Justin A. Lemkul wrote:
Then it seems clear to me that your installation of Gromacs is faulty.
Have you tried running the test set (available on the wiki site)? If
you can describe your computer system (OS, version, compilers used,
configuration options, etc.) then perhaps someone on the li
Thanks a lot Justin for the reply.
I have already seen that post. But the problem is that there is no clear answer
in it. Hess says that there NO G43b1 force-field now in GROMACS and G43b1 was
just a modified version of G43a1 but with no residue charges. So this means
that there in no vacuum for
Dear Song,
I guess that the problem you encountered does not matter the GROMACS. On
contrary, I think that you must have edited the pdb file and made mistakes of
the file format so that pdb2gmx can not tell it correctly. I wish this
information can help you to deal with the problem.
xiao
> >> heiko...@web.de wrote:
> >>> Hello all,
> >>>
> >>> I am doing a cg minimization with Gromacs-4.0.3.
> >>> It is compiled on a Linux system with gcc 3.4.6
> >>>
> >>> All frames in the trajectory are identical to the starting configuration,
> >>> except for the final one, which is clearly diff
Dear all;
I ran a simulation using two tabulated potentials for two energy groups but it
seems that
Gromacs is not generating any potential because LJ energies = 0. in every
step.
The groups are TET and HS and they are represented in index.ndx. Their
tabulated potentials
are table_TET_T
Then it seems clear to me that your installation of Gromacs is faulty. Have you
tried running the test set (available on the wiki site)? If you can describe
your computer system (OS, version, compilers used, configuration options, etc.)
then perhaps someone on the list can spot a potential p
Dear Justin:
Thank you so much for your help earlier. I updated my GROMACS to
4.0.4. When I run pdb2gmx using the following two files. I still got
the similar error message:
Opening library file ffoplsaa.rtp
Opening library file /packages/gromacs-4.0.4/share/gromacs/top/aminoacids.dat
Opening lib
Ragnarok sdf wrote:
Hello, I was following the steps in Justin Lemkul's tutorial for
insertion of a protein in a lipid bilayer and have come accross a
problem right after using inflategro's script from Tieleman's website.
It says there that I should run an energy minimization and then
continue
Hello, I was following the steps in Justin Lemkul's tutorial for
insertion of a protein in a lipid bilayer and have come accross a
problem right after using inflategro's script from Tieleman's website.
It says there that I should run an energy minimization and then
continue with the steps of the tu
Stefano Meliga wrote:
Hi everybody,
Whilst attempting to compile gromacs 4 on my MacOSX I encountered a
problem.
I successfully configured with ./configure but the 'make' command
doesn't work. It displays:
MBSTEFANO:gromacs-4.0.4 Stefano$ make
make: *** No targets specified and no makefile
Hi everybody,
Whilst attempting to compile gromacs 4 on my MacOSX I encountered a problem.
I successfully configured with ./configure but the 'make' command
doesn't work. It displays:
MBSTEFANO:gromacs-4.0.4 Stefano$ make
make: *** No targets specified and no makefile found. Stop.
Any sugges
From the archives, a simple search for "43b1 4.0":
http://www.gromacs.org/pipermail/gmx-users/2008-December/038463.html
-Justin
Anirban Ghosh wrote:
Hi ALL,
I want to do a MD simulation of a GPCR protein using GROMACS vacuum force field. I want to use the old force field G43b1 (vacuum simulat
Hi ALL,
I want to do a MD simulation of a GPCR protein using GROMACS vacuum force
field. I want to use the old force field G43b1 (vacuum simulation)
which is not there in GROMACS4.0.3. I would like to know which is the
substitute for this G43b1 force field
from the present menu:
Select the Forc
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