Hi Luciane,
David van der Spoel has replied saying:
there is a problem compiling gromacs using gcc 4.x that may cause this. see
a recent bugzilla entry about it.
Did you compile using the 4.x gcc? In that case, recompile with an
older version (3.x). That solution was suggested in the same
di
Hi All
Is there any way to use gamess-us for Hybrid QM/MM calculation with
Gromacs instead of using CPMD, GAMESS-uk or gaussion?
Thanks
Dhiraj
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Yes of course I looked at the output but I thought is I specify energy
groups it will output only those specified and not the whole system.
However I tried a short run and it did output both. For the crash it
turned out it is because all the nodes try to read the huge trajectory
file at the sam
George Abadir wrote:
Hi all,
I am running simulations of carbon nanotubes and amino acids in
water. I need to calculate the potential energies for the whole system
as well as the interaction energy between the CNT and amino acid. What
I am tried to do is to calculate the energy for th
Probably, you've broken your line endings transferring to/from a Windows
machine.
Mark
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Please search the archive at http://www.gromacs.org/search befo
There is a niche for implicit solvent if you need to do more
extensive conformational sampling than you can achieve with
atomically detailed solvent---and if you can plausibly argue that you
are not introducing such egregious systematic errors that you are
just sampling more junk.
At 09:23 AM
--
Message: 4
Date: Wed, 18 Jul 2007 16:50:22 -0400
From: "srinivas aripirala" <[EMAIL PROTECTED]>
Subject: [gmx-users] How to include Mg in the input file?
To: gmx-users@gromacs.org
Message-ID:
<[EMAIL PROTECTED]>
Content-Type: tex
srinivas aripirala wrote:
Hello everybody,
I am attaching both the pdb and the inp. while i was trying to run the
inp file.
It errors our saying the Mg (magnesium )
ERROR PCM SPHERE(S) MUST HAVE A POSITIVE RADIUS
Guys when i diagonize i see that there it has included radius for MG
John Mercer wrote:
Hi,
I am a beginning user of GROMACS, and am just now trying to get a
functional installation. There is something not quite right about the
installations I have tried. I have spent considerable time testing
ideas about what might be the problem, but have not nailed it. I
Hello everybody,
I am attaching both the pdb and the inp. while i was trying to run the inp
file.
It errors our saying the Mg (magnesium )
ERROR PCM SPHERE(S) MUST HAVE A POSITIVE RADIUS
Guys when i diagonize i see that there it has included radius for MG as 0.
has anybody come acros
Hi,
I am a beginning user of GROMACS, and am just now trying to get a
functional installation. There is something not quite right about
the installations I have tried. I have spent considerable time
testing ideas about what might be the problem, but have not nailed
it. I am hoping some
[EMAIL PROTECTED] wrote:
Selon Erik Lindahl <[EMAIL PROTECTED]>:
Hi,
On Jul 18, 2007, at 5:08 PM, David van der Spoel wrote:
The version used by Alan Mark has never made it into gromacs.
Rather, Erik Lindahl started the implementation of this stuff but
did never finish it completely, due to
Selon Erik Lindahl <[EMAIL PROTECTED]>:
> Hi,
>
> On Jul 18, 2007, at 5:08 PM, David van der Spoel wrote:
>
> > The version used by Alan Mark has never made it into gromacs.
> > Rather, Erik Lindahl started the implementation of this stuff but
> > did never finish it completely, due to other prior
Mikael Lund wrote:
Reading the mailing list and the wiki as well, I see that GROMACS has
little support for implicit solvent. However, I'm interested in
simulating charged polymers (small spheres connected with springs) in an
aqueos salt solution (more spheres). Assuming no dielectric boundarie
Reading the mailing list and the wiki as well, I see that GROMACS has
little support for implicit solvent. However, I'm interested in
simulating charged polymers (small spheres connected with springs) in
an aqueos salt solution (more spheres). Assuming no dielectric
boundaries -- i.e. a uni
Hi Jim,
That system should scale quite well with a fast network (infiniband)
since you don't seem to be using PME, and the CVS 3.99 version is
even better.
However, as David already mentioned, the gigabit network is likely
limiting you. If you test the CVS code there are timing reports th
Hi,
On Jul 18, 2007, at 5:08 PM, David van der Spoel wrote:
The version used by Alan Mark has never made it into gromacs.
Rather, Erik Lindahl started the implementation of this stuff but
did never finish it completely, due to other priorities I presume.
We should however take out the vari
It's a 3.712 cube containing 1722 tip4p water molecules at 300 deg K and
density = 1000kg/l
Regards,
Jim Kress
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Stéphane Téletchéa wrote:
Moore, Jonathan (J) a écrit :
I asked for and received the code a couple of years ago.
As the paper indicates, it's in an ancient version of GROMACS...which
creates challenges. Also, the different models (Still, etc.) are
implemented in independent versions of the cod
Moore, Jonathan (J) a écrit :
I asked for and received the code a couple of years ago.
As the paper indicates, it's in an ancient version of GROMACS...which
creates challenges. Also, the different models (Still, etc.) are
implemented in independent versions of the code. Also, the GB part is
ac
Dear all,
I am having problem with genion.
I have already search the gmx archive, and got the following message:
While using genion with -np 3, i get 2 lines of Replacing sol. xxx with Na and
it hangs up. With -np 1 it works fine and replaces 1 SOL with Na. I thought it
might be my system, so
You can get a typical mdp file from some tutorials.
By the way, I think the topology is wrong.
Thanks.
On 7/18/07, Christopher Stiles <[EMAIL PROTECTED]> wrote:
I am trying to simulate a single wall CNT in a box filled with water for
about 500 ps and 300K just to start and I am having trouble
I asked for and received the code a couple of years ago.
As the paper indicates, it's in an ancient version of GROMACS...which
creates challenges. Also, the different models (Still, etc.) are
implemented in independent versions of the code. Also, the GB part is
actually implemented in FORTRAN.
Dear all
Sorry for repeating this message. I have found what appears to be an
error in the files ffG53a(5 and 6).rtp related to the ACE group topology.
Maybe it is a trivial error, or a change due to something I am missing.
I’m sure you experts will ponder it much better than me.
I was constru
If you REALLY want implicit solvent then i suggest you contact the authors
and ask them about it, however i (like most others i think) have never
needed to use implicit solvent.
Tom
--On Wednesday, July 18, 2007 16:17:01 +0200 Ran Friedman
<[EMAIL PROTECTED]> wrote:
Dear Tom,
The paper is
Dear Tom,
The paper is available and was mentioned in the list. The model,
however, isn't available AFAIK.
Ran.
TJ Piggot wrote:
> Hi,
>
> Just to let people know in case they are unaware there is a paper
> where implicit solvent models have been implemented in GROMACS, the
> paper can be found
I am trying to simulate a single wall CNT in a box filled with water for
about 500 ps and 300K just to start and I am having trouble with the mdp
file, basicly what should and should not be in it. I just want it generic to
start and tune it up later. Here is what I have done so far along with links
Hi,
Just to let people know in case they are unaware there is a paper where
implicit solvent models have been implemented in GROMACS, the paper can be
found using the following link:
http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=15814616
Tom
--On Wednesday, July 1
SeungPyo Hong wrote:
Thank you for your kind reply, Stephane.
Anyhow it is a little disappointing that Generalized-Born is not
implemented in Gromacs.
I've put it on the development TODO list (feel free to volunteer)
http://wiki.gromacs.org/index.php/Implicit_Solvent
The reason it is not t
Thank you for your kind reply, Stephane.
Anyhow it is a little disappointing that Generalized-Born is not implemented
in Gromacs.
Sincerely,
Seungpyo Hong
On 7/16/07, Stéphane Téletchéa <[EMAIL PROTECTED]> wrote:
SeungPyo Hong a écrit :
> Dear gmx-users,
>
> Recently I want to perform MD for p
Erik Lindahl wrote:
Hi,
Great that you solved it.
For the record, this is an excellent example why you should never, ever,
use "soft" NFS mounts. If you stick to "hard" mounts the clients might
hang while the server isn't responding, but at least you won't lose data.
of course you will hav
Hi,
Great that you solved it.
For the record, this is an excellent example why you should never,
ever, use "soft" NFS mounts. If you stick to "hard" mounts the
clients might hang while the server isn't responding, but at least
you won't lose data.
Cheers,
Erik
On Jul 18, 2007, at 2:48
Thanks to Tsjerk Wassenaar, Yang Ye and Chris Neale.
My simulation is running very well! ;)
I put that to run on a computer with local HD.
Really, the problem was overload of NFS server.
Thanks again.
Fernando Lopes
Dept. of Physics
UNESP - São José do Rio Preto - SP - Brazil
--- Tsjerk Was
Hi,
Can we use other (native windows) c preprocessor ?
As it says explicitly in the manual, you can use any preprocessor you
want. The default force fields have #include and #define statements
meant for a C preprocessor, but it's just a matter of pushing the
input files through the specifi
If cpp is not runnable, I would wonder what those GCC guys are working
and how you have compiled GROMACS?
On 7/18/2007 4:23 PM, Utkal Ranjan Pradhan wrote:
…. OK.
Again, the shipping Win32 version of cpp.exe is perfectly working with Gromacs
64-bit on a opetron m/c which is a x86-64 box.
But I
.. OK.
Again, the shipping Win32 version of cpp.exe is perfectly working with
Gromacs 64-bit on a opetron m/c which is a x86-64 box.
But I guess it (the above cpp.exe) may not work on pure x64 m/c as its not a
valid x64 application.
Is there a x64 port of cpp.exe is available ?
Can we use other (na
Hi Utkal,
Cpp.exe is called by grompp to preprocess the topology.
Tsjerk
On 7/18/07, Utkal Ranjan Pradhan <[EMAIL PROTECTED]> wrote:
Thank you for your reply.
But still confused WHY CPP.EXE IS REQUIRED AT RUNTIME ?
(Note that, I can build gromacs without cpp.exe with MS VS 2005, but wh
Thank you for your reply.
But still confused WHY CPP.EXE IS REQUIRED AT RUNTIME ?
(Note that, I can build gromacs without cpp.exe with MS VS 2005, but while
running applications like mdrun, it looks for cpp.exe L)
Thank You;
URPradhan At Gmail Dot Com
David van der Spoel wrote:
>
Jim Kress wrote:
I ran a parallel (mpi) compiled version of gromacs using the following
command line:
$ mpirun -np 5 mdrun_mpi -s topol.tpr -np 5 -v
At the end of the file md0.log I found:
M E G A - F L O P S A C C O U N T I N G
Parallel run - timing based on wallclock.
David van der Spoel wrote:
Utkal Ranjan Pradhan wrote:
Friends
As I know cpp.exe is a GNU port for C Preprocessor for Windows and
which is required to compile the Gromacs code.
But I’m confused, Why it is required during runtime of Gromacs
applications ?
And I have the Win32 version of
Utkal Ranjan Pradhan wrote:
Friends
As I know cpp.exe is a GNU port for C Preprocessor for Windows and which
is required to compile the Gromacs code.
But I’m confused, Why it is required during runtime of Gromacs
applications ?
And I have the Win32 version of cpp.exe, will it work for x
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