An acceptance ratio of 0.2/0.3 is normally best. The problem with high
acceptance ratio is that it means that a large portion of the exchanges are
just back and forth exchanges between consecutive exchange and are thus
disturbing the system more that actually helping sampling.
I do not know
Okay Sir, I will try two-three combinations this time and will report back
to you ...
On Thu, May 16, 2013 at 5:25 PM, XAvier Periole x.peri...@rug.nl wrote:
An acceptance ratio of 0.2/0.3 is normally best. The problem with high
acceptance ratio is that it means that a large portion of the
You have to convince yourself, not me :)) But I can give you my opinion …
On May 16, 2013, at 10:33 AM, bharat gupta bharat.85.m...@gmail.com wrote:
Okay Sir, I will try two-three combinations this time and will report back
to you ...
On Thu, May 16, 2013 at 5:25 PM, XAvier Periole
Hi,
The new server is up and running. Let us know if you see issues.
Cheers,
Rossen
On 5/12/13 8:56 PM, Rossen Apostolov wrote:
Dear users and developers,
On Wednesday the redmine server will be upgraded and moved to a new
VM. Thus expect downtime of 1-2 hours (if it all goes well :-) ).
Hi
I am unable to use cmake to install 4.6.1 on my macbook. I got cmake from
macports, the version is 2.8.8. The command being used is:
sudo cmake /Users/hkhandel/Downloads/gromacs-4.6.1/src/
Xcode and gcc are installed.
The errors are something like this:
CMake Error at
With ACPYPE I can convert any Amber *.prmtop and *.crd to Gromacs, but it
doesn't mean it will work straightforward (but I am working for that).
For example, I am wondering how Gromacs team will port the Amber FF12SB,
since now we have atom types like '2C', '3C' (ie. starting with a number),
and
Dear Sir,
Here's the result of three different runs :
Temperature distribution for three trials
Repeat-1 280 298 317 337 359 382 406 432 460 489 520 554 589 627
Repeat-2 280 299 319 340 363 388 414 441 471 503 536 572 611
Repeat-3 280 300 322 345 370 397 426 457 490 526 564 605 649
md.log
On 5/16/13 6:11 AM, khandelia wrote:
Hi
I am unable to use cmake to install 4.6.1 on my macbook. I got cmake from
macports, the version is 2.8.8. The command being used is:
sudo cmake /Users/hkhandel/Downloads/gromacs-4.6.1/src/
You shouldn't have to invoke sudo to do work in your own
Dear All,
I have a system with two solutes (A and B) with water and ions. For
pressure coupling in index file I defined two groups: Solute and Solvent,
where solute consists of A+B and solvent consists of water+ions
Due to some reasons I need to apply position restraints on Solute A only
for few
On 5/16/13 8:12 AM, gromacs query wrote:
Dear All,
I have a system with two solutes (A and B) with water and ions. For
pressure coupling in index file I defined two groups: Solute and Solvent,
where solute consists of A+B and solvent consists of water+ions
Due to some reasons I need to apply
Hi All,
Has anyone performed MD simulation on fluids in reduced units with GROMACS?
I just wandering how the obtained density values through the box should be
converted in the SI unit (Kg/m3).
Thanks
Rasoul
--
gmx-users mailing listgmx-users@gromacs.org
Indeed the Repeat-3 seems good. But I would guess you did not run too long,
right! That would explain the distribution of values!
On May 16, 2013, at 2:04 PM, bharat gupta bharat.85.m...@gmail.com wrote:
Dear Sir,
Here's the result of three different runs :
Temperature distribution for
Okay, now I can start with large production runs .
On Thu, May 16, 2013 at 11:10 PM, XAvier Periole x.peri...@rug.nl wrote:
Indeed the Repeat-3 seems good. But I would guess you did not run too
long, right! That would explain the distribution of values!
On May 16, 2013, at 2:04 PM, bharat
On Thu, May 16, 2013 at 2:04 PM, bharat gupta bharat.85.m...@gmail.comwrote:
Dear Sir,
Here's the result of three different runs :
Temperature distribution for three trials
Repeat-1 280 298 317 337 359 382 406 432 460 489 520 554 589 627
Repeat-2 280 299 319 340 363 388 414 441 471 503
Does manual 2.3 help?
On Thu, May 16, 2013 at 2:51 PM, Rasoul Nasiri nasiri1...@gmail.com wrote:
Hi All,
Has anyone performed MD simulation on fluids in reduced units with GROMACS?
I just wandering how the obtained density values through the box should be
converted in the SI unit (Kg/m3).
Sorry to ask this simple question but how to read the replica_index and
replica_temp files. I tried to search a lot but didn't find any
information. As I have concatenated all log files and demuxed them. Here's
first 10 lines from both files:-
replica_index:
0 012345
They show which structure is in which ensemble, and the inverse. Look at
the exchange events reported in the .log files and work out which is which.
Mark
On Thu, May 16, 2013 at 5:25 PM, bharat gupta bharat.85.m...@gmail.comwrote:
Sorry to ask this simple question but how to read the
On Thu, May 16, 2013 at 12:37 PM, Alan alanwil...@gmail.com wrote:
With ACPYPE I can convert any Amber *.prmtop and *.crd to Gromacs, but it
doesn't mean it will work straightforward (but I am working for that).
For example, I am wondering how Gromacs team will port the Amber FF12SB,
Dear all,
if one performs a parallel calculation on a single node / computer with
more than 1 core, is there a speed difference between MPI and Threads?
Problem is for gromacs 4.6.1 i'm facing problems to link it to OpenMpi.
A serial version (without threads) worked, so i think i should be
cmake -DGMX_THREAD_MPI=on is intended to provide maximum performance for
your case, i.e. a single node. It's on by default for a reason ;-)
Mark
On Thu, May 16, 2013 at 6:57 PM, Thomas Schlesier schl...@uni-mainz.dewrote:
Dear all,
if one performs a parallel calculation on a single node /
I'm not sure what you mean by threads. In GROMACS this can refer to
either thread-MPI or OpenMP multi-threading. To run within a single
compute node a default GROMACS installation using either of the two
aforementioned parallelization methods (or a combination of the two)
can be used.
--
Szilárd
PS: if your compute-nodes are Intel of some recent architecture
OpenMP-only parallelization can be considerably more efficient.
For more details see
http://www.gromacs.org/Documentation/Acceleration_and_parallelization
--
Szilárd
On Thu, May 16, 2013 at 7:26 PM, Szilárd Páll
Dear all,
I have just updated the GROMACS installation at a local cluster which
have 2 GPUs. I installed CUDA 5 with no problems and it was detected by
cmake. No problems during installation.
With GROMACS 4.5 I was able to use the GPUs of this same cluster, but
now GROMACS 4.6 says that
Hi
I want to store Z coordinates of atoms at the beginning of each time step
when I am doing 'mdrun -rerun'. I am not able to find the line and file in
the source code where I can implement this. Can anyone please help me with
that?
Thanks
Sikandar
--
gmx-users mailing list
On 5/16/13 9:14 PM, Leandro Bortot wrote:
Dear all,
I have just updated the GROMACS installation at a local cluster which
have 2 GPUs. I installed CUDA 5 with no problems and it was detected by
cmake. No problems during installation.
With GROMACS 4.5 I was able to use the GPUs of
Hi,
I have a system composed of POPC/peptide/water/ions. I aim to study ion
conduction through the peptide using umbrella sampling.
I built the system and ran EM, NVT, NPT successfully, but have not run md yet.
I' d like to know if the system is required of passing a few nanoseconds md? Or
I
Respected sir
Which command do we use to determine Interaction spectra of
inhibitor–residue pair in the protein–inhibitor complexes as we have
g_hbond to determine the hydrogen bond between protein and ligand
--
Thanking You with Regards.
Arunima Shilpi
Ph. D Research Scholar(Cancer
Do you need it in the code? g_traj would help you do that on the trajectory.
On May 17, 2013, at 3:17 AM, Sikandar Mashayak symasha...@gmail.com wrote:
Hi
I want to store Z coordinates of atoms at the beginning of each time step
when I am doing 'mdrun -rerun'. I am not able to find the
Are you sure lattice cell set up in f.c.c structure has been explained
there for the positions of molecules?
On Thu, May 16, 2013 at 3:28 PM, Mark Abraham mark.j.abra...@gmail.comwrote:
Does manual 2.3 help?
On Thu, May 16, 2013 at 2:51 PM, Rasoul Nasiri nasiri1...@gmail.com
wrote:
Hi
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