The topology with the below params produced that 118 errors during
grompp processings ( after pdb2gmx processing the geoetry of the
mollecule was correct )
[CRN]
[ atoms ]
CG2 CA-0.0900 0
CD1 CA-0.0800 1
CD2 CA-0.0800 2
CE1 CA-0.2800 3
CE2 CA-0.2800 4
CZ CA 0.4500 5
Looks like it is not an issue in the mpi version, but the normally-threaded
gromacs-4.6 beta2 version dies at 1.07 us as well.
--
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On 12/14/12 3:20 PM, James Starlight wrote:
Justin,
in the case of the system with the atom types assigned from that paper
the grompp produced above 118 errors of non standard bond, angle as
well as dihedral types ;o So it' seems that some 118 addition terms
must be added to the ffbonded.itp t
Justin,
in the case of the system with the atom types assigned from that paper
the grompp produced above 118 errors of non standard bond, angle as
well as dihedral types ;o So it' seems that some 118 addition terms
must be added to the ffbonded.itp to the existing charmm parameters(
it's uncommon
On 12/14/12 2:28 PM, James Starlight wrote:
Today I've tried to rename atoms from Swiss's params specific names to
the standard charmm names and obtain the set of the same errors
No default Improper Dih. types
No default U-B types
No default Bond types
Its strange to me because chromophore
Today I've tried to rename atoms from Swiss's params specific names to
the standard charmm names and obtain the set of the same errors
No default Improper Dih. types
No default U-B types
No default Bond types
Its strange to me because chromophore itself consist of only one
uncommon bond (in cyc
On 12/14/12 2:22 PM, Eduardo Oliveira wrote:
Hi,
I'm trying to use AMBER03 force field with my protein but when i run pdb2gmx i
get a fatal error message:
Fatal error:
Incomplete ring in HIS415
The problem is, when I open the structure on pymol i can't see any missing
atoms. Does anybody h
Hi Eduardo,
Some visualization softwares completes the structure, even if it's broken.
I suggest you to look at the .pdb file directly in notepad and check out
the composition of your HIS415.
Regards
--
Marcelo Depólo Polêto
Molecular Animal Infectology Laboratory - LIMA
Department of Biochemis
Hi,
I'm trying to use AMBER03 force field with my protein but when i run pdb2gmx i
get a fatal error message:
Fatal error:
Incomplete ring in HIS415
The problem is, when I open the structure on pymol i can't see any missing
atoms. Does anybody had the same problem?
Regards,
Eduardo
--
gmx-us
On 12/14/12 12:40 PM, Dr. Vitaly Chaban wrote:
If you have a correct temperature for the particle of interest,
everything is correct.
One important caveat, of course, is a given thermostat's ability to produce
velocities that belong to a real NVT ensemble. This is not the case, for
instan
Hi all,
I've had problems before with waters placed within a beta-sandwich
protein by genbox. Although it is theoretically a matter of running the
simulation and waiting for the waters to "come out", in practice this took
about 30 ns and destroyed a considerable amount of the beta-strands.
Hi,
The fact that GPUs are detected at configure-time does not imply that these
GPUs will also work fine at run-time and you see this in action in your
case. The current CMake configure script only looks at whether there is any
NVIDIA GPU device connected, but does not check other conditions that
Thanks Dr. Vitaly
Yeap !
>From that point of view I'm seeing the correct temperature drift and
it reaches nicely to 300 K after say, 300ps.
But is it a good integrator ( SD ) to perform this job ? Or, should I
opt for other, like Lep-frog or MD-VV with let say , Berendsen
thermostat?
Please expla
On Fri, Dec 14, 2012 at 3:46 PM, Thomas Schlesier wrote:
> Dear all,
> i have a small question regarding the '-nosum' option of 'mdrun'.
> The manual states:
>
> For a global thermostat and/or barostat the temperature and/or pressure
> will also only be updated every nstlist steps. With this optio
That does indeed sound like a bug now. The combination of PD, distance
restraints and lincs has likely never been tested :-( Sadly, there are far
too many combinations of algorithms to ever test. Please file an issue at
redmine.gromacs.org, and please include .tpr files with and without lincs
(and
I think the same way as you. They do bring in errors but this is acceptable
in normal MD because we already have lots of approximations. BTW, -sum has
been dropped from 4.5, in other words, Gromacs won't calculate global
Energy every step by default now.
dawei
On Fri, Dec 14, 2012 at 9:46 AM, Th
Dear gromacs users,
I run into problems when I try to use the NVIDIA tesla K10 GPUs with mdrun.
Looking at the cmake log file I find this lines:
-- Looking for NVIDIA GPUs present in the system
-- Number of NVIDIA GPUs detected: 2
-- Found CUDA: /usr/local/cuda (found suitable version "4.2", req
Dear all,
i have a small question regarding the '-nosum' option of 'mdrun'.
The manual states:
For a global thermostat and/or barostat the temperature and/or pressure
will also only be updated every nstlist steps. With this option the
energy file will not contain averages and fluctuations over
Dear Mark
Here it is some information that may be useful. I checked all my -pd, with
distance restraints MD runs. It seemed that crash usually happened when
protons and the carbon they attached were in different processors.
best,
dawei
On Thu, Dec 13, 2012 at 4:12 PM, Da-Wei Li wrote:
> Dear
Morning Shine and Tsjerk,
Sorry for the missing links (here and here), I was refering to PyMol wiki's and
a blog:
http://macosxpostdoc.blogspot.mx/2012/04/dssp-through-pymol.html
http://www.pymolwiki.org/index.php/DSSP_Stride
But what Tsjerk mentions is far more relevant, I was thinking staticall
Hey Julio, Shine,
I would like to see the 'here' and 'here'. Pymol has two routines for
determining secondary structure, one of which uses the same approach as
dssp to classify helices and sheets. A relevant question is, what is a
helix? Is a helix a stretch of residues that is defined by dssp as
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