Hello,
I was wondering what the scale up was with GROMACS 3.3.1 on 8 or 16
processors. Here are my benchmarks:
Hardware: Dell PowerEdge 2950, 2x 2,66Ghz Intel Woodcrest CPUs, 8 GB Ram, 2x
Gigabit Ethernet
GROMACS 3.3.1: 24 atoms, PME, 1.0 nm real cutoff
processors ns/day
1 0.141
2
Hi all,
I am trying to simulate multiple (2 or 3) tetrapeptides in a cage with
Gromacs.
However, I would like to constrain the peptides to the centre of the box by
enforcing a wall potential in which each of the atoms of the peptide feels a
repulsive potential with respect to the edge of the box
From: "maria goranovic" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users
To: gmx-users@gromacs.org
Subject: [gmx-users] No scale up beyond 4 processors for 24 atom system
Date: Tue, 9 Oct 2007 12:09:50 +0200
Hello,
I was wondering what the scale up was with GROMACS 3.3.1
Thanks Alan
in fact I've already added the option -machinefile, here's the script:
cat $PBS_NODEFILE >/home/liuxin/mpd.hosts
/home/liuxin/mpich2/bin/mpdboot -n 6 -f mpd.hosts
/home/liuxin/mpich2/bin/mpiexec -machinefile $PBS_NODEFILE -np 12
/home/liuxin/
programs/gromacs33mpi/bin/mdrun -v -s 12np
Berk Hess schrieb:
Hi all,
So this is 4 cores sharing one ethernet connection?
perhaps the two Gigabit NICs were bundled somehow. But I guess this
doesn't work out-of-the-box&plug'n'play. And latency and not bandwidth
may be limiting in this case.
With such a setup you will never get goo
Yeah.
Check the machinefile tells mpich what you think it does. It looks pretty
certain to be an issue with mpich rather than gromacs. Unfortunately, I don't
use mpich any more because I find LAM better. Standard procedure, turn up the
verbosity on everything, check the outputs, re-read the r
Thanks for your quick comment Alan :)
On 10/9/07, Alan Dodd <[EMAIL PROTECTED]> wrote:
>
> Yeah.
> Check the machinefile tells mpich what you think it does. It looks pretty
> certain to be an issue with mpich rather than gromacs. Unfortunately, I
> don't use mpich any more because I find LAM be
Dear Gromacs users (and developpers)
I need to use a force field, derived from ab initio methods, for which
the non-bonded interactions between the different atom types is a
modified 3-parameters LJ potential.
As this kind of potential is not implemented within Gromacs I am using
fully tabulated
From: "Adrien Leygue" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users
To: gmx-users@gromacs.org
Subject: [gmx-users] limit on energygrp_table
Date: Tue, 9 Oct 2007 18:13:21 +0300
Dear Gromacs users (and developpers)
I need to use a force field, derived from ab initio methods
Did you noticed that the number of TIP5P water molecules is about half
of what's needed to fill the box. I think that's why your box
collapsed.
JW
On 4/23/07, kitty ji <[EMAIL PROTECTED]> wrote:
>
>
>
>
> Dear GMX user,
>
>
>
> Explicated model of Poly (vinyl methyl ether) was built with ether
>
Hello,
I'm very new to Gromacs, and I am interested in simulating the interactions
of 2 hexadecane (C16H34) molecules in water (SPC/E specificall). I've spent
some time experimenting with tutorials in Gromacs, but I've found little
help in non-protein simulations like this one.
I have built topo
Hi,
I am trying to compile version 3.3.2 in the parallel mode. I use the following
options to configure:
./configure --prefix=dir --disable-float -enable-mpi
and receive the following error message:
checking size of int... configure: error: cannot compute sizeof (int)
Note: The non paral
[Tsjerk] why do you write velocities and forces every 10 ps?
Third world country my friend, energy supply is not that stable over
here. Also the queue to run a process is huuuge, so every hour is
important. In the end I do a trjconv to reduce # of frames.
Great "Doing Restarts" whoever wrote it :
Hi,
On Oct 9, 2007, at 6:21 PM, Triguero, Luciano O wrote:
Hi,
I am trying to compile version 3.3.2 in the parallel mode. I use
the following options to configure:
./configure --prefix=dir --disable-float -enable-mpi
and receive the following error message:
checking size of int... configu
Hi Erik,
Thank for your help.
Luciano
Dr. Luciano Triguero College of Art and Science Department of Physics and
Chemistry Cox Science Building 1301 Memorial Drive, Room 146 P.O Box 249118
Coral Gables, FL 33124-0431 Cellular: 305-904-2419 Office: 305-284-3938
_
hi... i have been trying to do grompp for the following file but am getting
this error:
There were 1 error(s) processing your inputWARNING 3 [file "popc.top", line
32]: 7380 non-matching atom names atom names from popc.top will be used atom
names from popc.pdb will be ignored
double-checking
ERROR: The cut-off length is longer than half the shortest box vector
or longer than the smallest box diagonal element. Increase the box
size or decrease rlist.
try to "Increase the box size or decrease rlist." <= as ERROR message suggests
On 10/9/07, pragya chohan <[EMAIL PROTECTED]> wrote:
hi... i have been trying to do grompp for the following file but am
getting this error:
There were 1 error(s) processing your inputWARNING 3 [file
"popc.top", line 32]: 7380 non-matching atom names atom names from
popc.top will be used atom names from popc.pdb will be ignored
Your top
Low cost tip:
Ask your cluster administrator if it is possible apply channel bonding
to the Gigabit interfaces. You need two network switches for that to
be efficient (a cut-through switch may also help). It increases
network bandwidth by 70%. It also helps to use Cat6 cables.
You may try this MPI
ERROR: The cut-off length is longer than half the shortest box vector
or longer than the smallest box diagonal element. Increase the box
size or decrease rlist.
try to "Increase the box size or decrease rlist." <= as ERROR
message suggests
Yes, technically you could decrease rlist (rcoulomb
Dear GROMACS Users,
I'm trying to use GROMACS to get some MD snapshots for single-point quantum
mechanical calculations, trying to observe HOMO-LUMO gap of a protein immersed
in water with counterions, at a given salt concentration (4600 atoms in total).
I'd like to know if they are reliable en
GMX users,
In 3.3.1, I used "trjconv -ur compact -pbc whole " to convert a
rhombic dodecahedron box so it could be displayed properly in VMD.
This does not appear to be working in 3.3.2. Is there another way to
convert a box so it displays properly in a visualization program?
This is the comman
Hey,
Now I'm simulating infinite molecules. I want to change the box size a lit
bit every time step so as to induce some stress in this system.
Is there any way in gromacs to do this, apart from modifying the code?
Thanks in advance.
Yours Sincerely,
Using "trjconv -ur compact -pbc atom" worked.
JW
On 10/9/07, JW Feng <[EMAIL PROTECTED]> wrote:
> GMX users,
>
> In 3.3.1, I used "trjconv -ur compact -pbc whole " to convert a
> rhombic dodecahedron box so it could be displayed properly in VMD.
> This does not appear to be working in 3.3.2. Is
Hi,
I have a problem using Gromacs. When I use the pdb2gmx command to
generate the .top and .gro files, I got the error:
:-) G R O M A C S (-:
Gyas ROwers Mature At Cryogenic Speed
:-) VERSION 3.3.2 (-:
Haining,
Did you check the structure for missing atoms/residues (REMARK 465/470)?
Tsjerk
On 10/10/07, Haining Liu <[EMAIL PROTECTED]> wrote:
>
> Hi,
>
> I have a problem using Gromacs. When I use the pdb2gmx command to
> generate the .top and .gro files, I got the error:
>
>
Tsjerk,I just started to learn Gromacs. But how do I check the missing atoms?Thanks,HainingOn Wed, 10 Oct 2007 06:41:31 +0200 "Tsjerk Wassenaar" <[EMAIL PROTECTED] />wrote: > Haining, > > Did you check the structure for missing atoms/residues (REMARK 465/470)? > > Tsjerk > > On 10/10/07, Haining Li
Hi Haining,
This has nothing to do with gromacs. The information is in the .pdb file
(use a text viewer/editor). Before starting any simulation, you have to know
what you're intending to simulate. The model, the .pdb file of it. How the
structure was solved, etc., etc. The paper should also state
Dear gmx-users, I used anisotropic p-coupling for lipid bilayers and annealed
the system from 330K-300K at the ratio of 2 degree/ns.And the x dimension and y
dimension increased with time in the whole procedure, but actually the
area/lipid should decrease when tempreture decreases. I think there
Q733 wrote:
> Dear gmx-users, I used anisotropic p-coupling for lipid bilayers and
> annealed the system from 330K-300K at the ratio of 2 degree/ns.And the x
> dimension and y dimension increased with time in the whole
> procedure, but actually the area/lipid should decrease when tempreture
> d
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