On 7/12/2011 11:31 AM, Surya Prakash Tiwari wrote:
Dear Gromacs users,
I am simulating a charged system with periodic boundary conditions. My
system has 506 water molecules and one ion.
I am trying to calculate the free energy of an ion.
I do not want to use any counter-ions to neutralize the sy
Hi Chris,
You can also try with open64. Let us know in case you face any issues
in compiling and running. We will be glad to help you.
Thanks
Anupama
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
Behalf Of chris.ne...@utoronto.c
On 7/12/2011 6:20 AM, Chris Neale wrote:
Dear users:
can I use a .tpr file created with an intel icc compilation of grompp
and then do mdrun under a pathscale compilation of mdrun ? (same
version of gromacs)
You can run any .tpr with any mdrun regardless of OS, architecture,
endianness or
Thank you Matthew.
your suggestion for the hanging .o compilation sounds good. I didn't
try it because in the end the intel compiler produced the fastest
executables in any event.
For those interested, here are my benchmarking speeds for one of my
simulation systems (270,000 atoms) on 48
Should work just fine.
As far as compilation hanging...maybe hand-compile that .o with less
aggressive optimization flags, then try "make" again?
MZ
On Tue, Dec 6, 2011 at 2:20 PM, Chris Neale wrote:
> Dear users:
>
> can I use a .tpr file created with an intel icc compilation of grompp and
> t
Surya Prakash Tiwari
On Tue, Dec 6, 2011 at 20:34, Justin A. Lemkul wrote:
>
>
> Surya Prakash Tiwari wrote:
>>
>> Hi,
>>
>> I think you simply use #include "spce.itp" in your topology file.
>> Please see http://www.gromacs.org/Documentation/Include_File_Mechanism
>>
>
> This will not give D2O
Surya Prakash Tiwari wrote:
Hi,
I think you simply use #include "spce.itp" in your topology file.
Please see http://www.gromacs.org/Documentation/Include_File_Mechanism
This will not give D2O - the SPC/E water model is for H2O. I would suggest to
the OP to search for a suitable D2O model.
Hi,
I think you simply use #include "spce.itp" in your topology file.
Please see http://www.gromacs.org/Documentation/Include_File_Mechanism
Thanks.
Surya Prakash Tiwari
On Tue, Dec 6, 2011 at 19:53, cuong nguyen wrote:
> Dear GROMACS users,
>
> I usually use spce.itp file for water solvent
Hi all,
Just as the title, can Gromacs do Targeted MD simulations? If Yes, how
to set up the simulation procedure?
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Dear GROMACS users,
I usually use spce.itp file for water solvent in my simulation. However,
now I want to change this solvent to deuterium monoxide (D2O).
Please let me know if I have to change this itp file? if yes, where can I
find this file?
Thank you very much.
Best regards,
Nguyen Van C
Dear Gromacs users,
I am simulating a charged system with periodic boundary conditions. My
system has 506 water molecules and one ion.
I am trying to calculate the free energy of an ion.
I do not want to use any counter-ions to neutralize the system,
because I don't have force-field between my ion
>
> Message: 2
> Date: Wed, 07 Dec 2011 00:12:19 +1100
> From: Mark Abraham
> Subject: Re: [gmx-users] RE: logfile size
> To: Discussion list for GROMACS users
> Message-ID: <4ede14b3.8040...@anu.edu.au>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
> On 6/12/2011 8:48 PM, lloyd
Section 5.3.3 of the manual.
Catch ya,
Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu
+61 3 9903 9304
-
When the only tool you own is
Dear users:
can I use a .tpr file created with an intel icc compilation of grompp
and then do mdrun under a pathscale compilation of mdrun ? (same
version of gromacs)
I'm wondering if there would be some strange behaviour. It seems like it
should be ok, but I wanted to be sure.
I ask beca
Not the main problem, but your dt=0.0002 (0.2fs), is it what you want?
Javier
El 06/12/11 15:59, Mark Abraham escribió:
On 7/12/2011 12:12 AM, Mark Abraham wrote:
On 6/12/2011 8:48 PM, lloyd riggs wrote:
Dear All,
Hope this is not tooo stupid a question. I recenttly reduced my
file sizes b
Hi,
I am inexperienced with gromacs and I would like to figure out the format of all
parts of a .top file, needed for Gromacs. I am trying to understand the input
format so I can write a program for automatic setup for small molecule ligands
with Gromacs, using the oplsaa force field. I have recen
Hi,
Thanks for the reply, I check the path and everything still I get this error.
Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!
-Original Message-
From: Javier Cerezo
Sender: gmx-users-boun...@gromacs.org
Date: Tue, 06 Dec 2011 13:30:55
To: Discussion
Dear colleagues,
We would like to announce the availability of mmView - the web-based
application which allows to comfortably explore the structural data of
biomacromolecules stored in the mmCIF (macromolecular Crystallographic
Information File) format. The mmView software system is primarily
inte
Sorry but the help does not help me... In anycase, the help of
g_rmsdist say: "g_rmsdist computes the root mean square deviation of
atom distances, which
has the advantage that no fit is needed like in standard RMS deviation as
computed by g_rms..."; so no fit is needed, for me it means that t
On 6/12/2011 9:09 PM, Efrat Exlrod wrote:
Hi everyone,
I have installed Gromacs 4.5.5 following the online installation guide without
and with mpi.
My configure lines (after few tries) were:
./configure CC=/private/gnss/local/bin/gcc CXX=/private/gnss/local/bin/g++
--prefix=/private/gnss/Grom
On 7/12/2011 12:12 AM, Mark Abraham wrote:
On 6/12/2011 8:48 PM, lloyd riggs wrote:
Dear All,
Hope this is not tooo stupid a question. I recenttly reduced my file
sizes by increasing the time between writing. However, if I do an
Umbrella run I get the following to my logfile output, which m
On 6/12/2011 8:48 PM, lloyd riggs wrote:
Dear All,
Hope this is not tooo stupid a question. I recenttly reduced my file sizes by
increasing the time between writing. However, if I do an Umbrella run I get
the following to my logfile output, which makes my log file in the end larger
than my
Are you sure that fftw was installed in /home/fftw? According to the
instructions you used to install fftw, it seems that it's been done in
the standard location (maybe /usr/local/fftw?), anyway in such a case
the system should normally find the libraries without additional
CPPFLAGS and LDFLAGS
Dear All,
Hope this is not tooo stupid a question. I recenttly reduced my file sizes by
increasing the time between writing. However, if I do an Umbrella run I get
the following to my logfile output, which makes my log file in the end larger
than my trajectory;
Dispersion correction
Hi everyone,
I have installed Gromacs 4.5.5 following the online installation guide without
and with mpi.
My configure lines (after few tries) were:
./configure CC=/private/gnss/local/bin/gcc CXX=/private/gnss/local/bin/g++
--prefix=/private/gnss/Gromacs_455 --disable-float --with-fft=fftw3
--
Hi Gromacs users,
Am trying to install gromacs-4.5.5 version on IBM cluster with Linux
platform and am getting an error such as configure: error: Cannot find
fftw3f library.
The steps i followed-
Installed fftw-3.3 version
./configure --enable-threads --enable-float
make
make install
setenv C
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