On 25.07.2013 04:25, Carlos Bueno wrote:
I added all the repositories and installed all you told me.
And that solved the problem for one of the computers
The others still have an error in make:
[ 55%] Building NVCC (Device) object
src/mdlib/nbnxn_cuda/./nbnxn_cuda_generated_nbnxn_cuda.cu.o
/home
On Jul 24, 2013, at 5:53 PM, battis...@libero.it wrote:
> Dear Carsten
>
> could you give me more information about your suggestions?
> I tried but probably I did not understand well what you meant.
Hi Anna,
I suggested to use the enforced rotation module of Gromacs 4.6
to restrain the orientati
> Date: Wed, 24 Jul 2013 09:35:26 -0400
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Calculate interaction energy dynamically
>
>
>
> On 7/24/13 9:25 AM, Davit Hakobyan wrote:
> > Thank you again for your time and help.
> >
> > Performing "rerun" on the origin
I read the report (http://redmine.gromacs.org/issues/1110)
and tried some combinations. This was my last failing
attempt:
- - - 8< - - - - - - - - - - - - - - - - - - - - - - - - - -
#!/bin/sh
export GMXVERSION=gromacs-4.6.3
export GMXTARGET=/opt/gromacs463
MINC=/opt/intel/mkl/include
MLIB=/opt
What doesn't work about the install guide instructions: 'Using MKL
with icc 11 or higher is very simple. Set up your compiler environment
correctly, perhaps with a command like source /path/to/compilervars.sh
intel64 (or consult your local documentation). Then set
-DGMX_FFT_LIBRARY=mkl when you run
On 7/25/13 12:44 AM, Jonathan Saboury wrote:
Hm, I am probably completely wrong about this, but can you do implicit
solvent and Periodic Box Conditions?
That's not typical. I suppose one could do an NVT simulation, but the only
stable way I have found to run in implicit solvent is to use i
On 7/25/13 12:51 AM, Albert wrote:
Hello:
I notice that the manual or tutorial in Gromacs (FEP, unbralla sampling, TI
and so on) website for binding energy evaluation are all for protein in water. I
am just wondering how can we evaluate the protein/ligand binding affinity for
membrane system
After running for 100 ps, I visualized the pullf_umbrella.xvg, in this plot I
found the F value around 100 kJ/mol/ns. But force constant which I had set in
md_US.mdp file was 4000 KJ/mol/ns. Does this difference show me that the US has
not done properly?
;define = -DPOSRES
integrato
On 7/25/13 7:52 AM, Shima Arasteh wrote:
After running for 100 ps, I visualized the pullf_umbrella.xvg, in this plot I
found the F value around 100 kJ/mol/ns. But force constant which I had set in
md_US.mdp file was 4000 KJ/mol/ns. Does this difference show me that the US has
not done proper
Vitaly has it upside down - it is normally required to build a static
binary on Crays.
cmake .. -DBUILD_SHARED_LIBS=off just works for building static
binaries for me with 4.6.3 on lindgren, a Cray XE6, when using
PrgEnv-gnu/4.0.46
Mark
On Wed, Jul 24, 2013 at 8:58 AM, Andrew R Turner wrote:
>
Think your .mdp-file looks reasonable.
If you are totaly unsure you could determine the PMF of two water
molecules. As a reference one can use the radial distribution function
g(r) and calculate the PMF as
V_pmf(r) = -kT LN(g(r))
One side note:
Since the force constant you are using is relativ
Dear All,
I am working on some molecule and I have defined atom types with OPLSaa and
all atom types really exist in oplsaa and well chosen so no approximation
in choosing atom types. During grompp, I found there are dihedral param
missing. e.g.
N CT CT NT
N CT CT N3
Is there any 'good' way of fi
On 7/25/13 8:25 AM, gromacs query wrote:
Dear All,
I am working on some molecule and I have defined atom types with OPLSaa and
all atom types really exist in oplsaa and well chosen so no approximation
in choosing atom types. During grompp, I found there are dihedral param
missing. e.g.
N CT CT
Dear Justin,
Thanks this paper is quite explained and requires much detailed study
(sorry am escaping!)
As I have these two params missing, is there any tool that can help me in
this regard or may be some approximation method I may use?
thanks
On Thu, Jul 25, 2013 at 3:28 PM, Justin Lemkul wro
On 7/25/13 8:41 AM, gromacs query wrote:
Dear Justin,
Thanks this paper is quite explained and requires much detailed study
(sorry am escaping!)
As I have these two params missing, is there any tool that can help me in
this regard or may be some approximation method I may use?
It is very ha
Dear Justin,
>> Parameterization is a hard road that takes a lot of time
I agree and thanks for reply
On Thu, Jul 25, 2013 at 3:47 PM, Justin Lemkul wrote:
>
>
> On 7/25/13 8:41 AM, gromacs query wrote:
>
>> Dear Justin,
>>
>> Thanks this paper is quite explained and requires much detailed
On 25.07.2013 12:28, Mark Abraham wrote:
What doesn't work about the install guide instructions: 'Using MKL
with icc 11 or higher is very simple. Set up your compiler environment
correctly, perhaps with a command like source /path/to/compilervars.sh
intel64 (or consult your local documentation).
Dear users,
For some unknown reasons checkpoint file are not
being created if -cpo is not mentioned (in 4.5.3). Now
I have a trajectory of ~10ns without a checkpoint file.
I tried the following -
tpbconv option to create a new .tpr file so that I can
start form the point I stopped. But manual ment
On Thu, Jul 25, 2013 at 2:55 PM, Mirco Wahab
wrote:
> On 25.07.2013 12:28, Mark Abraham wrote:
>>
>> What doesn't work about the install guide instructions: 'Using MKL
>> with icc 11 or higher is very simple. Set up your compiler environment
>> correctly, perhaps with a command like source /path/t
Mark,
A bit of testing has revealed that it is the
"-DGMX_PREFER_STATIC_LIBS=ON" flag that makes the difference. With
this flag you end up with dynamic executables that do not work (I
think due to some glibc problem I have not yet tracked down) whereas
if I exclude this option then I get
That combo is supposed to generate a CMake warning.
I also get a warning during linking that some shared library will have
to provide some function (getpwuid?) at run time, but the binary is
static.
Mark
On Thu, Jul 25, 2013 at 4:21 PM, Andrew R Turner wrote:
> Mark,
>
> A bit of testing has re
Dear gmx-users,
My system is composed of an ion(CL-) and waters.
In the .top file the charge of CL is -1.
PME-USER is used to deal with electrostatics.
Now I would like set CL charge as 0 in the source code,
in order to turn off the ELECTROSTATIC FORCE of Reciprocal part between CL
and waters
Dear users,
Please take a moment to check out Gromacs on Rescale.
http://blog.rescale.com/run-gromacs-faster-on-rescale-with-parallelization/
We would really appreciate any feedback you might have for us.
Best,
Joris
*Joris Poort*
Rescale
jo...@rescale.com
--
gmx-users mailing listgmx-us
Dear gromacs users,
I know similar issues have been raised many times on the list but I am unable to
solve the problem so I am seeking your advice. I am trying to simulate a protein
in a dodecahedron box. The system size is ~30k atoms. I have followed the
methodology given in the lysozyme tutorial
Dear Amin,
I did such things in the past, and had similar issues. First of, somone may have beter suggestions. The coupling time will bring it down a bit in the .mdp file (0.2 Vs 2 picoseconds. However, I have found that you will still see large fluctuations around a mean once equilibrate
Dear Justin,
Thanks for your answer...
I move so far...
My aim was to ask gromacs to read directly a modify protein SOL+NA, not
protein SOL NA
But I have not succeed so far.
Best regards
Collins
On Wed, Jul 24, 2013 at 8:38 AM, wrote:
> Send gmx-users mailing list submissions to
>
Hi everybody,
I was wondering if you could answer a quick question I had. Where does the
axis in a box with PBC lie in Gromacs? I thought 0, 0, 0 was the corner of
the box, but if that was true none of the x, y, z values for position should
be negative. However in my trajectory I see a value with
If the box is periodic, then it is everywhere. mdrun makes no promises
about its output being mapped to a particular box.
Mark
On Thu, Jul 25, 2013 at 9:56 PM, Neha wrote:
> Hi everybody,
>
> I was wondering if you could answer a quick question I had. Where does the
> axis in a box with PBC lie
Please don't reply to the whole digest.
On 7/25/13 1:47 PM, Collins Nganou wrote:
Dear Justin,
Thanks for your answer...
I move so far...
My aim was to ask gromacs to read directly a modify protein SOL+NA, not
protein SOL NA
But I have not succeed so far.
I don't understand what you're a
I am running GROMACS 4.6.2 on a GPU cluster in our reasearch group. I am trying
to bench mark some systems, and I am getting this message:
NOTE: The number of threads is not equal to the number of (logical) cores
and the -pin option is set to auto: will not pin thread to cores.
This c
On 7/25/13 6:09 PM, Tim Moore wrote:
I am running GROMACS 4.6.2 on a GPU cluster in our reasearch group. I am trying
to bench mark some systems, and I am getting this message:
NOTE: The number of threads is not equal to the number of (logical) cores
and the -pin option is set to auto:
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