Dear All,
I am a new user for GROMACS, and I meet one problem when
installing the code.
When I run
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
Check the following link, may be helpful
Dear list,
I discovered something strange today. In my hbond search i find only HW1 of the
water forming a hydrogen bond as donor hydrogen and never HW2. Is this due to
the fact that I am using SPC water? I can see the atom IDs of HW2 in the [
donors_hydrogens_Water ] entry in the ndx file. So
Dear All,
I am a new user for GROMACS, and I meet one problem when installing
the code.
When I run
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
I obtain the following errors:
On 5/1/15 11:27 AM, Ebert Maximilian wrote:
Dear list,
I discovered something strange today. In my hbond search i find only HW1 of the
water forming a hydrogen bond as donor hydrogen and never HW2. Is this due to
the fact that I am using SPC water? I can see the atom IDs of HW2 in the [
Hello,
I wish to turn off the secondary structure restraint in half of the peptide
while using martinze.py.
Is there any way in which this can be done.
I have tried to delete the columns in .dssp file which tell about the
structure and character of the peptide but I still get a completely
I used the tool g_cluster of gromacs (4.5.1) to obtain clusters from my
simulations. As option of g_cluster, you can chose the cluster algorithm
gromos.
gromos: use algorithm as described in Daura et al. (Angew. Chem. Int. Ed.
1999, 38, pp 236-240). Count number of neighbors using cut-off,
Is there any handy way to decouple two molecules (defined as the same
group or anyhow) upon free energy calculation?
The case is applicable to ionic systems, for instance.
=
If molecules for decoupling are submitted via an index file:
Fatal error:
Did not
On 5/1/15 1:26 PM, V.V.Chaban wrote:
Is there any handy way to decouple two molecules (defined as the same
group or anyhow) upon free energy calculation?
The case is applicable to ionic systems, for instance.
=
If molecules for decoupling are submitted
With opls-aa, incorrect densities and diffusivities were calculated
entirely away from the critical point for several liquids.
Alex
On May 1, 2015 11:40 AM, V.V.Chaban vvcha...@gmail.com wrote:
This problem is natural. Even small change in (T,P) in the
supercritical range results in a huge
This problem is natural. Even small change in (T,P) in the
supercritical range results in a huge change of density and, hence,
all other properties.
You need either to alter (T,P) or to adjust the force field model
(both change will be slight, but will bring large changes of density).
If you
Yup, that would likely be pretty publishable.
It kind of goes beyond just CO2. If you look at the report I mentioned
above, there were also benzene and heptane, all wrong. I would then think
that many other compounds relevant to fuel technology are also inadequately
described.
I'd say that a lot
Hello Tsjerk,
Thanks for the reply.
I have a 21 amino acids helical peptide, I want to first 10 amino acids to
not having secondary structure restraints while coarse graining using
martinize.py and the rest to remain helical.
I reverse coarse the peptide to see if my trials while playing around
Hi sxn,
What do you mean with reverse coarse graining?
You can specify the secondary structure also as string, which is doable if
the peptide is not too long, e.g. using -ss HHHLLL. Otherwise, you
can put the secondary structure you want in a simple file, and pass that
with the option
Hi sxn,
With martinize.py -ss LLLHH
you'll get the secondary structure you want.
Cheers,
Tsjerk
On Fri, May 1, 2015 at 10:24 PM, shivangi nangia shivangi.nan...@gmail.com
wrote:
Hello Tsjerk,
Thanks for the reply.
I have a 21 amino acids helical peptide, I want to first
If no good model of CO2 still exists, we can publish a right one. It
is very simple. I assume that C-O bond polarity is significantly
different in the supercritical state and in the gas state.
On Fri, May 1, 2015 at 3:30 PM, Alex nedoma...@gmail.com wrote:
I wasn't talking about the initial
Dear Justin,
Thanks for the clarification. :)
Regards,
Sapna
On 4/30/15, Justin Lemkul jalem...@vt.edu wrote:
On 4/30/15 10:12 AM, SAPNA BORAH wrote:
Dear all,
I have some doubts regarding pbc being new to gromacs. Since my protein
was
breaking into fragments, I introduced pbc options
The point is that any metastable state in numerical simulations
requires fine-tuned Hamiltonians.
On Fri, May 1, 2015 at 2:47 PM, Alex nedoma...@gmail.com wrote:
With opls-aa, incorrect densities and diffusivities were calculated entirely
away from the critical point for several liquids.
I wasn't talking about the initial post. I was talking about the fact
that in _very stable_ states the same numerical simulation with a
supposedly well-established set of interactions produces garbage.
VVC The point is that any metastable state in numerical simulations
VVC requires fine-tuned
Does anyone know if any of the typical CO2 force fields are parameritized for
supercritical CO2? But if anyone does publish (or have) a good model, I would
very much appreciate the parameters.
Thanks again for all the input.
Jarrett
-Original Message-
From:
A cursory search yields:
http://www.sciencedirect.com/science/article/pii/0009261496003971#
http://www.sciencedirect.com/science/article/pii/S0009261403006407
http://link.springer.com/article/10.1007%2Fs11814-011-0248-5
The first one has some parameters, maybe trying them would be a start.
Alex
Dear Gromacs users,
I am looking for ready made heme B parameters for use in md runs of CYP enzymes.
Heme is defined in Gromos54a7 ff, but I am looking for a definition for
amber99sb-star-ildn as I am planning to use QM charges pre-calculated (and
published - doi: 10.10002/jcc.21922) for the
It's on the second paragraph of the Experimental Section. The entire
paragraph.
Note: the middle of cluster from g_cluster is not the same as the method's
center of cluster.
Best,
João
On Fri, May 1, 2015 at 8:27 AM, Antonio De Nicola adenic...@unisa.it
wrote:
I used the tool g_cluster of
22 matches
Mail list logo
