Dear all,
I am a beginner to performing simulations and my system consists of protein+
cholesteryl ester +phospholipid and drug. Papers involving lipids are in
general united atom, while those involving drug-protein systems are all-atom
mostly. Kindly suggest me which of these, all-atom or
Dear Users,
I have been trying to carry out FEP calculations for a long time for
mutation of
Glutamine to Aspartic acid using gromacs 4.5.5. Unfortunately, some
questions and problems arises during calculations.
Here is the question of mine.With glutamine, the
protein charge is -12. To neutralize
I've found GTX Titat with 6gb of RAM and 384 bit. The price of such card is
equal to the price of the latest TESLA cards. Could it give me better
performance in gromacs ?
Also assuming that 1 such card need 600 WATT power supply what supply I
need for desktop with two such cards?
2013/5/28 Ehud
Thank you.
Can you tell me whether there was such a problem in earlier versions?
If not, I could use for example version 4.5.7. Because I think it isn't very
important at first stage of experiment.
Best regards,
David
--
View this message in context:
Look for my papers. At least, two dozens of them are about non-biophysical
stuff.
Gromacs can. The question is whether you can provide an adequate
Hamiltonian to describe your systems involving Al-surface.
Dr. Vitaly Chaban
On Mon, May 27, 2013 at 10:59 PM, Jeya vimalan
In my mind, MARTINI is a decent option to build your particular topology
upon.
Dr. Vitaly Chaban
On Tue, May 28, 2013 at 8:22 AM, Revthi Sanker revthi.san...@yahoo.comwrote:
Dear all,
I am a beginner to performing simulations and my system consists of
protein+ cholesteryl ester
Dear Justin Thank you for your Previous reply,
I have
Downloaded gromacs 4.6
I have configured well using the following command
cmake .. -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs4.6 -DGMX_DOUBLE=ON
-DGMX_BINARY_SUFFIX=_d
and
What other people do?
2013/5/28 Dr. Vitaly Chaban vvcha...@gmail.com
In my mind, MARTINI is a decent option to build your particular topology
upon.
Dr. Vitaly Chaban
On Tue, May 28, 2013 at 8:22 AM, Revthi Sanker revthi.san...@yahoo.com
wrote:
Dear all,
I am a beginner to
The actual error message is higher up, but my guess would be your compiler
in 10.04 is too old to be useful. Per the installation instructions, you
will want the latest version of gcc you can get, and ones that came with
10.04 will very likely be wrong or slower than the latest ones.
Mark
On
On 2013-05-28 14:39, massimo sandal wrote:
What other people do?
Read literature. Gromacs allows you to choose many. If you need detailed
results use an atomistic force field.
2013/5/28 Dr. Vitaly Chaban vvcha...@gmail.com
In my mind, MARTINI is a decent option to build your particular
10.04 comes with gcc 4.3 and 4.4 which should both work (we even test
them with Jenkins).
Still, you should really get a newer gcc, especially if you have an
8-core AMD CPU (= either Bulldozer or Piledriver) both of which are
fully supported only by gcc 4.7 and later. Additionally, AFAIK the
On 5/28/13 1:01 AM, Ishwor wrote:
Dear all
I want to study the simulation of Carbonmonoxide in water. I have seen the
Lennard Jones parameters, force constant and partial charges of water in the
file spce.itp inherent in gromacs but couldnt get the parameters for CO .I
will be pleased if
On 5/28/13 6:03 AM, DavidPO wrote:
Thank you.
Can you tell me whether there was such a problem in earlier versions?
If not, I could use for example version 4.5.7. Because I think it isn't very
important at first stage of experiment.
I have no idea. Try 4.5.7 and see. If it does work in
On 28.05.2013 13:39, vidhya sankar wrote:
cmake .. -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs4.6 -DGMX_DOUBLE=ON
-DGMX_BINARY_SUFFIX=_d
please try
cmake .. -DGMX_CPU_ACCELERATION=SSE4.1
-DCMAKE_INSTALL_PREFIX=/usr/local/gromacs4.6 -DGMX_DOUBLE=ON
-DGMX_BINARY_SUFFIX=_d
I remember to have
Thank you Mirco Wahab and Other Gromacs users
As you
Mailed Me I have compiled gromacs 4.6
I have installed using the command As posted in mail But I have AMD 8 Core
black Edition
When I run the mdrun I saw a warning
On 5/28/13 11:11 AM, vidhya sankar wrote:
Thank you Mirco Wahab and Other Gromacs users
As you
Mailed Me I have compiled gromacs 4.6
I have installed using the command As posted in mail But I have AMD 8 Core
black
On 28.05.2013 17:11, vidhya sankar wrote:
As you Mailed Me I have compiled gromacs 4.6
I have installed using the command As posted in mail
But I have AMD 8 Core black Edition
When I run the mdrun I saw a warning
Note: file tpx version 73, software tpx version 83
Using 8 MPI threads
Compiled
Dear Sir,
Thank
you so much for your reply. To be specific, my system has only four
lipid moities- 2 cholesteryl oleates and 2 phosphotidyl cholines. But I
was not able to get all atom parameters for these lipids from the lipid
book( only united atom parameters were available). So I had
without knowing full details of your simulated system and the goals you
pose, I cannot advise anything more definite than I did before.
if I were you and my system were yours, I would start with MARTINI FF.
I wish you a success in your endeavor.
Dr. Vitaly Chaban
On Tue, May 28, 2013 at
Chaban, why are you advising MARTINI? It is a coarse-grained force field,
one should be well aware of the limitations etc. before deciding to choose
it, it's not just another force field.
2013/5/28 Dr. Vitaly Chaban vvcha...@gmail.com
without knowing full details of your simulated system and
That'll likely work, but whether Vidhya wants to use it depends whether he
cares about his simulation performance on this machine.
Mark
On Tue, May 28, 2013 at 4:05 PM, Mirco Wahab
mirco.wa...@chemie.tu-freiberg.de wrote:
On 28.05.2013 13:39, vidhya sankar wrote:
cmake ..
You'll still need to do some reading. If your moieties have never been used
in all-atom simulations, you'll have a big task of parameterization, or
have to accept some approximation in your model. Even if they have been
used, you'll want to read up on how they were parameterized and whether
Dear all,
As far as I understand, the OP is interested in hardware for *running*
GROMACS 4.6 rather than developing code. or running LINPACK.
To get best performance it is important to use a machine with hardware
balanced for GROMACS' workloads. Too little GPU resources will result
in CPU
On 2013-05-28 18:09, Revthi Sanker wrote:
Dear Sir,
Thank you so much for your reply. To be specific, my system has only
four lipid moities- 2 cholesteryl oleates and 2 phosphotidyl cholines.
But I was not able to get all atom paramters for these lipids from the
lipid book( only united atom
On Sat, May 25, 2013 at 2:16 PM, Broadbent, Richard
richard.broadben...@imperial.ac.uk wrote:
I've been running on my Universities GPU nodes these are one E5-xeon (6-cores
12 threads) and have 4 Nvidia 690gtx's. My system is 93 000 atoms of DMF
under NVE. The performance has been a little
On Tue, May 28, 2013 at 10:14 AM, James Starlight
jmsstarli...@gmail.com wrote:
I've found GTX Titat with 6gb of RAM and 384 bit. The price of such card is
equal to the price of the latest TESLA cards.
Nope!
Titan: $1000
Tesla K10: $2750
Tesla K20(c): $3000
TITAN is cheaper than any Tesla and
Dear Dr. Pali,
Thank you,
Stephan Watkins
Gesendet:Dienstag, 28. Mai 2013 um 19:50 Uhr
Von:Szilrd Pll szilard.p...@cbr.su.se
An:Discussion list for GROMACS users gmx-users@gromacs.org
Betreff:Re: Re: [gmx-users] GPU-based workstation
Dear all,
As far as I understand, the OP is
Hello All,
Does anybody have any script to arrange the molecules in the sphere?
Actually, I need to set up a LDL (has hydrophobic core and monolayer of PC
around).
Thanks,
Dariush
--
View this message in context:
http://gromacs.5086.x6.nabble.com/arrange-the-atoms-in-sphere-tp5008599.html
Use packmol.
On Wed, May 29, 2013 at 1:32 AM, dariush d.mohammady...@gmail.com wrote:
Hello All,
Does anybody have any script to arrange the molecules in the sphere?
Actually, I need to set up a LDL (has hydrophobic core and monolayer of PC
around).
Thanks,
Dariush
--
View this
Dear all,
I am doing PCA on a 110ns run.
When calculating the subspace overlap from independent PCA performed in
different time windows, I expect the overlap to be 1 only when the time
interval is equal to 110ns, since both covariance matrices are identical.
However, I found that from the
Compiling GROMACS w CUDA 5.0 problem
I did this a few days. i will share my how to do. i used gromacs 4.6.1.
assuming u have the nvidia gpu also
1.$ tar xfz gromacs-4.6.tgz
$ cd gromacs-4.6
$ mkdir build-cmake
$ cd build-cmake
$sudo apt-get install cmake
$ cmake ..
$cmake .. -DGMX_GPU=ON
Dear Dr. Pall!
Thank you for your suggestions!
Asumming that I have budget of 5000 $ and I want to build gpu-based desktop
on this money.
Previously I've used single 4 core i5 with GTX 670 and obtain average 10
ns\day performance for the 70k atoms systems (1.0 cutoffs, no virtual sites
, sd
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