Dear All,
I am planning to perform a QM/MM calculation of my protein system. Can
anybody suggest me whether gromacs-4.5.5 can be patched with any latest
version of CPMD? If not, then please suggest me some combination of the
gromacs-cpmd versions.
I came across this tutorial, but there, both groma
Dear All,
I am planning to perform a QM/MM calculation of my protein system. Can
anybody suggest me whether gromacs-4.5.5 can be patched with any latest
version of CPMD? If not, then please suggest me some combination of the
gromacs-cpmd versions.
I came across this tutorial, but there, both groma
Thank you Mark.
Sent from my Ultrafast Samsung Galaxy S4 on Three
Original message
From: Mark Abraham
Date: 17/06/2013 08:02 (GMT+00:00)
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Gromacs 4.5.5
On Jun 16, 2013 7:58 PM, "Emmanuel, Alaina&qu
On Jun 16, 2013 7:58 PM, "Emmanuel, Alaina"
wrote:
>
> Dear All,
>
> I've had to re-install my gromacs on my computer and I'm having issues
getting past the "Making all in Man7" during the "make" stage.
There is no error in the output you show. Grepping for "error" doesn't
really help when there
Dear All,
I've had to re-install my gromacs on my computer and I'm having issues getting
past the "Making all in Man7" during the "make" stage. Below (at the end) are 2
copies of different outputs I get during my installation. The first copy is
from the "make.log" file. The second copy is from
Thanks for your help!I will try .
--
xiaohong
-- Original --
From: "Justin Lemkul";
Date: Thu, Nov 29, 2012 10:43 AM
To: "Discussion list for GROMACS users";
Subject: Re: [gmx-users] gromacs 4
On 11/28/12 9:21 PM, Kdead wrote:
When I use the Do_dssp module to collect the data from --.trr ,It report
segment fault.
The other common module is normol.WHY?? Thanks!
The input options in the DSSP executable changed. This is a known problem and
has been around for a long tim
When I use the Do_dssp module to collect the data from --.trr ,It report
segment fault.
The other common module is normol.WHY?? Thanks!
--
xiaohong--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please sear
Gromacs-4.5.5 is built on GPU with OpenMM-4.1.1 binary package. But
the standard gromacs gpu benchmark - dhfr failed with "Floating point
exception".
The benchmark name is : dhfr/GPU/dhfr-impl-1nm.bench
Error Output:
Reading file topol.tpr, VERSION 4.5.1-dev-20100917-b1d66 (single precision)
W
:42 +1000
From: mark.abra...@anu.edu.au
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] gromacs 4.5.5 on Cygwin
On 22/04/2012 9:30 AM, vijaya subramanian wrote:
Hi
I am trying to install gromacs 4.5.5 on cygwin following the
On 22/04/2012 9:30 AM, vijaya subramanian wrote:
Hi
I am trying to install gromacs 4.5.5 on cygwin following the
instructions in the wiki.
I first installed fftw3 using the following commands:
./configure --enable-float
make
make install
I then tried installing gromacs using:
./configure --dis
Hi
I am trying to install gromacs 4.5.5 on cygwin following the instructions in
the wiki.
I first installed fftw3 using the following commands:
./configure --enable-float
make
make install
I then tried installing gromacs using:
./configure --disable-threads
as well as
./configure --disable-th
Hi,
Could you compile in Debug mode and run mdurn-gpu in gdb, it will tell
more about the location and type of exception.
--
Szilárd
On Mon, Mar 12, 2012 at 8:47 AM, TH Chew wrote:
> Hi all,
>
> I am trying to get the GPU version of gromacs running. I manage to install
> OpenMM, compile and i
e for target `all-recursive' failed
make: *** [all-recursive] Error 1
- Forwarded Message -
From: Mark Abraham
To: Discussion list for GROMACS users
Sent: Monday, 12 March 2012 1:21 PM
Subject: Re: [gmx-users] gromacs 4.5.5 cygwin installation error message
On 12/03/2012 1
Hi all,
I am trying to get the GPU version of gromacs running. I manage to install
OpenMM, compile and install mdrun-gpu. However when I ran mdrun-gpu on any
of the benchmark files, I got this:
./run.sh: line 2: 14224 Floating point
exception/usr/local/gromacs-4.5.5-cuda/bin/mdrun-gpu -v
Any ide
ftwf_destroy_plan'
.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2bb5): undefined
reference to `_fftwf_destroy_plan'
.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2bcb): undefined
reference to `_fftwf_destroy_plan'
...
----- Forwarded Message -
*From:* Mark Abraham
*To:* Dis
ft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2b8a): undefined
> > reference to `_fftwf_destroy_plan'
> > .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2b9f): undefined
> > reference to `_fftwf_destroy_plan'
> > .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2bb5): undefine
__
> From: Mark Abraham
> To: Discussion list for GROMACS users
> Sent: Monday, 12 March 2012 10:21 AM
> Subject: Re: [gmx-users] gromacs 4.5.5 cygwin installation error message
>
>
> On 12/03/2012 8:14 AM, Wholly Peach wrote:
> Dear All,
> >
> &
s/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2bb5): undefined reference to
>`_fftwf_destroy_plan'
>.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2bcb): undefined reference to
>`_fftwf_destroy_plan'
>...
>
>
>- Forwarded Message -
>From: Mark Abraha
7;
.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2bcb): undefined
reference to `_fftwf_destroy_plan'
.......
----- Forwarded Message -
*From:* Mark Abraham
*To:* Discussion list for GROMACS users
*Sent:* Sunday, 11 March 2012 6:26 PM
*Subject:* Re: Fw: [gmx-users] gromacs 4.5.5 cygwin
defined reference to
`_fftwf_destroy_plan'
.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2bb5): undefined reference to
`_fftwf_destroy_plan'
.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2bcb): undefined reference to
`_fftwf_destroy_plan'
...
- Forwarded Message -----
Fro
] Error 2
make[1]: Leaving directory
`/cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src'
Makefile:347: recipe for target `all-recursive' failed
make: *** [all-recursive] Error 1
- Forwarded Message -
*From:* Peter C. Lai
*To:* Wholly Peach ; Discussion list for
GROMACS users
*Sent
ard to getting a reply from you.
>
> Cheers,
> Wholley
>
>
>
> From: Peter C. Lai
> To: Wholly Peach ; Discussion list for GROMACS users
>
> Sent: Sunday, 11 March 2012 11:20 AM
> Subject: Re: [gmx-users] gromacs 4.5.5 cygw
cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src'
Makefile:347: recipe for target `all-recursive' failed
make: *** [all-recursive] Error 1
- Forwarded Message -
From: Peter C. Lai
To: Wholly Peach ; Discussion list for GROMACS users
Sent: Sunday, 11 March 2012 11:54 AM
Subj
--disable-threads?
>
> Wholley
>
>
>
> From: Mark Abraham
> To: Discussion list for GROMACS users
> Sent: Sunday, 11 March 2012 11:43 AM
> Subject: Re: [gmx-users] gromacs 4.5.5 cygwin installation error message
>
> On 11/03/2012 1
Hi Mark,
If for Gromacs I use disable --disable-threads, for fftw3 show I also use
--disable-threads?
Wholley
From: Mark Abraham
To: Discussion list for GROMACS users
Sent: Sunday, 11 March 2012 11:43 AM
Subject: Re: [gmx-users] gromacs 4.5.5 cygwin
On 11/03/2012 12:20 PM, Peter C. Lai wrote:
Is fftw3 properly installed in /usr/local/lib?
And of the right precision, like reading the installation guides will
warn you...
Mark
On 2012-03-10 03:51:12PM -0800, Wholly Peach wrote:
Dear All,
For Gromacs installation, my configure co
Is fftw3 properly installed in /usr/local/lib?
On 2012-03-10 03:51:12PM -0800, Wholly Peach wrote:
> Dear All,
>
> For Gromacs installation, my configure command is:
>
> ./configure --enable-shared LDFLAGS='-L/usr/local/lib' --disable-threads.
> After make, the error message is as following
Dear All,
For Gromacs installation, my configure command is:
./configure --enable-shared LDFLAGS='-L/usr/local/lib' --disable-threads.
After make, the error message is as following.
I am looking forward to getting a reply from you on how to avoid the error
message.
Wholly
.
.libs/g
Hi everyone!
I am trying to install Gromacs 4.5.5 using Cygwin. I have succesfully compiled
and installed fftw-3.2.2 according to the instructions provided below.
I previously installed a Gromacs-4.5.3 using the same procedure and is still
available but as a separate folder.
http://lists.g
Hi everyone!
I am trying to install Gromacs 4.5.5 using Cygwin. I have succesfully compiled
and installed fftw-3.2.2 according to the instructions provided below:
http://lists.gromacs.org/pipermail/gmx-users/2009-September/044792.html
However, when I am at the step after running "make" (and af
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