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Thank you Rossen, that worked.
When I compile, should I be including my FFTW as per normal? I didn't
do that since it was not mentioned and during the build, I get "--
Using internal FFT library - fftpack"
--- original message ---
Hi Chris,
## what I did:
module purge
module load gcc/
My messages haven't been going through since yesterday, testing to see if this
one makes it.
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (54
This sounds like you, or your sysadmin, killed the job. It is also
possible if you are using a cluster that there is a walltime limit and
you exceeded that, so your job was sent the term signal.
You should restart the run. Check the manual on how to do that since
it depends on what version
Thanks a lot for the help, that will do well enough, but require me to redo
some things I did before. As far as you know there is no way to have multiple
constraints using the center masses of the peptides? Thanks.
_One thing which you could do is to write your three proteins into
one
Hi,
I'm resending the message below from last week because it didn't make it
to the list due to some problem with the server.
Rossen
-
Hi Mark,
It will be definitely important to have the regressiontests working
properly and extended as the development of Gromacs con
Hi,
The GPU version uses the CUFFT libraries that come with CUDA, and no
external or internal CPU libraries are actually being used. You can
safely ignore the message.
Rossen
On 8/6/10 9:31 PM, chris.ne...@utoronto.ca wrote:
Thank you Rossen, that worked.
When I compile, should I be inclu
Hi Mark,
It will be definitely important to have the regressiontests working
properly and extended as the development of Gromacs continues. We
discussed that with Berk, and here are some suggestions about the
structure of the suite.
1. Make all current tests 3.3.4 compliant. There _is_ actu
leila karami wrote:
Hi gromacs users
I obtained pdb input file for gromacs from STRAP program. this pdb
file coantains protein and dna. this pdb file was obtaind form
superposition of 2 other pdb files. there is one problem: when I see
pdb file obtained from STRAP program by VMD, some bonds ar
Dear All,
I'm putting together a new Dell Xeon cluster running ROCKS 5.3 which
uses CENTOS (6 I believe). This is currently ~20 dual quad-cores with
roughly 16 GB of RAM each.
In any case, I wanted to inquire about hyperthreading. Does anyone
have experience on similar machines with vs. without h
Hi,
These are nehalem Xeons I presume?
Then you get 15 to 20% more performance in Gromacs running 2 vs 1 thread or
process per physical core.
Berk
> Date: Fri, 6 Aug 2010 09:24:11 -0500
> From: dmob...@gmail.com
> To: gmx-users@gromacs.org
> Subject: [gmx-users] hyperthreading
>
> Dear All,
>
giving this a bump .. any suggestions please ?
On Mon, Aug 2, 2010 at 12:39 PM, maria goranovic
wrote:
> Friends
>
> Why are the phase shifts while making dihedral parameters always 0 or 180,
> for example near the unsaturated bond of a lipid ? I am trying to fit a
> function to a dihedral, and m
This surprised me since most of the systems that I am interested in
have improper dihedrals. Is it possible that I did something wrong here?
### Error message from mdrun-gpu:
Program mdrun-gpu, VERSION 4.0.99-dev-20100315
Source code file:
/project/pomes/cneale/GPC/exe/intel/GPUgromacs/groma
Hi,
Could you provide the compiler versions you used? I really hope it's
not gcc 4.1.x again...
Cheers,
--
Szilárd
On Thu, Aug 5, 2010 at 8:26 PM, Elio Cino wrote:
>
> Since the charmm force field has some instances with large charge groups
> (grompp warns you for it) it is advisable to use a
NG HUI WEN wrote:
Dear gmxusers,
I have a very basic question here which I hope someone could help me
with. I was running a couple of simulations over the weekend on a shared
cluster and both came to a stop for the same reasons:
Program mdrun_mpi, VERSION 4.0.7
Source code file: trnio.c,
Hi,
I am planing to use 53a6 ff for my membrane protein system. And I can
use Kukol 2009 lipid or Roger 2010 lipids so I wonder is there any
problem about 53a6 force field and what is the most suitable force
field for membrane protein systems?
1) Kukol, A., 2009. Lipid models for united-atom mol
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Has anyone else tried this ?
The single precision version is fine with icc.
Thanks
David
__
Fujitsu Laboratories of Europe Limited
Hayes Park Central, Hayes End Road, Hayes, Middlesex,
This was already reported, there is a bugzilla filed already and we
are looking at fixing it.
http://bugzilla.gromacs.org/show_bug.cgi?id=495
Rossen
On 8/6/10 2:45 PM, david.groc...@uk.fujitsu.com wrote:
Has anyone else tried this ?
The single precision version is fine with icc.
Thanks
Da
Hi,
I want to use the pme algorithm in GROMACS. Thge size of my box is
8.2x8.2x8.2 in reduced units. I am considering a collection of 1000
of CO2 molecules. If I am using reduced units, the values of the
parameters "rcoulomb=0.9" I think should be converted to reduced
units "rcoulomb=2.45" (my \si
This is a VMD issue, it estimates which atoms are bonded together by the
distance that the atoms are separated. Obviously, the bonds that you
see "disappear" are due to them being separated by a distance larger
than what VMD would say is "bonded".
Catch ya,
Dr. Dallas Warren
Drug Delivery, Dispo
Hi everyone,
I want to calculate the RMSD, and a few minutes to start the calculation,
appears that Fatal Error:
calloc for bond_mat[i] (nelem=50001, elsize=4, file gmx_rms.c, line 650)
I don't have any idea what is the problem.
Thanks in advance!!!...
Deisy Y. Rodriguez S.
Practicante de Comp
Hi, this is the first time I have messaged this group, so please bear with me.
I have had little trouble with previous versions (4.0.7 for example), however
with this version the pdb2gmx program gives a segmentation fault error if run
stand-alone, even with no input. When compiled with debug, id
Hi Elton,
But I have neither killed the job nor I pressed Ctrl-C in the foreground. The
job was practically running background.
Thanks
Atanu
From: Elton Carvalho
To: Discussion list for GROMACS users
Sent: Thu, August 5, 2010 1:59:39 PM
Subject: Re: [gmx-use
Samrat Pal wrote:
Hi all,
I have been running a simulation of 200 ns length and it
suddenly stoped at 67 ns showing the following line -
Received the TERM signal, stopping at the next step
I have checked the time steps properly and there is no error. What
should I do now? Please
I haven't tried mdrun -nt based hyperthreading, but I have tested
using -np 16 on an 8 core box. I get an 8% to 18% performance increase
when using -np 16 and optimizing -npme as compared to -np 8 and
optimizing -npme. This is on a cluster of Intel Xeon E5540 aka
"Nehalem" with 2 quad cores
Hi,
The message is quite obvious about what happened: mdrun received a
TERM signal and therefor it stopped (see: man 7 signal or
http://linux.die.net/man/7/signal).
Figuring out the reason who and why sent a TERM signal to your mdrun
will be your task, but I can think of 2 basic scenarios: (I) yo
Hi,
In Gromacs 4.5 there is no difference, since it does not use real thread
parallelization.
Gromacs 4.5 has a built-in threaded MPI library, but openmpi also has an
efficient
MPI implementation for shared memory machines. But even with proper thread
parallelization I expect the same 15 to 20%
Hi,
for implicit solvent, people generally use longer cut-offs, as you noted.
There can be many reasons for your seg. fault, however.
Did you do energy minimization before starting md?
Please also test the same system with using a cut-off to see if that works.
/Per
8 aug 2010 kl. 22.36 skrev
Sounds like you killed the job, or your sysadmin killed it, or it
timed out if you are on a cluster with a walltime limit.
-- original message --
Hi all,
I have been running a simulation of 200 ns length and it suddenly
stoped at 67 ns showing the following line -
Received the TERM
This time from gmail.
David.
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deisy yurley rodriguez sarmiento wrote:
Hi everyone,
I want to calculate the RMSD, and a few minutes to start the
calculation, appears that Fatal Error:
calloc for bond_mat[i] (nelem=50001, elsize=4, file gmx_rms.c, line 650)
I don't have any idea what is the problem.
Sounds like a memory
On 05/08/10 17:37, Samrat Pal wrote:
Hi all,
I have been running a simulation of 200 ns length and it suddenly
stoped at 67 ns showing the following line -
Received the TERM signal, stopping at the next step
I have checked the time steps properly and there is no error. What should I
Nisha,
The approach is dictated by the goal. What do you want from this? and
why are you doing it? e.g. if you want to test the FF, then it is a
good idea to at least include US as a part of your strategy; if you
want to determine if 100 ns of equilibrium sampling is sufficient to
converg
Dear Per:
Thanks for your reply.
I did start the simulation from an equilibrated structure. Instead of
setting them to 0, if I simply use a large cut-off (say 1.6),
everything works just fine.
Best,
Bin
Hi,
for implicit solvent, people generally use longer cut-offs, as you
In tis case it must have been your sysadmin or your queueing system.
Check the other answers in this thread.
On Thu, Aug 5, 2010 at 10:30 PM, Samrat Pal wrote:
> Hi Elton,
> But I have neither killed the job nor I pressed Ctrl-C in the foreground.
> The job was practically running background.
> T
Hi all
I am trying to install the latest version. I have installed fftw3 with
-enable float and enable thread options, but I am still getting a fftw3
error.
the fftw/lib location has all these files:
libfftw3f.a libfftw3f_threads.la* libfftw3_threads.la*
../ libfftw3f.la*
Alpay Temiz wrote:
checking for fftw3.h... yes
checking for main in -lfftw3... no
configure: error: Cannot find fftw3 library
[temi...@abcc1 gromacs-4.5-beta2]$ echo $LDFFLAGS
The proper environment variable is LDFLAGS, not LDFFLAGS.
-Justin
-L/users/n2000546794/temizna/software/fftw/li
Okay so I tried to analyze the torsion using g_chi and g_rama for one
glycine zwitterion in water. for g_rama I didn't see anything in
xmgrace, and same for g_chi. I used this command for g_chi
g_chi -f traj.xtc -s gly.gro -phi -psi
When I run the command it says 1 residue with dihedrals fou
nishap.pa...@utoronto.ca wrote:
Okay so I tried to analyze the torsion using g_chi and g_rama for one
glycine zwitterion in water. for g_rama I didn't see anything in
xmgrace, and same for g_chi. I used this command for g_chi
g_chi -f traj.xtc -s gly.gro -phi -psi
When I run the command it
So is there a way I can test for convergence for my zwitterion for 100ns run?
Quoting "Justin A. Lemkul" :
nishap.pa...@utoronto.ca wrote:
Okay so I tried to analyze the torsion using g_chi and g_rama for
one glycine zwitterion in water. for g_rama I didn't see anything
in xmgrace, and
nishap.pa...@utoronto.ca wrote:
So is there a way I can test for convergence for my zwitterion for 100ns
run?
I'm not yet clear what you're assessing or how you define convergence. In
addition to what Chris said, you can look at dihedral transitions with g_angle.
Surely there are a few
Well I guess, what I am trying to get at is, for my system I want to
make sure that 100ns has covered all the conformational changes within
the molecule, although I know there is not that much conformational
changes for glycine molecule, but I just wanted to confirm. I did run
g_angle comma
nishap.pa...@utoronto.ca wrote:
Well I guess, what I am trying to get at is, for my system I want to
make sure that 100ns has covered all the conformational changes within
the molecule, although I know there is not that much conformational
changes for glycine molecule, but I just wanted to co
thank you!
On Mon, Aug 9, 2010 at 4:40 PM, Justin A. Lemkul wrote:
>
>
> Alpay Temiz wrote:
>
>
>
>
> checking for fftw3.h... yes
>> checking for main in -lfftw3... no
>> configure: error: Cannot find fftw3 library
>> [temi...@abcc1 gromacs-4.5-beta2]$ echo $LDFFLAGS
>>
>
> The proper environm
Nisha:
Simply applying available tools and seeing if the distribution looks
okay is not a good plan. You should have a very well-defined idea of
what you are trying to test and then pick a tool to get that done.
For example, perhaps you have a reference that provides the converged
distrib
Hi all,
I think the gromacs tools 4.5 may have a bug. So far I experienced that
several tools trjconv, g_rms, grmsf, g_covar, g_anaeig crash with a
segmentation fault if the trajectory read in does not have the same atom
number as the atom number in the .tpr file. It seems to be a systematic
- Original Message -
From: Xiaohu Hu
Date: Tuesday, August 10, 2010 10:26
Subject: [gmx-users] A bug in gromacs tool 4.5
To: gmx-users@gromacs.org
> Hi all,
>
> I think the gromacs tools 4.5 may have a bug. So far I
> experienced that several tools trjconv, g_rms, grmsf, g_covar,
> g_a
- Original Message -
From: david.groc...@uk.fujitsu.com
Date: Tuesday, August 10, 2010 1:25
Subject: [gmx-users] Double Precision Gromacs 4.5 beta 2 on Intel Xeon
"Woodcrest"
To: gmx-users@gromacs.org
> Hi, this is the first time I have messaged this group, so please
> bear with me.
>
>
Dear Gromacs,
I want to combine two separately equilibrated solvents into one mixed
solvent file. How can I do that? I want to check the mixing effect of
those solvents and try to check the density and volume change before
and after mixing those solvents. I have equilibrated and run MD for
Dear all
I have been looking for water mediated hydrogen bond in my simulation when i
use
g_hbond the -ins option it dose not showing the water mediated hydrogen bond
could you please tell me how to get the hydrogen mediated hydrogen bond in
gromacs ? is there any way to calculate hydrogen medi
Dear all
I have been looking for water mediated hydrogen bond in my simulation when i
use
g_hbond the -ins option it dose not showing the water mediated hydrogen bond
could you please tell me how to get the hydrogen mediated hydrogen bond in
gromacs ? is there any way to calculate hydrogen medi
Hi There,
I want to benchmark the scalability and speed for gromacs-4 on our cluster.
I want to know if there is any benchmarking activity already goin on? I have
browsed and got benchmarking for gromacs-3 and it seems that gromacs-4 is
much more scalable and faster than gromacs-3.
Can somebody sug
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