Dear Justin
Thanks for your reply.
My system contains dopc lipid. ns.xtc and ns.tpr files contain all atoms
related to dopc molecule.
I want to obtain number of atoms in a first group (C38 atom in dopc) which
are located in special distance (0.74 nm) of the second group (rest of
atoms in dopc).
You have to define the B state parameters for your deprotonated state
explicitly.
The following line in your topology does not have the parameters for the B
state.
16 opls_270 77GLUHE2 5 0.45 1.008
You have to set the charges zero in the B state (if you want to cons
Thanks. It'd be nice if MSVC did what it claims to do, and create more
pages on demand for such allocations.
Mark
On Wed, Jan 29, 2014 at 6:59 PM, Mirco Wahab <
mirco.wa...@chemie.tu-freiberg.de> wrote:
> On 29.01.2014 15:06, Mirco Wahab wrote:
>
>> A test run (martini small vesicle system,
>>
Hi Anders,
This mail belongs to the users' list.
This type of error is typically a sign of the CUDA kernel failing due
to a nasty bug in the code or hardware error. The dmesg message is
suspicious and it may be a hint of hardware error (see
https://www.kubuntuforums.net/showthread.php?64133-kwin-
Hi,
I uploaded fixes for both issues:
https://gerrit.gromacs.org/#/c/3040/
https://gerrit.gromacs.org/#/c/3041/
Thanks for the feedback.
Roland
On Wed, Jan 29, 2014 at 12:59 PM, Mirco Wahab <
mirco.wa...@chemie.tu-freiberg.de> wrote:
> On 29.01.2014 15:06, Mirco Wahab wrote:
> > A test run (
On 29.01.2014 15:06, Mirco Wahab wrote:
A test run (martini small vesicle system,
250K atoms) did start promising but crashed
after 15 min without any indication. (I'll
try without gpu later).
I identified the problem. It is the same problem
that also required a patch in the 4.6.x versions
on W
Hi,
Did you use g_dist to measure, quantitatively, the distance between NAMD
and formate?
If you see the drastic movement, from the trajectory file, then I would
suggest you to convert the traj to a new .xtc file using trjconv -nojump
and then check whether the same thing is happening or not.
Best
Hi Mark,
Thank you so much for your kind response! If you have time, may I please
ask a follow-up question?
In your response below, you said that three of the features that I asked
about (leapfrog integration, Nose-Hoover thermostat, and Ewald sum with
dipole correction) are, in fact, now suppor
On 1/29/14, 10:10 AM, SEMRAN İPEK wrote:
Dear Users;
I am really in need of your help regarding to the MD results for
ligand-enzyme system.
I have done MD calculations for 10 ns. for Formate, FDH and NADP ternary
structure. Before MD, formate ligand has been docked to the NADP to ensure
the b
On 1/29/14, 10:02 AM, Albert wrote:
Hello:
I am going to simulate a membrane system without wrap at z direction (pbc=xy).
it claimed that it requires a wall. I try to add the following parameters into
.mdp file:
pbc = xy
nwall= 2
wall-type = 12-6
cutoff-scheme = Verlet
but
Thanks Bipin for the reply.
I went through the Gromacs manual, and thought that I managed to incorporate
two states (protonated and deprotonated) in my topology file. Can anyone who
has done it before tell me if I defined both A and B states correctly in my
.top file.
;
; File 'GLUA_p
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On 1/29/14, 9:13 AM, Atila Petrosian wrote:
Dear Justin
Thanks for your reply.
To obtain modified trajectory and then comparing with original trajectory,
I do not know exactly which of none, mol, res, atom, nojump, cluster or
whole is appropriate for me.
In a simple case like this, many of
On 1/29/14, 9:19 AM, shahab shariati wrote:
Hi all
I used trjorder -f ns.xtc -s ns.tpr -n ns.ndx -o ns.pdb -nshell ns.xvg -r
0.74
I encountered with Fatal error:
An atom number in group is larger than the number of atoms in the
trajectory
What means of this error? How to fix it?
It mea
Dear Users;
I am really in need of your help regarding to the MD results for
ligand-enzyme system.
I have done MD calculations for 10 ns. for Formate, FDH and NADP ternary
structure. Before MD, formate ligand has been docked to the NADP to ensure
the binding the ligand to the pocket of NADP.
Form
Hello:
I am going to simulate a membrane system without wrap at z direction
(pbc=xy). it claimed that it requires a wall. I try to add the following
parameters into .mdp file:
pbc = xy
nwall= 2
wall-type = 12-6
cutoff-scheme = Verlet
but it failed with grompp with messages:
Dear Justin
Thanks for your reply.
To obtain modified trajectory and then comparing with original trajectory,
I do not know exactly which of none, mol, res, atom, nojump, cluster or
whole is appropriate for me.
Best wishes
--
Gromacs Users mailing list
* Please search the archive at
http://ww
Hi all
I used trjorder -f ns.xtc -s ns.tpr -n ns.ndx -o ns.pdb -nshell ns.xvg -r
0.74
I encountered with Fatal error:
An atom number in group is larger than the number of atoms in the
trajectory
What means of this error? How to fix it?
Any help will highly appreciated.
--
Gromacs Users mail
On 29.01.2014 11:15, Mark Abraham wrote:
* lots of internal cleaning of the house
* various bug fixes
Status report on windows:
Build Perfectly!
Builds error-free out-of-the-box using
Visual C++ 2012 (VC11), cmake 2.8.12.1,
Cuda 5.5, already installed Boost 1.55,
already installed fftw3.3.3,
Dear Carlo,
I thought people who use plumed with gromacs would look into my post.
Thanks for looking at it. :)
Gareth Tribello has suggested me to use few options related to the pbc
implementation on COLVARS. I'm working on that.
cheers,
Tarak
On Wed, Jan 29, 2014 at 5:04 PM, Carlo Camilloni
w
On 1/29/14, 5:44 AM, Atila Petrosian wrote:
Dear kannan
Thanks for your reply
Are you sure there is not pbc problem in my case.
For example, can I do g_dist tool to obtain distance between protein and
cnt? Is output for g_dist true and rational?
g_dist, like most Gromacs tools, accounts f
Daer kannan
Thanks for your reply
Picture relating to g_dist is in the following link:
https://www.dropbox.com/s/c86ubhdguy9ai8b/g_dist.bmp
Distance between protein and cnt was increased in during 1000-2500 ps,
exactly those
frame are unusaul in VMD (in my opinion, pbc problem).
Best wishes
--
On Wed, Jan 29, 2014 at 4:46 AM, Trayder Thomas
wrote:
> Curses! Kinda seemed intuitive that way. I assume the philosophy being
> worked towards is that every unique run should have a unique .tpr file that
> it is reproducible from?
>
> Curiously, I ran and checked a first batch on a different clu
Hi Albert,
Check g_cluster -h
Cheers,
Tsjerk
On Wed, Jan 29, 2014 at 11:21 AM, Albert wrote:
> Hello:
>
> I am using g_cluster to cluster a peptide conformation from Gromacs. It
> generate a black/white .xpm file and a .log file.
>
> However, it doesn't generate an average structure for each
Dear Tarak,
I think this message would me more appropriate for the PLUMED mailing list.
plumed-us...@googlegroups.com
Best wishes,
Carlo
> Message: 3
> Date: Wed, 29 Jan 2014 11:17:46 +0530
> From: tarak karmakar
> To: plumed-us...@googlegroups.com,Discussion list for GROMACS users
>
On Jan 29, 2014 4:59 AM, "Trayder Thomas" wrote:
>
> Curses! Kinda seemed intuitive that way. I assume the philosophy being
> worked towards is that every unique run should have a unique .tpr file
that
> it is reproducible from?
It has that effect, which is very useful for debugging. I think of t
Dear kannan
Thanks for your reply
Are you sure there is not pbc problem in my case.
For example, can I do g_dist tool to obtain distance between protein and
cnt? Is output for g_dist true and rational?
Best wishes
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Gromacs Users mailing list
* Please search the archive at
http://www.gromac
Hi people,
Teemu's done some quick work getting bash completions more or less in
shape. Please try out the new 5.0-beta2 and let us know how it works. You
will need to source GMXRC and both gmx-completion* files
Thanks,
Mark
On Thu, Jan 23, 2014 at 7:10 AM, Tsjerk Wassenaar wrote:
> +1 for b
Hi,
trjconv -s topol.tpr -f traj -pbc mol -o traj_modified
select '0' for the entire system
You can try using either 'mol' or 'nojump' depending on your visualization
needs.
cheers,
Tarak
On Wed, Jan 29, 2014 at 3:39 PM, Atila Petrosian
wrote:
> Dear Gromacs users
>
> I did simulation of a sy
Hello:
I am using g_cluster to cluster a peptide conformation from Gromacs. It
generate a black/white .xpm file and a .log file.
However, it doesn't generate an average structure for each cluster. So,
I am just wondering, how can we also export one avarage structure for
each cluster?
thank
Hi GROMACS users,
The second beta release of GROMACS 5.0 is available! We are making this
available to you to get an early taste of how GROMACS 5.0 will look and
work, and most importantly to get feedback from you about how well things
work. While we try our hardest to keep the quality of GROMACS
Dear Gromacs users
I did simulation of a system containing protein and cnt using gromacs 4.5.6.
When I see trajectory by VMD, in some frames, protein atoms exit one side
of box
and enter opposite side of box (pbc problem). I know I should use -pbc
option of
trjconv tool. But I do not know exactly
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