tried fiddling with the
parameters in the .m2p file such as matrix spacing and X-axis minimum
and maximum
You cannot mix the .gro and .pdb formats within the same file. One
approach is to direct the GROMACS tool to write the output in pdb
format simply by naming the output file with a .pdb suffix. Then you
can do such a pasting operation, and if you've preserved the format
correctly, proceed to use the
On 9/10/13 5:30 AM, Neha Gandhi wrote:
Hi Gromacs mailing list supporters,
I had previously posted query on xpm2ps.
http://lists.gromacs.org/pipermail/gmx-users/2013-April/080729.html
There are 100 frames in the simulations. I tried fiddling with the
parameters in the .m2p file such as ma
Thanks Mark,
I am now set and rolling down.
Cheers.
On Tue, Sep 10, 2013 at 11:55 AM, Mark Abraham wrote:
> You cannot mix the .gro and .pdb formats within the same file. One
> approach is to direct the GROMACS tool to write the output in pdb
> format simply by naming the output file with a .pdb
On 9/10/13 6:43 AM, Neha Gandhi wrote:
Hi Justin,
I am sorry to forward the files to your id but gromacs mailing list
wouldn't allow attachments.
Regardless, please keep the discussion on the list. An .m2p file is small
enough that it can be copied and pasted into an email. Everything el
Hi Justin,
This is another type of error while running energy minimization:
what to do for these type of errors.
ERROR 218 [file topol.top, line 23487]:
No default Ryckaert-Bell. types
ERROR 219 [file topol.top, line 23499]:
No default Ryckaert-Bell. types
ERROR 220 [file topol.top, line
On 9/10/13 9:21 AM, Rama Krishna Koppisetti wrote:
Hi Justin,
This is another type of error while running energy minimization:
what to do for these type of errors.
They're exactly the same as the dihedral error from before. You're using
parameters that don't exist in the force field.
-J
Hi Justin,
It is which part in the force field. Exactly which file I have to look to
overcome this errors.
Thanks
--Rama
On Tue, Sep 10, 2013 at 8:25 AM, Justin Lemkul wrote:
>
>
> On 9/10/13 9:21 AM, Rama Krishna Koppisetti wrote:
>
>> Hi Justin,
>>
>> This is another type of error while run
On 9/10/13 9:33 AM, Rama Krishna Koppisetti wrote:
Hi Justin,
It is which part in the force field. Exactly which file I have to look to
overcome this errors.
Go to the line number in the .top indicated in the error message and determine
the atom types. This will tell you the sequence of a
On 10.09.2013 08:20, shahid nayeem wrote:
I am installing gromacs -4.6.3 on cygwin with following commands
tar -xvzf gramcs-4.6.3.tar.gz
cd gromacs-4.6.3
mkdir build
cd build
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_DOUBLE=on
It runs fine and write file in build directory.
when I run make command
Adding parameters can be a little bit of a pain, you could instead change
the atom types in the molecule parameter, to ones that have defined angles
and bond types with each other. Of course, you would need to make sure that
you dont assign sp2 with sp3 atoms, or aromatic with non aromatic etc.
Che
On 9/10/13 1:28 PM, Rafael I. Silverman y de la Vega wrote:
Adding parameters can be a little bit of a pain, you could instead change
the atom types in the molecule parameter, to ones that have defined angles
and bond types with each other. Of course, you would need to make sure that
you dont a
Hi,
Sorry to bother you again regarding this. But I am not sure, as to why
freeze + constraints should not work during a NPT simulation?
The update algorithm as shown in the manual does not say anything that
would fundamentally prevent this. In fact, one can use freezegroups +
constraints in NVT.
On 9/10/13 3:55 PM, Rama Krishna Koppisetti wrote:
Hi Justin,
There is no errors in dihedral but I got 4 warnings in ffbonded.itp. Is
there any suggestions from you.
You've constructed the force field such that you have repeating entries that
override parameters. You still haven't said wh
How so? If there is an atom type that has a reasonable similarity to the
one that doesnt have the default bondtypes, what makes using that worse
than coming up with entirely new parameters that are not necessarily based
on physical data or quantum calculations? Isnt copying angles and force
constan
Hi Justin,
There is no errors in dihedral but I got 4 warnings in ffbonded.itp. Is
there any suggestions from you.
WARNING 1 [file ffbonded.itp, line 2817]:
Overriding Proper Dih. parameters.
Use dihedraltype 4 to allow several multiplicity terms.
old: 180 5.86 1 180 5.86 1
new: LNL LH
On 9/10/13 3:54 PM, Rafael I. Silverman y de la Vega wrote:
How so? If there is an atom type that has a reasonable similarity to the
one that doesnt have the default bondtypes, what makes using that worse
than coming up with entirely new parameters that are not necessarily based
on physical dat
On 9/10/13 2:59 PM, HANNIBAL LECTER wrote:
Hi,
Sorry to bother you again regarding this. But I am not sure, as to why
freeze + constraints should not work during a NPT simulation?
The update algorithm as shown in the manual does not say anything that
would fundamentally prevent this. In fact,
Hi,
The near-silence has been deafening, so these issues are regarded as
closed. Anybody wanting a significant deviation from that plan will
find the onus on them to do the work! :-)
Cheers,
Mark
On Wed, Aug 14, 2013 at 5:06 PM, Mark Abraham wrote:
> Hi gmx-users and gmx-developers,
>
> There
I would think that too. However, that is not what happens. If you freeze a
group it gets scaled according to the box vectors during a npt simulation.
Hence in order to keep the group (in my case a carbon nano tube) of fixed
diameter i use position restraints. This protocol works fine with with npt
On 9/10/13 5:17 PM, HANNIBAL LECTER wrote:
I would think that too. However, that is not what happens. If you freeze a
group it gets scaled according to the box vectors during a npt simulation.
Are the positions of the atoms actually changing? If they are, that's a bug.
It shouldn't happen,
On 9/10/13 4:35 PM, Rama Krishna Koppisetti wrote:
H
i Justin,
The force field that I constructed with OPLS + Berger lipids
.
Similar to
your Bilayer tutorial.
Presumably you are following Chris Neale's half-epsilon, double pairlist method
then? In any case, you're defining the same inter
Hi,
How to convert normal dihedrals to so-called Ryckaert-Bellemans
potential dihedrals. Is there any script available for that.
Thanks
Rama
On Tue, Sep 10, 2013 at 3:44 PM, Justin Lemkul wrote:
>
>
> On 9/10/13 4:35 PM, Rama Krishna Koppisetti wrote:
>
>> H
>> i Justin,
>>
>> The force fie
On 9/10/13 6:10 PM, Rama Krishna Koppisetti wrote:
Hi,
How to convert normal dihedrals to so-called Ryckaert-Bellemans
potential dihedrals. Is there any script available for that.
Periodic dihedrals and R-B dihedrals have different functional forms. See the
manual.
-Justin
--
===
Hi All.
I work on a simulation of a membrane protein in a model membrane
(DPPC) with a total of 26,859 atoms. In a step of NPT equilibration,
my mdp file is used for a 100 ps NPT and it has a reference pressure
of 1 bar.
At the end of simulation, I obtained a result of the average
pressure
H
i Justin,
The force field that I constructed with OPLS + Berger lipids
.
Similar to
your Bilayer tutorial.
Thanks
--Rama
On Tue, Sep 10, 2013 at 3:26 PM, Rama Krishna Koppisetti <
ramkishn...@gmail.com> wrote:
>
>
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.or
On 9/10/13 9:12 PM, Dwey wrote:
Hi All.
I work on a simulation of a membrane protein in a model membrane
(DPPC) with a total of 26,859 atoms. In a step of NPT equilibration,
my mdp file is used for a 100 ps NPT and it has a reference pressure
of 1 bar.
At the end of simulation, I obta
Part answer is provided at
http://www.gromacs.org/Documentation/Terminology/Pressure
Have you plotted how the pressure changes with time during your simulation?
What you will notice is that the pressure is oscillating between something like
+300 bar and -300 bar. With such large variations lik
Hi Dallas and Justin,
Thanks for the reply. Yes, I did plot pressure changes over time by
g_energy and I have been aware of the note at
http://www.gromacs.org/Documentation/Terminology/Pressure
I am concerned about the average pressure is because our experiment shows
that our target membrane
Hello,
i am trying to compile gromacs-4.6.1 on a linux machine. I used already the
following compile script and it worked
export CCDIR=/usr/bin/gcc
export MPICCDIR=/usr/mpi/gcc/openmpi-1.4.1/bin
export CXX=mpicxx
export CC=mpicc
cd /home/fbafti/CODE
tar -xvf gromacs-4.6.1.tar.gz
cd mv gr
On 9/10/13 10:56 PM, Dwey Kauffman wrote:
Hi Dallas and Justin,
Thanks for the reply. Yes, I did plot pressure changes over time by
g_energy and I have been aware of the note at
http://www.gromacs.org/Documentation/Terminology/Pressure
I am concerned about the average pressure is because
Also remember that here you are dealing with the measurement of a macroscopic
property on a microscopic scale.
As Justin has alluded to, the only manner in which you can make the variation /
fluctuations in the pressure smaller is by increase the total number of
particles in the system.
Catch
>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. Pressure fluctuations decrease on the orde
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':
"/usr/bin/ld:
/usr/local/mvapich2-1.9a-gcc/lib/libmpich.a(mvapich_malloc.o): relocation
R_X86_64_32 against `.bss' can not be used when making a shared object;
recompile
Thanks Wahab
I followed your instruction and added #define HAVE_SYS_TIME_H
at the very top of the file gmxlib/thread_mpi/impl.h.
Then again in make command I got following errors.
[ 53%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwCSTab_G
38 matches
Mail list logo
