Hi,
Well, I didn't shuffle or sort my system prior to running. I am running in
parallel, would that be part of the problem?
I have tryed -fit or -pbc but the structure comes out bad the same way. The
exact problem is that I have two structures. Each comes from individual
dynamics job. Now I need to
Jussi Lehtola wrote:
Hi,
I'm doing a Fedora package of GROMACS. Does GROMACS have runtime CPU
capability detection, i.e. if the package is compiled on a SSE-capable
processor and run on an i586 (hope not), will it work?
Yes it does. It should work, but e.g. debuggers tend to dislike illegal
in
Hi There,
I am trying to run MD simulation for screening my docking result, but I am
not aware of what are the parameters and analysis we can do for docking by
using MD simulation.
If anybody have tried the similiar things using GROMACS, Please help me in
this regard.
With Thanks,
VIvek
__
Hi,
I'm doing a Fedora package of GROMACS. Does GROMACS have runtime CPU
capability detection, i.e. if the package is compiled on a SSE-capable
processor and run on an i586 (hope not), will it work?
The safe way is, of course, to disable all assembly loops, which would
hurt performance a lot...
Hi Fabricio,
You can also sue the option -dump 1 to extract a frame. But it's
not related to your error.
Have you done any fitting and pbc related stuff or did you
shuffle/sort your system prior to running?
Cheers,
Tsjerk
On Tue, Sep 30, 2008 at 5:02 PM, Ragnarok sdf <[EMAIL PROTECTED]> wro
I have some (hopefully) clarifying commments to my previous post now:
First to answer your question regarding pme.c. My compilation was done
from v. 1.125
Line 1037-
if ((kx>0) || (ky>0)) {
kzstart = 0;
} else {
kzstart = 1;
From: Laercio Pol Fachin <[EMAIL PROTECTED]>
Date: September 30, 2008 9:50:48 AM EDT
To: gmx-users@gromacs.org
Subject: [gmx-users] Hydrogen Bond Lifetime
Reply-To: [EMAIL PROTECTED], Discussion list for GROMACS
users
Hi, all.
I am analyzing the hydrogen bond lifetime of water molecules
Laercio Pol Fachin wrote:
Hi, all.
I am analyzing the hydrogen bond lifetime of water molecules around
polar atoms of my molecule. However, I have faced different HB lifetime
definitions in different sources. A sample of what I obtained employing
g_hbond is below:
"g_hbond -f .xtc -s .tpr -
Hello,
I have ran a simulation with gromac but can't seem to be able to extract a
single structure of a determined frame from my .trr file. I wish to obtain a
pdb file good for reading in CHIMERA, for example.
I tryed the following command:
trjconv -f sim.trr -s trjtop.tpr -o pdbiwant.pdb -b 1
Hi, all.
I am analyzing the hydrogen bond lifetime of water molecules around polar atoms
of my molecule. However, I have faced different HB lifetime definitions in
different sources. A sample of what I obtained employing g_hbond is below:
"g_hbond -f .xtc -s .tpr -n .ndx -ac .xvg -b 0 -e 1"
vivek sharma wrote:
hi All,
My apologies for putting a question out of gromacs.
I was trying to superimpose pdb entry of one molecule over other, I
tried it using PYMOL, CHIMERA and vmd ..they are simply opening one
molecule over other.
Is there any specific function in any of the visualizati
Hi.
I've checked with the person who did the test and the system is 36000 atoms
large, it seems small, doesn't it? Maybe that's the problem, coupled with
the high latency of GbE connection.
What I find strange though, is that for many computers in the Top 500, this
is sufficient.
Best regards,
hi All,
My apologies for putting a question out of gromacs.
I was trying to superimpose pdb entry of one molecule over other, I tried it
using PYMOL, CHIMERA and vmd ..they are simply opening one molecule over
other.
Is there any specific function in any of the visualization tool, that can
solve my
Hi,
Is there a possibility to calculate the kinetic energy separately for
the each specified (energy) groups?
I have not found such option in g_energy. One only can treat the total
Kinetic-En. Is it anywhere else or not?
Thanks for suggestions.
Vitaly
--
Vitaly V. Chaban
School of Chemistry
shahrbanoo karbalaee wrote:
Dear justin
Hi,
In my simulation with ff53a5 when I do this command pdb2gmx -f
name.pdb -ter -ignh -water spce .I find this error .C-terminus: None
Now there are 14 residues with 138 atoms
Making bonds...
Opening library file /usr/local/gromacs/share/gromacs/top/
Dear justin
Hi,
In my simulation with ff53a5 when I do this command pdb2gmx -f
name.pdb -ter -ignh -water spce .I find this error .C-terminus: None
Now there are 14 residues with 138 atoms
Making bonds...
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
Number of bonds w
I see.
I was looking to do my dissertation for my Masters course in GPGPU on
cientific calculation programs and GROMACS seemed appropriate.
Would any of the developers be interested in collaborating with me to make
this happen, or should I look elsewhere, to OpenMM, like Jose Duarte said?
Best r
Ok, tks Jose!
I will be looking into this project then, maybe it's what I'm looking for.
Best regards,
Tiago Marques
On Tue, Sep 30, 2008 at 9:17 AM, Jose Duarte <[EMAIL PROTECTED]> wrote:
> Hi Tiago
>
> I think this is precisely what the [EMAIL PROTECTED] people are
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Yes.
Cheers,
Erik
On Sep 29, 2008, at 3:18 PM, himanshu khandelia wrote:
Is there an implementation in gromacs for using a uniform
neutralizing plasma with PME, to avoid use of counterions?
Thank you
-Himanshu
___
gmx-users mailing listgmx-u
Hi,
Please search the list - all this stuff will be available in Gromacs
once we have neighborlists and PME working, but that's non-trivial
work ;-)
Cheers,
Erik
On Sep 30, 2008, at 10:17 AM, Jose Duarte wrote:
Hi Tiago
I think this is precisely what the [EMAIL PROTECTED] people are do
Hi Tiago
I think this is precisely what the [EMAIL PROTECTED] people are doing.
Apparently the just released a preview of the OpenMM API and they intend
to release gromacs code using the API in December:
https://simtk.org/project/xml/news.xml?group_id=161
Maybe somebody on the list more fami
Hi,
I have to correct myself.
The PME fix is in the 4.0 rc2 release, but was not in the CVS.
Now it is also in CVS.
So you can try changing the line, or you can download 4.0 rc2.
Berk
From: [EMAIL PROTECTED]
To: gmx-users@gromacs.org
Subject: RE: [gmx-users] Possible bug in parallelization,
Hi,
In 4.0 rc1 there is a bug in PME.
Erik mailed that this has been fixed in 4.0 rc2, but actually this is not the
case.
The fix was in the head branch of CVS, but not in the release tree.
I have committed the fix now.
Could you check if the crash is due to this?
After line 1040 of src/mdlib/pm
Just addin my drop here:
Just did the same, both single and double precision, not parallel anyway.
What I get is the following:
*aurora down/gmxtest 41%* ./gmxtest.pl all
All 16 simple tests PASSED
FAILED. Check files in dec+water
1 out of 14 complex tests FAILED
All 63 kernel tests PASSED
All 4
Hi Sudheer,
It depends mainly on what it is you want to look at. You cannot
exclude though, that the version has an effect on your results.
Therefore you either have to do all simulations using the same
version, or you have to randomize the versions over the simulations. I
do hope that you meant t
Hi Users,
I want to compare the protein results by simulating six systems in personal
computer has Gromacs version 3.3.1, due to delay of running jobs in a single
computer,I want to run some of my systems in another computer contain
Gromacs version 3.3.3 but processor speed machine type everything
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