Hi, Mark:
I made the index file and call two methanes as methane1 and methane2 , then
I set energygrp_excl = methane1 methane2, but when I run grompp, it said
methane1 is not an energy group. What do you understand this problem?
Thanks. -Xianghong Qi
On Wed, Nov 19, 2008 at 2:17 AM, xianghong qi
Yes, Mark. I now understand. I use united atom model. In my system, protein
includes only methane pair. I still need those parameter to control
protein/solvent, solvent/solvent interaction. Thanks so much for your great
help. I will do it now.
Best, -Xianghong Qi
On Wed, Nov 19, 2008 at 1:48 AM
xianghong qi wrote:
Thanks, Mark. That means I can set energygrp_excl = Protein Protein,
then I can get rid of those parameter which are related to
electrostatics, Vdw( like rcoulomb, vdw-type, rvdw, rvdw-switch, etc).
Am I right?
No. Section 7.3.19 indicates how this should be done. I thi
Thanks, Mark. That means I can set energygrp_excl = Protein Protein, then I
can get rid of those parameter which are related to electrostatics, Vdw(
like rcoulomb, vdw-type, rvdw, rvdw-switch, etc). Am I right?
Thanks so much.
-Xianghong Qi
On Tue, Nov 18, 2008 at 7:19 PM, Mark Abraham <[EMAIL
Hello,
(I remind you that my initial system is a monoclinic crystal, which is a sub
categorie to triclinic boxes)
compiling gromacs 4.0.2 with fftw3.2 and having the skew problem, now even in
less steps than before, I face this:
Not all bonded interactions have been properly assigned to the do
Nicholas Geraedts wrote:
Jussi - I tried installing the packages from the EPEL repo. I removed
the old LAM installation so there's no remnants of it, but now I can't
find mpirun anywhere. It's not listed in the path, nor can I find it in
any of the "usual" installation locations. Any thoughts?
Suman Chakrabarty wrote:
Now when I try to follow his script posted at
http://www.gromacs.org/pipermail/gmx-users/2008-November/037973.html ,
I find that it does not work for me. Error is:
checking for mpxlc... mpcc -q64 -compiler xlc_r
checking whether the MPI cc command works... configure: er
xianghong qi wrote:
Dear all:
I have a simple system which has two methane molecules with water. Now I
need turn off the intermolecular interactions between these two methanes
and just run
simulation. So I can get the random placement of two methanes. The
question is how to turn off the int
On Tue, 2008-11-18 at 14:02 -0800, Nicholas Geraedts wrote:
> Jussi - I tried installing the packages from the EPEL repo. I removed
> the old LAM installation so there's no remnants of it, but now I can't
> find mpirun anywhere. It's not listed in the path, nor can I find it
> in any of the "usual"
Jussi - I tried installing the packages from the EPEL repo. I removed the
old LAM installation so there's no remnants of it, but now I can't find
mpirun anywhere. It's not listed in the path, nor can I find it in any of
the "usual" installation locations. Any thoughts? gromacs and gromacs-mpi
insta
On Tue, Nov 18, 2008 at 9:19 AM, Q. Y. HUAN <[EMAIL PROTECTED]> wrote:
> Dear gmx users and developers,
>
> Currently I am installing Grace into my computer, but the problem is that I
> found difficulty to install it because there is no complete version of
> installation file of it. After i insta
Dear all:
I have a simple system which has two methane molecules with water. Now I
need turn off the intermolecular interactions between these two methanes and
just run
simulation. So I can get the random placement of two methanes. The question
is how to turn off the intermolecular interaction.
On Tue, Nov 18, 2008 at 7:59 PM, Mark Abraham <[EMAIL PROTECTED]> wrote:
>
> If you know its name, GROMACS is 99% likely to run on it.
>
> Mark
Should be, but one must know the compilers and appropriate flags for
compilation on obscure systems. I am having real tough time compiling
Gromacs on an
On Tue, Nov 18, 2008 at 5:48 PM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote:
>
>
> Suman Chakrabarty wrote:
>>
>> But now I have problem with the parallel (MPI) version. When I issue
>> the command:
>> ./configure --prefix=/home/hpcscratch/csdsuman/Gromacs/GMX402
>> --disable-largefile --enable-mpi
On Wed, 2008-11-19 at 01:46 +1100, Mark Abraham wrote:
> > Jussi - I'm trying to compile the packages myself since the pre-made
> > RPM's don't seem to install the libraries needed. Furthermore, the LAM
> > RPM would constantly complain about not being able to find gcc-g77 - a
> > package found
Ah, sorry, I did not read your mail carefully enough.
A bug with the -maxh option was fixed in 4.0.2.
But you are refering to the ns/day performance.
This is indeed incorrect (based on nsteps, not on
the actual number of steps performed).
I will fix it.
Berk
> Date: Tue, 18 Nov 2008 16:30:47 +01
As you can see in the attachment (the full output of the testrun), I am
using GMX 4.0.2
Are there different versions of 4.0.2 ?
On Tue, 2008-11-18 at 16:21 +0100, Berk Hess wrote:
> Yes, this is a bug.
> And it has been fixed already in 4.0.2.
>
> Berk
>
> > Date: Tue, 18 Nov 2008 16:10:51 +01
Yes, this is a bug.
And it has been fixed already in 4.0.2.
Berk
> Date: Tue, 18 Nov 2008 16:10:51 +0100
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Wrong calculation of runtime
>
> Hi.
>
> I use GMX4.0.2 on a Linux cluster.
>
> When I start my System (242224
Hi.
I use GMX4.0.2 on a Linux cluster.
When I start my System (242224 atoms on 8CPUs), I can calculate about 1
ns/day. This is also shown at the end of the mdrun output(output is
marked by "#"):
# NODE (s) Real (s) (%)
# Time:344.000344.000100.0
#
Nicholas Geraedts wrote:
Mark - I've followed the instructions on the wiki. The last step says to
email the mailing list, as I have done. I'm not sure about your comment
for not needing a complete make if we're looking for MPI. There are
situations where the program will be used in single-proce
Marudachalam S wrote:
Hi,
Thanks. What about RHEL? Will Gromacs run on it?
If you know its name, GROMACS is 99% likely to run on it.
Mark
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Please s
Hello,
thanks for the tip about -pname flag for genion - that was the problem in the
first place.
While I was waiting for the reply I set -maxwarn=1 and ran the simulation. At
the end I got the gro file with the following lines
. . . .
31598SOL OW 5239 7.367 10.098 9.759 -0.9983 -0.837
DimitryASuplatov wrote:
Hello,
thanks for the tip about -pname flag for genion - that was the problem in the
first place.
While I was waiting for the reply I set -maxwarn=1 and ran the simulation. At
the end I got the gro file with the following lines
. . . .
31598SOL OW 5239 7.367 1
Suman Chakrabarty wrote:
I have solved the reported problem by adding --disable-largefile to
the configure options. Now the non-parallel version compiles and
installs fine. What is the file size limit now? Is it 2 GB?
But now I have problem with the parallel (MPI) version. When I issue
the com
Kwee Hong wrote:
Hi. When I was trying to do the test run for my installed gromacs, I got
message below return to me even though i've source GMXRC (source
/usr/local/gromacs/bin/GMXRC). Can some one tell me why? Thanks.
"Permission denied" means you're not allowed to write files to those d
On Tue, 2008-11-18 at 02:13 -0800, Nicholas Geraedts wrote:
> Mark - I've followed the instructions on the wiki. The last step says
> to email the mailing list, as I have done. I'm not sure about your
> comment for not needing a complete make if we're looking for MPI.
> There are situations where t
Mark - I've followed the instructions on the wiki. The last step says to
email the mailing list, as I have done. I'm not sure about your comment for
not needing a complete make if we're looking for MPI. There are situations
where the program will be used in single-processor mode, as well as MPI. I'
On Tue, 2008-11-18 at 09:39 +0100, Antoine Migeon wrote:
> Hello,
>
> I have many problem for install Gromacs in Centos 5.2, without MPI for
> the moment.
>
> I tried you solution, but the package contain only binary prefixed by
> "g_", and the test set doesn't find grompp.
> (after source /usr/b
On Tue, 2008-11-18 at 13:49 +0530, Marudachalam S wrote:
> Hi,
>
> Thanks. What about RHEL? Will Gromacs run on it?
Yes. You can even use the ready-compiled RPMs available from Fedora
EPEL:
Forwarded Message
From: Jussi Lehtola <[EMAIL PROTECTED]>
Reply-To: Discussion list for
Hi,
This errors means that one of your box dimensions has shrunk by more than 20%
or a skewness change caused such an effects.
Normally you would have to lower the -dds option of mdrun.
But the skew_fac I determined from your box is 0.73, i.e. twice as high.
Therefore I guess you are using 4.0,
Hi,
On Tuesday, 18. November 2008, Bhawana Gupta wrote:
> hello everyone,
> i m getting problem with in finding grace as instead of default path.
> My path is home/bhawana/gromacs/bin/..
> so i have to plot my .xvg files by using xmgrace but i m not getting where
> it is
> otherwise by default its
hello everyone,
i m getting problem with in finding grace as instead of default path.
My path is home/bhawana/gromacs/bin/..
so i have to plot my .xvg files by using xmgrace but i m not getting where
it is
otherwise by default its path is
/usr/local/grace/bin/xmgrace.
what shd i do.
whether there
Hello,
I have many problem for install Gromacs in Centos 5.2, without MPI for
the moment.
I tried you solution, but the package contain only binary prefixed by
"g_", and the test set doesn't find grompp.
(after source /usr/bin/GMXRC)
What the problem ?
Antoine Migeon
Université de Bourgogn
Hi,
Thanks. What about RHEL? Will Gromacs run on it?
Marudachalam.
> Marudachalam S wrote:
>> Hello,
>>
>> Can someone tell me if Gromacs will run on SuSe linux enterprise
>> edition,
>> with an AMD opteron processor?
>
> Yes.
>
> Mark
> ___
> gmx-us
Hi,
Thanks. What about RHEL? Do you know if Gromacs will run on it?
Marudachalam.
> On Tue, 2008-11-18 at 12:19 +0530, Marudachalam S wrote:
>> Hello,
>>
>> Can someone tell me if Gromacs will run on SuSe linux enterprise
>> edition,
>> with an AMD opteron processor?
>
> Yes, it will.
> --
> -
Marudachalam S wrote:
Hello,
Can someone tell me if Gromacs will run on SuSe linux enterprise edition,
with an AMD opteron processor?
Yes.
Mark
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