Hello:
I've got two polar residues which make H-bond directly. However, I
found that this Hbond can be broken by solvent molecules: sometimes
there is 1 water molecule stucked in the middle during the simulation
and sometimes 2 even 3. But those water molecules can bridge this two
residues
Thanks for the tip about nstlist, I will make good use of it.
I also tried the NPT and the NVT ensembles with different temperatures and
pressures, and I always had blow-up and large energies. Now I tried
decreasing the time step up to 10 times, but still have blow-up problem and
the potential
Not easily - a complex geometric criterion is needed to define a
multi-molecule H-bonding bridge.
g_hbond can probably be made to do the simple case with 1 bridging water,
but anything more complex than that will need the functionality of g_select.
Mark
On Fri, Nov 30, 2012 at 10:31 AM, Albert
Dear All,
I have successfully compiled the beta1 of gromacs 4.6 on my macbook pro with
mountain lion.
I used the latest cuda and the clang/clang++ compilers in order to have access
to the AVX instructions.
mdrun works with great performances!! great job!
two things:
1. the compilation was
Hi,
As the new Verlet cut-off scheme, also used on the GPU, uses separate non-bonded
coordinate and force buffers, implementing this will require very little code
changes.
All real variables in the nbnxn_atomdata_t data structure and in all code
operating
on them should be replaced by floats.
Hi everyone,
Ithought I should share something that I've noticed about some of the outputs
of g_hbond, in case it's confused anyone else. I'd noticed that there is a
significant difference in the length distribution plots (-dist) produced by
version 3.3.3 and all of the 4 family, including
On Fri, Nov 30, 2012 at 5:01 AM, Carlo Camilloni
carlo.camill...@gmail.comwrote:
Dear All,
I have successfully compiled the beta1 of gromacs 4.6 on my macbook pro
with mountain lion.
I used the latest cuda and the clang/clang++ compilers in order to have
access to the AVX instructions.
On 11/29/12 10:25 PM, Szilárd Páll wrote:
On Fri, Nov 30, 2012 at 3:20 AM, Justin Lemkul jalem...@vt.edu wrote:
Hooray for being the first to report a problem with the beta :)
We have a cluster at our university that provides us with access to some
CPU-only nodes and some CPU-GPU nodes.
On 11/30/12 4:45 AM, escajarro wrote:
Thanks for the tip about nstlist, I will make good use of it.
I also tried the NPT and the NVT ensembles with different temperatures and
pressures, and I always had blow-up and large energies. Now I tried
decreasing the time step up to 10 times, but still
30 nov 2012 kl. 12.24 skrev Cara Kreck:
Hi everyone,
Ithought I should share something that I've noticed about some of the outputs
of g_hbond, in case it's confused anyone else. I'd noticed that there is a
significant difference in the length distribution plots (-dist) produced by
I do have constraints, all the bond lengths are fixed and they are specified
in the topology file. Am I doing something wrong? I copy here the definition
of one of the models I use. I also tried using in the input the line:
constraints = all-bonds
instead of
constraints
Date: Thu, 29 Nov 2012 08:58:50 -0500
From: jalem...@vt.edu
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Electrostatic field in atoms - GROMACS is not
reading table interaction functions for bonded interactions
On 11/29/12 8:18 AM, Ariana
Hi,
On Fri, Nov 30, 2012 at 5:01 AM, Carlo Camilloni
carlo.camill...@gmail.comwrote:
1. the compilation was easy but not straightforward:
cmake ../ -DGMX_GPU=ON
-DCMAKE_INSTALL_PREFIX=/Users/carlo/Codes/gromacs-4.6/build-gpu
-DCMAKE_CXX_COMPILER=/usr/bin/clang++
On 11/30/12 8:21 AM, escajarro wrote:
I do have constraints, all the bond lengths are fixed and they are specified
in the topology file. Am I doing something wrong? I copy here the definition
of one of the models I use. I also tried using in the input the line:
constraints =
Dear Berk:
Thanks a lot for your positive comments.
I'm very happy the mixed calculation option will be realised in
near future.
Regards,
Makoto
--
View this message in context:
Dear gromacs users,
in the Gromacs manual pages (version 4.5.3 page 211) there are the
criteria to have an Hbond.
r 0.35 nm, where r is the Donor-Acceptor distance
alpha 30°, where alpha is the Hydrogen-Donor-Acceptor angle
in the Manual page for g_hbond (version 4.5.3 page 275) it is
On 11/30/12 10:41 AM, Velia Minicozzi wrote:
Dear gromacs users,
in the Gromacs manual pages (version 4.5.3 page 211) there are the criteria to
have an Hbond.
r 0.35 nm, where r is the Donor-Acceptor distance
alpha 30°, where alpha is the Hydrogen-Donor-Acceptor angle
in the Manual page
On Fri, Nov 30, 2012 at 3:20 AM, Justin Lemkul jalem...@vt.edu wrote:
Hooray for being the first to report a problem with the beta :)
:) Thanks!
We have a cluster at our university that provides us with access to some
CPU-only nodes and some CPU-GPU nodes. I'm having problems with
On Fri, Nov 30, 2012 at 2:35 PM, Justin Lemkul jalem...@vt.edu wrote:
On 11/30/12 8:21 AM, escajarro wrote:
I do have constraints, all the bond lengths are fixed and they are
specified
in the topology file. Am I doing something wrong? I copy here the
definition
of one of the models I
On 11/30/12 11:00 AM, Mark Abraham wrote:
On Fri, Nov 30, 2012 at 2:35 PM, Justin Lemkul jalem...@vt.edu wrote:
On 11/30/12 8:21 AM, escajarro wrote:
I do have constraints, all the bond lengths are fixed and they are
specified
in the topology file. Am I doing something wrong? I copy here
Dear All,
I have copied and patched the plumed script plumed_gromacs-4.5.5.sh,
given in the patches directory. But after doing that, while running
some umbrella sampling it's not printing the COLVAR file, only the
simple md is running there.
So, can anyone help me in this regard?
Thanks
--
Thanks. http://redmine.gromacs.org/issues/1053 created.
Mark
On Fri, Nov 30, 2012 at 5:16 PM, Justin Lemkul jalem...@vt.edu wrote:
On 11/30/12 11:00 AM, Mark Abraham wrote:
On Fri, Nov 30, 2012 at 2:35 PM, Justin Lemkul jalem...@vt.edu wrote:
On 11/30/12 8:21 AM, escajarro wrote:
I
Hi Roland,
so, the problem is not fixed by changing to
-DCUDA_NVCC_HOST_COMPILER=/usr/bin/g++ ,
I still have to change by hand clang to clang++ in that single link.txt file,
while everything works fine by checking out the revision you suggested.
Best,
Carlo
Message: 3
Date: Fri, 30 Nov 2012
Hi Carlo,
thanks for the feedback!
Roland
On Fri, Nov 30, 2012 at 1:35 PM, Carlo Camilloni
carlo.camill...@gmail.comwrote:
Hi Roland,
so, the problem is not fixed by changing to
-DCUDA_NVCC_HOST_COMPILER=/usr/bin/g++ ,
I still have to change by hand clang to clang++ in that single
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