Dear All,
How do I incorporate the 1-4 scaling factor ( e.g., 1.0 for CHARMM and
0.833 in AMBER) in gromacs? Or, is it internally taken care of by gromacs
while specifying the -ff flag?
NAMD input file uses the following keyword
1-4scaling 1.0 (for charmm force field)
Thanks,
Tara
Hai
In Hydrogen Bonding Analysis, I want to know about the the
interpretation of option -life and -ac (autocorrelation) I cannot understand
what the columns P(t) and t p(t) describe and how to interpret this. Similarly
after tagging -ac option in .xvg file I am getting @ s0 leg
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 wrote:
> Does manual 2.3 help?
>
>
> On Thu, May 16, 2013 at 2:51 PM, Rasoul Nasiri
> wrote:
>
> > Hi All,
> >
> > Has anyone performed MD
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 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 line and file in
> t
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 & Epige
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 mi
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 t
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 listgmx-users@gromacs.
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
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 wrote:
> I'm not su
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
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 wrote:
> Dear all,
> if one performs a parallel calculation on a single node / computer with
> more
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 abl
On Thu, May 16, 2013 at 12:37 PM, Alan 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,
>
There's no plan to do
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 wrote:
> Sorry to ask this simple question but how to read the replica_index and
> replica_tem
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
Does manual 2.3 help?
On Thu, May 16, 2013 at 2:51 PM, Rasoul Nasiri 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).
>
> Thanks
> Ras
On Thu, May 16, 2013 at 2:04 PM, bharat gupta wrote:
> 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
> Rep
Okay, now I can start with large production runs .
On Thu, May 16, 2013 at 11:10 PM, XAvier Periole 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 gupta
> wro
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 wrote:
> Dear Sir,
>
> Here's the result of three different runs :
>
> Temperature distribution for three trials
>
> Re
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
http://lists.gromacs.org/mailman/listi
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
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 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 dire
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 fi
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 G
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 gmxlib/CMakeLists.txt
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 :-) ).
C
You have to convince yourself, not me :)) But I can give you my opinion …
On May 16, 2013, at 10:33 AM, bharat gupta 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 wrote:
>
>>
>> An acc
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 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 exchanges are
>
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 p
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