Check this: http://manual.gromacs.org/online/editconf.html
editconf -align
On Fri, Jan 25, 2013 at 1:12 PM, 申昊 wrote:
> Dear GMX users,
>
>I have a question about aligning my molecules along specific coordinate
> axis ,such as Z-axis.
>Does anyone know the codes?
>
>
> Best regards,
>
Mark,
as I told previously to Justin ( lets to consider the problems with
g_anaeig only in that topic to avoid producing doubles ) the problem
is not in the average structure (it looks fine) but in the
filter.xtc trajectory produced by g_anaeig. When I load that xtc to
any structure in vmd I obtai
Szilárd,
thanks for suggestions.
IT's only not quite understand for me in what GPU ( gtx or tesla) I'll
get best performance with the typical ssystem consisted of 50-80k
atoms with explicit solvent and PME ( assuming that I'm using small
cut-offs as you told). For example on the 400$ gtx 670 I
Dear GMX users,
I have a question about aligning my molecules along specific coordinate axis
,such as Z-axis.
Does anyone know the codes?
Best regards,
Hao
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archiv
Justin,
the problem is not in the average structure (it looks fine) but in the
filter.xtc trajectory produced by g_anaeig. When I load that xtc to
any structure in vmd I obtained dynamics picture of my protein with
broken geometry (its look loke my protein was shrunken). But when I
compared eigenv
Thanks for your reply.
I want to chose one of the 5 conformers from a NMR PDB. As I studied in
literature, the average structure could be selected regarding RMSD values and
the go on with selected one to simulate in in water, lipid bilayer.
All right, I may make a matrix, but how would I chose
Thank you for the clarification.
On Fri, Jan 25, 2013 at 12:40 AM, Justin Lemkul wrote:
>
>
> On 1/24/13 11:03 AM, Kavyashree M wrote:
>
>> Dear users,
>>
>> I have a little confusion -
>> The hbmap.xpm file gives the existence of each hydrogen bond.
>> The file mentions -
>> " c #FF " /*
On Mon, Jan 14, 2013 at 7:20 PM, James Starlight wrote:
> 1)As I understood from nvidia site at present time GPU's from the
> tesla serie are the best for the calculations like md. For instasnce
> NVIDIA Tesla C2075 have performance ~ 1 TFLOPS in the
> single-precission calculations. I wounder to
Hi,
Typically, the fastest the GPU the better. On a more detailed level, less
multiprocessors (that's not "cores"!) with faster clock speeds help in
achieving higher performance with small systems. As GPUs are highly
parallel processors, 20-30k atoms/GPU can be considered small-ish -
especially wi
Hi Berk,
I am running membrane simulations using both the CHARMM36 and MARTINI v. 2.1
parameters.
So both those cut-off treatments are important to me, but if there are ways
around it I'd be happy to explore them to be able to use the GPUs. The place it
would be most effective would probably be
Hi,
I am not a fan of especially switching the potential, as that produces
artifacts.
Shifting is less harmful, but unnecessary in nearly all cases.
But I do realize some force fields require this (although you can probably find
a cut-off
setting at which results would be very similar).
Another
Dear GMX developers,
Thanks so much for the GMX 4.6 release. Testing on GPUs has shown impressive
speed-ups.
I have a question however, regarding the missing "switching and shifting" for
non-bonded interactions.
I looked at the developer zone website and saw this comment below:
http://www.grom
On Tue, Jan 22, 2013 at 8:22 PM, James Starlight wrote:
> Dear Gromacs users!
>
>
> There is some bug with g_anaeig the souce of which I could not fully
> understand.
Good Advice: until you can almost write a code patch to fix it, be very
hesitant in suggesting any software has a bug. The best
If your trajectory halves were fully converged then you would observe no
difference in their PCs. Since differences exist, your simulations cannot
possibly have converged. Convergence implies the same covariance matrix,
but unfortunately even if you had the same PCs, it's still a leap in the
dark t
On 1/24/13 6:12 AM, dakoenig wrote:
Hi Justin,
thank you so far. Now I got some more specific questions regarding g_msd
I got my trajectory from 0-30ns. So far it should to be "correct".
I was analyzing this trajectory with g_msd and the following command:
g_msd -f mdrun.xtc -s mdrun.tpr -ni
On Thu, Jan 24, 2013 at 7:09 PM, Christoph Junghans wrote:
> > Date: Thu, 24 Jan 2013 01:07:04 +0100
> > From: Szil?rd P?ll
> > Subject: Re: [gmx-users] Problem with gromacs-4.6 compilation on
> > Debian
> > To: Discussion list for GROMACS users
> > Message-ID:
> > xwqyn3xwoeujj
On 1/24/13 9:44 AM, James Starlight wrote:
Justin,
thanks. I've not known that posres were defined in the tpr file as well.
Sure, how else would mdrun know what to do? :)
By the way could you make your suggestion in my another topic which
I've posted some days ago about problem with the g
On 1/24/13 10:26 AM, Raghuvir R. S. Pissurlenkar wrote:
Hi
I have tried to write a grompp.mdp file for simulated annealing of a peptide
(~30 aa) in implicit solvent.
Please someone could tell me if the parameters set are fine for the same.
On 1/24/13 11:03 AM, Kavyashree M wrote:
Dear users,
I have a little confusion -
The hbmap.xpm file gives the existence of each hydrogen bond.
The file mentions -
" c #FF " /* "None" */,
"o c #FF " /* "Present" */,
Meaning -
character "" in white colour means Hbond not present
chara
> Date: Thu, 24 Jan 2013 15:55:13 +0100
> From: Szil?rd P?ll
> Subject: Re: [gmx-users] Problem with gromacs-4.6 compilation on
> Debian
> To: Discussion list for GROMACS users
> Message-ID:
>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Let me add two more things.
>
> Note
On Thu, Jan 24, 2013 at 6:48 PM, James Starlight wrote:
> Justin, Szilárd, thanks for suggestion!
>
> It will be easily for me to found a better card :)
>
> By the way in other topics some developments told me that the Plumed
> plugin for methadynamics will be realised in gromacs 4.6. I've checked
On Thu, Jan 24, 2013 at 5:08 PM, Ali Alizadeh wrote:
> Dear All users
>
> How can i use only Buckingham potential(non bonded interaction) for my
> system? Is it possible?
>
Yes. First you need a force field that implements it, and then you need to
look in chapters 4 and 5 of the manual for the d
> Date: Thu, 24 Jan 2013 01:07:04 +0100
> From: Szil?rd P?ll
> Subject: Re: [gmx-users] Problem with gromacs-4.6 compilation on
> Debian
> To: Discussion list for GROMACS users
> Message-ID:
>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi all,
>
> Let me clarify one thing
Justin, Szilárd, thanks for suggestion!
It will be easily for me to found a better card :)
By the way in other topics some developments told me that the Plumed
plugin for methadynamics will be realised in gromacs 4.6. I've checked
for it in manual but could not find any notions about it . Have it
you can make a simple script which calculates all the pairwise RMSD
values with g_rms. By doing this you can make a "RMSD matrix".
The usefulness of this depends on what you are trying to see, which
wasn't clearly stated to us. I did it once because I wanted to know how
similar the 20 co
Hi KT,
This is caused by another problem. Your system blew up. Check messages
before this one, and check the log for LINCS warnings.
Cheers,
Tsjerk
On Thu, Jan 24, 2013 at 9:11 AM, Kieu Thu Nguyen wrote:
> Dear All,
>
> My MD simulation has an error
>
> Warning: Only triclinic boxes with the
Dear users,
I have a little confusion -
The hbmap.xpm file gives the existence of each hydrogen bond.
The file mentions -
" c #FF " /* "None" */,
"o c #FF " /* "Present" */,
Meaning -
character "" in white colour means Hbond not present
character "o" in red colour means Hbond is present
Hi
I have tried to write a grompp.mdp file for simulated annealing of a peptide
(~30 aa) in implicit solvent.
Please someone could tell me if the parameters set are fine for the same.
-
; Preprocessing
define = -DFLE
HI Erik:
thanks a lot for kind advices, I will try it.
best
Albert
On 01/24/2013 03:00 PM, Erik Marklund wrote:
g_traj -nox -noy if I recall correctly.
On Jan 21, 2013, at 4:10 PM, Albert wrote:
hello:
I would like to make statics for an atom along Z-axis. I am just
wondering how can I t
Dear Sir,
This is 4.5.3. I have not tried nomerge. I did not use
nomerge option in any of them, So if it has counted
it (Hbond b/w same donor and acceptor but with
different hydrogen) twice in one calculation then it will
be counted twice in another, So wont the result with/without
nomerge be the
Let me add two more things.
Note that we *always* compare performance and acceleration to our
super-tuned state-of-the-art CPU code, which I can confidently say that is
among the fastest if not the fastest to date, and never to some slow (CPU)
implementation. Therefore, while other codes might be
On Thu, Jan 24, 2013 at 3:28 PM, Justin Lemkul wrote:
>
>
> On 1/24/13 9:23 AM, James Starlight wrote:
>
>> oh that was simply solved by upgrading of G++ :)
>>
>> the only problem which remains is the missing of support of mu GPU :(
>> That time I've tried to start simulation on simply 2 cores CP
Justin,
thanks. I've not known that posres were defined in the tpr file as well.
By the way could you make your suggestion in my another topic which
I've posted some days ago about problem with the g_anaeig ( below I
coppy that issue).
There is some bug with g_anaeig the souce of which I could
On 1/24/13 9:23 AM, James Starlight wrote:
oh that was simply solved by upgrading of G++ :)
the only problem which remains is the missing of support of mu GPU :(
That time I've tried to start simulation on simply 2 cores CPU + geforce 9500
From md run I've obtained
NOTE: Error occurred dur
oh that was simply solved by upgrading of G++ :)
the only problem which remains is the missing of support of mu GPU :(
That time I've tried to start simulation on simply 2 cores CPU + geforce 9500
>From md run I've obtained
NOTE: Error occurred during GPU detection:
CUDA driver version is
On 1/24/13 7:21 AM, James Starlight wrote:
Dear Gromacs Users!
In the gromacs-4.6 version I have some problems with the trp files
obtained after reduction of atom subset via
tpbconv -f initial.tpr -n index -o reduced.tpr
where in index file reduced atom sub set was defined ( e.g c-alpha
ato
The values are OK, you obtain a value of RMSD of 0.2510229 . The value -1
refers time, and it is because you do not have a trajectory. You are comparing
only two .pdb structures, so it is consistent that you obtain only one value,
as you do not have more than one frame to compare.
Regards
Flor
g_traj -nox -noy if I recall correctly.
On Jan 21, 2013, at 4:10 PM, Albert wrote:
hello:
I would like to make statics for an atom along Z-axis. I am just
wondering how can I to do this in Gromacs?
thank you very much
best
Albert
--
gmx-users mailing listgmx-users@gromacs.org
http://l
Hi. What version was this? Have you tried with -nomerge?
Erik
On Jan 21, 2013, at 10:55 AM, Kavyashree M wrote:
Dear users,
While calculating hydrogen bonds for a simulation, it
was found that the average number of intra protein
hbonds was not equal to sum of MM, MS and SS
hydrogen bonds. (MM
After switching to gcc-4.6 I've obtained that error on the first step
of gromacs compilation
[ 0%] Building NVCC (Device) object
src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o
gcc: error trying to exec 'cc1plus': execvp: No such file or directory
CMake Error a
Dear Gromacs Users!
In the gromacs-4.6 version I have some problems with the trp files
obtained after reduction of atom subset via
tpbconv -f initial.tpr -n index -o reduced.tpr
where in index file reduced atom sub set was defined ( e.g c-alpha
atoms from the protein only )
then I'm using g_Co
Hi Justin,
thank you so far. Now I got some more specific questions regarding g_msd
I got my trajectory from 0-30ns. So far it should to be "correct".
I was analyzing this trajectory with g_msd and the following command:
g_msd -f mdrun.xtc -s mdrun.tpr -nice 0 -b 0 -e 3 -beginfit 15000
-endf
42 matches
Mail list logo
