rchert, Christopher B ERDC-RDE-ITL-MS
Contractor <christopher.b.borch...@erdc.dren.mil>
wrote:
> Unfortunately using your shortened cmake args, I still get fpic
> errors. But it does complete the build statically with
> -DGMX_BUILD_SHARED_EXE=OFF
>
> CC=cc CXX=CC cmake ../ -D
ompiler wrappers, the rest is most of the time unnecessary
for a "vanilla" build.
Cheers,
--
Szilárd
On Fri, Apr 6, 2018 at 8:32 PM, Borchert, Christopher B ERDC-RDE-ITL-MS
Contractor <christopher.b.borch...@erdc.dren.mil>
wrote:
> You are trying to give me a hint. :
es not need
> relocatable device code, so that should not be necessary.
> --
> Szilárd
>
>
> On Fri, Apr 6, 2018 at 6:33 PM, Borchert, Christopher B
> ERDC-RDE-ITL-MS Contractor <christopher.b.borch...@erdc.dren.mil>
> wrote:
>> Thanks Szilárd. My unders
ild?
--
Szilárd
On Thu, Apr 5, 2018 at 6:52 PM, Borchert, Christopher B ERDC-RDE-ITL-MS
Contractor <christopher.b.borch...@erdc.dren.mil>
wrote:
> Hello. I'm taking a working build from a co-worker and trying to add GPU
> support on a Cray XC. CMake works but make fails. Both 2016 and 2
Hello. I'm taking a working build from a co-worker and trying to add GPU
support on a Cray XC. CMake works but make fails. Both 2016 and 2018 die at the
same point -- can't find gromac's own routines.
2016.5:
/opt/cray/pe/craype/2.5.13/bin/CC-march=core-avx2 -O2 -fPIC -dynamic
-std=c++0x
is there any link where i can get to know the minimum cut
off values for these parameters and which value should be used for which
force field or condition
thanks
Nikita
Original Message
> Subject: Re: simulation_time
> From:
Thank you sir for the reply...
a few queries are still there
1) what are the parameters that change according to force fields??
2) and what are the minimum cut offs for the parameters that changes
according to force fields or is there any link where the information can
be retrieved.
Original Message
Subject: Re: simulation_time
From:"Ms. Nikita Bora" <nik...@tezu.ernet.in>
Date:Mon, May 16, 2016 9:42 am
To: nik.
Respected Sir,
Recently i followed your tutorial for simulation of a 50 ns final mdrun of
protein-ligand complex where the value of rvdw=rcoulomb=1.4 was used. The
simulation runned at aorund 10 ns/day . While for the same complex when
rvdw=rcoulomb=1 is made the run was 10 ns/day.
Sir i would
Sir, I am running a simulation for 50ns for a protein separately and also
with a ligand docked to the protein. The mdp files and all are same for
both the run , but however while running the protein its taking only
around 3 days while running the protein-ligand docked complex its taking
around 7
I am gluing this email exchange to my office wall. This is just awesome.
Thanks to you all.
On 3/9/15 10:19 AM, Tsjerk Wassenaar wrote:
Hi Brett,
Let's say you're sitting at your _desk_ writing that paper with a deadline
yesterday and you put a quick _meal_ next to you, wondering why on
On 2/27/15 10:21 AM, Vasiliy Znamenskiy wrote:
I hoped that the package (gromacs_win32.zip,
http://www.gromacs.org/Downloads/User_contributions/Gromacs_binaries/i686%2f%2fMS_Windows
), with programs, which are ready to execution, will accelerate my time of
study of the GROMACS program, but it
On 10/21/14 12:28 PM, Netaly Khazanov wrote:
Dear Gromacs Users,
I want to study folding of isolated unstructured domain of the protein.
Do you have any recommendations which Force Field could possibly be used
for this purpose?
Thank you in advance.
Netaly Khazanov.
You can start from this
Dear Gromacs users,
I am using Gromacs 4.6. I would like to plot the contacts (minimum
atom-atom distances) between some residue side chains and a ligand along
a trajectory. I thought I would find the solution in g_dist or
g_mindist, however, if I understand correctly:
- g_dist calculates
On 8/27/14 8:14 PM, Justin Lemkul wrote:
g_mindist will plot the minimum distance of any atom pairs frame by
frame.
In short, what's the best strategy to accomplish what I am trying to do?
g_mindist should handle all of this.
Thanks a lot! I will play with it then.
Massimo
--
Gromacs
Dear Gromacs users,
I am analyzing the RMSD evolution of a trajectory with g_rms and
clustering it with g_cluster (GROMOS, cutoff 0.1). I am noticing
something quite odd in the RMSD distribution. I link here the RMSD
evolution over time , the cluster ID over time, and the RMSD
distribution
.
Cheers,
Tsjerk
On Wed, Aug 13, 2014 at 3:14 PM, ms deviceran...@gmail.com wrote:
Dear Gromacs users,
I am analyzing the RMSD evolution of a trajectory with g_rms and
clustering it with g_cluster (GROMOS, cutoff 0.1). I am noticing something
quite odd in the RMSD distribution. I link here the RMSD
more sense then, thanks!
Is there a Gromacs command to get the histogram of RMSD against a single
reference structure, then?
thanks,
Massimo
Cheers,
Tsjerk
On Wed, Aug 13, 2014 at 3:44 PM, ms deviceran...@gmail.com wrote:
Hi Tsjerk,
On 8/13/14 3:19 PM, Tsjerk Wassenaar wrote:
You have
On 8/13/14 4:17 PM, Justin Lemkul wrote:
Aha! This makes much more sense then, thanks!
Is there a Gromacs command to get the histogram of RMSD against a single
reference structure, then?
You can construct histograms of any time series with g_analyze -dist.
OK, I forgot that. Thanks a lot,
Dear all,
Me and a collegue were wondering if -using the same identical set of
features, same input files, same random seed, running on a single CPU-
we could expect numerical reproducibility between Gromacs 4.6 and
Gromacs 5.0 ; that is, same output numbers and same trajectory. My bet
is on
On 7/8/14 12:35 PM, Yip Yew Mun wrote:
Hi all,
I wish to run a MD simulation with the protein in CG and the small organic
ligand in AA. Has anyone attempted this before? If so, can guide me on how to
generate the right topologies for such simulations?
Thanks, any help would be greatly
On 5/19/14 12:41 PM, atsutoshi.ok...@takeda.com wrote:
Dear all,
I would like to superimpose protein-ligand complex(including waters) after MD
simulation to initial structure of the complex(including water) with protein
backbone.
If you only want to visualize/save a PDB of the
On 4/23/14 9:55 AM, neha_bharty wrote:
Hello
I want to find the protein ligand interaction using gromacs.
Is it possible to perform protein-ligand docking with the help of gromacs or
I have to dock the protein and ligand with some tools like autodock and then
only I can view its interaction
On 4/23/14 10:11 AM, Kalyan Reddy wrote:
Neha:
GROMACS is not a tool for doing docking studies. You can perform docking
using Autodock/ GLIDE/ HADDOCK etc.
Well, in my group we actually do use Gromacs to predict ligand binding
poses, so technically this is not entirely true. But yes, we start
On 1/20/14 3:01 PM, Mark Abraham wrote:
Do you use this feature?
Do you use this feature with a shell other than bash?
This feature is not essential to me but it is for sure handy, I use it,
and I'd appreciate if it was supported. I also work on some clusters
with zsh, so support for non-bash
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