Dear Gromacs Users
It is a pleasure to announce two new PLUMED releases.
Release 2.0.4 is a maintenance release on the 2.0.x branch with a few fixes,
see: http://goo.gl/2Hyv7c.
If you are using the keyword BIASVALUE with replica exchange you should upgrade
to version 2.0.4 as soon as
What does the force in log file mean?Does it include bonded force and
non-bonded force?
xiexiao...@sjtu.edu.cn
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What does the force in log file mean?Does it include bonded force and
non-bonded force?
xiexiao...@sjtu.edu.cn
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Hi,
To which part of the log file do you refer? The Force part of the timing
breakdown does indeed refer to the combination of short-range non-bonded,
and bonded force + energy computation.
Mark
On Fri, Sep 19, 2014 at 11:11 AM, xiexiao...@sjtu.edu.cn
xiexiao...@sjtu.edu.cn wrote:
What does
Thanks.Do you know how to calculate the time consuming of non-bonded force that
run on gpu?
xiexiao...@sjtu.edu.cn
From: Mark Abraham
Date: 2014-09-19 18:37
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] force
Hi,
To which part of the log file do you refer? The Force part
On Fri, Sep 19, 2014 at 5:35 AM, Theodore Si sjyz...@gmail.com wrote:
Hi all,
I run gromacs 4.6 on 5 nodes(each has 16 CPU cores and 2 Nvidia K20m) and
4 nodes in the following ways:
5 nodes:
1. Each node has 8 MPI processes, and use one node as PME-dedicated node
2. Each node has 8 MPI
Hi,
Gridding the particles in x and y, and then binning in z. See Fig 2 and
text of http://www.sciencedirect.com/science/article/pii/S0010465513001975
Mark
On Fri, Sep 19, 2014 at 4:54 AM, Theodore Si sjyz...@gmail.com wrote:
Hi all,
In the page 34 of the manual:
The Verlet cut-off scheme
On Fri, Sep 19, 2014 at 2:50 AM, Dallas Warren dallas.war...@monash.edu
wrote:
Some scaling results that might be of interest to some people.
Machine = Barcoo @ VLSCI
2.7GHz Intel Sandybridge cores
256GB RAM
16 cores per node
Mellanox FDR14 InfiniBand switch
Systems = water and octanol
Hi,
Short answer: use a profiler, e.g. nvprof.
Long answer: Unless you are running on a single GPU (i.e. no domain
decomposition), due to CUDA limitations, we can not time internally
the GPU kernels. However, you can easily do that using the nvprof
tool that comes with the CUDA toolkit. If you
Hi.
If I change ensemble (say, from NVT to NPT) but use the same
thermostat/barostat, will the internal variables of the thermostat/barostat
stays the same (like how many step later to couple the system to
thermostat)?
If I want to continue from a particular saved frame of the simulation
(saved
On Fri, Sep 19, 2014 at 6:39 PM, Johnny Lu johnny.lu...@gmail.com wrote:
Hi.
If I change ensemble (say, from NVT to NPT) but use the same
thermostat/barostat, will the internal variables of the thermostat/barostat
stays the same (like how many step later to couple the system to
thermostat)?
Sorry for not being clear about the question.
1. If I start with NVT with thermostat A, and then continue with NPT with
thermostat A, and barostat B, will the internal variables of thermostat A
stays the same, upon transitioning from the NVT ensemble to NPT ensemble?
2. If I start with a NPT
On Fri, Sep 19, 2014 at 7:23 PM, Johnny Lu johnny.lu...@gmail.com wrote:
Sorry for not being clear about the question.
1. If I start with NVT with thermostat A, and then continue with NPT with
thermostat A, and barostat B, will the internal variables of thermostat A
stays the same, upon
I ran gmxcheck on an old cpt file:
Command line:
gmxcheck -f nve1.cpt
Checking file nve1.cpt
Precision mismatch for state entry box, code precision is float, file
precision is double
Precision mismatch for state entry x, code precision is float, file
precision is double
Precision mismatch for
I mean is the last frame ... time, the time for the frame of the cpt
file, or the frame right before the frame of the cpt file?
On Fri, Sep 19, 2014 at 3:28 PM, Johnny Lu johnny.lu...@gmail.com wrote:
I ran gmxcheck on an old cpt file:
Command line:
gmxcheck -f nve1.cpt
Checking file
Just do it! ;-)
mdrun -nsteps 1
Mark
On Fri, Sep 19, 2014 at 9:29 PM, Johnny Lu johnny.lu...@gmail.com wrote:
I mean is the last frame ... time, the time for the frame of the cpt
file, or the frame right before the frame of the cpt file?
On Fri, Sep 19, 2014 at 3:28 PM, Johnny Lu
On 9/18/14 4:45 PM, Carlos Navarro Retamal wrote:
Hi Justin,
First of all thanks for your reply.
It worked, but i’m getting weird results.
When i measured the RDF between:
Protein (COM) - Glycerol (the entire molecule) i got a huge pick at 0.022 nm,
which doesn’t make any sense (because i
On 9/19/14 8:43 AM, gromacs query wrote:
Hi All
I have some pdb file and I removed hydrogens. When I try to make ndx file
using some residue option then rather printing atom numbers in that residue
it prints line number where that residue starts and ends.
make_ndx -f no_H.pdb -o test.ndx
I Justin,
Thanks for your reply.
Sadly, that’s not the only bizarre peak,as you can see on the next image:
http://cl.ly/1B3B2y3I0o1R
This is how it looks when i don’t consideren the COM as a reference:
http://cl.ly/3m0d2W2y0N1Y
What; i your opinion, could be the problem?
I think i’ll just have to
Hi Justin
Hope it makes sense now :) Here is the link (small piece of some pdb
without hydrogens)
http://s000.tinyupload.com/?file_id=09348261523279878452
http://s000.tinyupload.com/index.php?file_id=09348261523279878452
I used this command: (note residue 2 is missing so using 'r 2' will not
On 9/19/14 5:15 PM, gromacs query wrote:
Hi Justin
Hope it makes sense now :) Here is the link (small piece of some pdb
without hydrogens)
http://s000.tinyupload.com/?file_id=09348261523279878452
http://s000.tinyupload.com/index.php?file_id=09348261523279878452
I used this command: (note
On 9/19/14 4:54 PM, Carlos Navarro Retamal wrote:
I Justin,
Thanks for your reply.
Sadly, that’s not the only bizarre peak,as you can see on the next image:
http://cl.ly/1B3B2y3I0o1R
This is how it looks when i don’t consideren the COM as a reference:
http://cl.ly/3m0d2W2y0N1Y
What; i your
Not at all. I’m using the .xtc file that comes from the simulation.
What do you mean with the nrexcl issue? Is there a way i can fix it?
--
Carlos Navarro Retamal
Bioinformatic engineer
Ph.D(c) in Applied Science, Universidad de Talca, Chile
Center of Bioinformatics and Molecular Simulations
then the make_ndx output matches the atom numbers in the coordinate file.
Thats true but its bit surprising make_ndx was made to read 'residue number
column' (as I said r 2 does not work) but not 'atom number column'. Though
not a big issue but one should be careful in such case.
best regards
Hi Justin,
Thanks again for all your help.
If the problem is related to periodicity, why if i consider the whole protein i
got ‘normal’ results?
In any case i centered the protein with the following command:
trjconv -f npt_production.xtc -s npt_production.tpr -center -pbc mol -o
On 9/19/14 6:07 PM, Carlos Navarro Retamal wrote:
Hi Justin,
Thanks again for all your help.
If the problem is related to periodicity, why if i consider the whole protein i
got ‘normal’ results?
A normal (non-COM-based) RDF is an atom-based RDF, so periodicity doesn't affect
the outcome.
Carlos,
You might want to try a PBC correction with -pbc nojump and another RDF
calculation with the corrected trajectory.
2014-09-19 19:10 GMT-03:00 Justin Lemkul jalem...@vt.edu:
On 9/19/14 6:07 PM, Carlos Navarro Retamal wrote:
Hi Justin,
Thanks again for all your help.
If the problem
Hi Marcelo,
Thanks for your reply.
Sadly it didn’t work either, so i’m trying to generate a new .tpr file by
changing the nrexcl values just as Justin suggest.
Hope this may works.
Thanks the two of you.
Best Regards,
Carlos
--
Carlos Navarro Retamal
Bioinformatic engineer
Ph.D(c) in Applied
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