Re: [gmx-users] MPI oversubscription
Seems like my last message got lost because the CMakeError.log was too big,
I attached that as a zip file.
If i call sysconf() without any arguments it returns 1.
Sysconf(_SC_NPROCESSOR_ONLN) complains that _SC_NPROCESSOR_ONLN is not
defined.
Also this comes up during make, which looks like trouble:
src/gromacs/gmxlib/gmx_detect_
hardware.c: In function ‘get_nthreads_hw_avail’:
src/gromacs/gmxlib/gmx_detect_hardware.c:414:1: warning: implicit
declaration of function ‘sysconf’ [-Wimplicit-function-declaration]
I built gromacs as described in:
http://www.gromacs.org/Documentation/Installation_Instructions/Cmake#MPI_build
with
cmake -DGMX_MPI=ON ../gromacs-src
make -j 8
I did not set anything else.
2013/2/5 Roland Schulz rol...@utk.edu
On Tue, Feb 5, 2013 at 8:58 AM, Berk Hess g...@hotmail.com wrote:
One last thing:
Maybe a macro is not set, but we can actually query the number of
processors.
Could you replace the conditional that gets triggered on my machine:
#if defined(_SC_NPROCESSORS_ONLN)
to
#if 1
So we can check if the actual sysconf call works or not?
My workaround won't work without OpenMP.
Did you disable that manually?
Also large file support is not turned on.
It seems like your build setup is somehow messed up and lot of features
are not found.
Could you post your CMakeFiles/CMakeError.log? That should show why those
features are disabled.
Roland
Cheers,
Berk
Date: Tue, 5 Feb 2013 14:52:17 +0100
Subject: Re: [gmx-users] MPI oversubscription
From: hypo...@googlemail.com
To: gmx-users@gromacs.org
Head of .log:
Gromacs version: VERSION 5.0-dev-20121213-e1fcb0a-dirty
GIT SHA1 hash: e1fcb0a3d2768a8bb28c2e4e8012123ce773e18c (dirty)
Precision: single
MPI library: MPI
OpenMP support: disabled
GPU support: disabled
invsqrt routine: gmx_software_invsqrt(x)
CPU acceleration: AVX_256
FFT library: fftw-3.3.2-sse2
Large file support: disabled
RDTSCP usage: enabled
Built on: Tue Feb 5 10:58:32 CET 2013
Built by: christian@k [CMAKE]
Build OS/arch: Linux 3.4.11-2.16-desktop x86_64
Build CPU vendor: GenuineIntel
Build CPU brand: Intel(R) Core(TM) i7-2600K CPU @ 3.40GHz
Build CPU family: 6 Model: 42 Stepping: 7
Build CPU features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx
msr
nonstop_tsc pcid pclmuldq pdcm popcnt pse rdtscp sse2 sse3 sse4.1
sse4.2
ssse3 tdt
C compiler: /home/christian/opt/bin/mpicc GNU gcc (GCC) 4.8.0
20120618 (experimental)
C compiler flags: -mavx -Wextra -Wno-missing-field-initializers
-Wno-sign-compare -Wall -Wno-unused -Wunused-value
-Wno-unknown-pragmas
-fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -O3
-DNDEBUG
C++ compiler: /home/christian/opt/bin/mpiCC GNU g++ (GCC) 4.8.0
20120618 (experimental)
C++ compiler flags: -mavx -std=c++0x -Wextra
-Wno-missing-field-initializers -Wnon-virtual-dtor -Wall -Wno-unused
-Wunused-value -Wno-unknown-pragmas -fomit-frame-pointer
-funroll-all-loops -fexcess-precision=fast -O3 -DNDEBUG
I will try your workaround, thanks!
2013/2/5 Berk Hess g...@hotmail.com
OK, then this is an unhandled case.
Strange, because I am also running OpenSUSE 12.2 with the same CPU,
but
use gcc 4.7.1.
I will file a bug report on redmine.
Could you also post the header of md.log which gives all
configuration
information?
To make it work for now, you can insert immediately after #ifdef
GMX_OMPENMP:
if (ret = 0)
{
ret = gmx_omp_get_num_procs();
}
Cheers,
Berk
Date: Tue, 5 Feb 2013 14:27:44 +0100
Subject: Re: [gmx-users] MPI oversubscription
From: hypo...@googlemail.com
To: gmx-users@gromacs.org
None of the variables referenced here are set on my system, the
print
statements are never executed.
What I did:
printf(Checking which processor variable is set);
#if defined(_SC_NPROCESSORS_ONLN)
ret = sysconf(_SC_NPROCESSORS_ONLN);
printf(case 1 ret = %d\n,ret);
#elif defined(_SC_NPROC_ONLN)
ret = sysconf(_SC_NPROC_ONLN);
printf(case 2 ret = %d\n,ret);
#elif defined(_SC_NPROCESSORS_CONF)
ret = sysconf(_SC_NPROCESSORS_CONF);
printf(case 3 ret = %d\n,ret);
#elif defined(_SC_NPROC_CONF)
ret = sysconf(_SC_NPROC_CONF);
printf(case 4 ret = %d\n,ret);
#endif /* End of check for sysconf argument values */
From /etc/issue:
Welcome to openSUSE 12.2 Mantis - Kernel \r (\l)
From uname -a:
Linux kafka 3.4.11-2.16-desktop #1 SMP PREEMPT Wed Sep 26 17:05:00
UTC
2012
(259fc87) x86_64 x86_64 x86_64 GNU/Linux
2013/2/5 Berk Hess g...@hotmail.com
Hi,
This is the same cpu I have in my workstation and this case
should
Re: [gmx-users] MPI oversubscription
And if the zip file did not get through: http://de.pastebin.ca/2311103
2013/2/6 Christian H. hypo...@googlemail.com
Seems like my last message got lost because the CMakeError.log was too
big, I attached that as a zip file.
If i call sysconf() without any arguments it returns 1.
Sysconf(_SC_NPROCESSOR_ONLN) complains that _SC_NPROCESSOR_ONLN is not
defined.
Also this comes up during make, which looks like trouble:
src/gromacs/gmxlib/gmx_detect_
hardware.c: In function ‘get_nthreads_hw_avail’:
src/gromacs/gmxlib/gmx_detect_hardware.c:414:1: warning: implicit
declaration of function ‘sysconf’ [-Wimplicit-function-declaration]
I built gromacs as described in:
http://www.gromacs.org/Documentation/Installation_Instructions/Cmake#MPI_build
with
cmake -DGMX_MPI=ON ../gromacs-src
make -j 8
I did not set anything else.
2013/2/5 Roland Schulz rol...@utk.edu
On Tue, Feb 5, 2013 at 8:58 AM, Berk Hess g...@hotmail.com wrote:
One last thing:
Maybe a macro is not set, but we can actually query the number of
processors.
Could you replace the conditional that gets triggered on my machine:
#if defined(_SC_NPROCESSORS_ONLN)
to
#if 1
So we can check if the actual sysconf call works or not?
My workaround won't work without OpenMP.
Did you disable that manually?
Also large file support is not turned on.
It seems like your build setup is somehow messed up and lot of features
are not found.
Could you post your CMakeFiles/CMakeError.log? That should show why those
features are disabled.
Roland
Cheers,
Berk
Date: Tue, 5 Feb 2013 14:52:17 +0100
Subject: Re: [gmx-users] MPI oversubscription
From: hypo...@googlemail.com
To: gmx-users@gromacs.org
Head of .log:
Gromacs version: VERSION 5.0-dev-20121213-e1fcb0a-dirty
GIT SHA1 hash: e1fcb0a3d2768a8bb28c2e4e8012123ce773e18c (dirty)
Precision: single
MPI library: MPI
OpenMP support: disabled
GPU support: disabled
invsqrt routine: gmx_software_invsqrt(x)
CPU acceleration: AVX_256
FFT library: fftw-3.3.2-sse2
Large file support: disabled
RDTSCP usage: enabled
Built on: Tue Feb 5 10:58:32 CET 2013
Built by: christian@k [CMAKE]
Build OS/arch: Linux 3.4.11-2.16-desktop x86_64
Build CPU vendor: GenuineIntel
Build CPU brand: Intel(R) Core(TM) i7-2600K CPU @ 3.40GHz
Build CPU family: 6 Model: 42 Stepping: 7
Build CPU features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx
msr
nonstop_tsc pcid pclmuldq pdcm popcnt pse rdtscp sse2 sse3 sse4.1
sse4.2
ssse3 tdt
C compiler: /home/christian/opt/bin/mpicc GNU gcc (GCC) 4.8.0
20120618 (experimental)
C compiler flags: -mavx -Wextra -Wno-missing-field-initializers
-Wno-sign-compare -Wall -Wno-unused -Wunused-value
-Wno-unknown-pragmas
-fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -O3
-DNDEBUG
C++ compiler: /home/christian/opt/bin/mpiCC GNU g++ (GCC) 4.8.0
20120618 (experimental)
C++ compiler flags: -mavx -std=c++0x -Wextra
-Wno-missing-field-initializers -Wnon-virtual-dtor -Wall -Wno-unused
-Wunused-value -Wno-unknown-pragmas -fomit-frame-pointer
-funroll-all-loops -fexcess-precision=fast -O3 -DNDEBUG
I will try your workaround, thanks!
2013/2/5 Berk Hess g...@hotmail.com
OK, then this is an unhandled case.
Strange, because I am also running OpenSUSE 12.2 with the same
CPU, but
use gcc 4.7.1.
I will file a bug report on redmine.
Could you also post the header of md.log which gives all
configuration
information?
To make it work for now, you can insert immediately after #ifdef
GMX_OMPENMP:
if (ret = 0)
{
ret = gmx_omp_get_num_procs();
}
Cheers,
Berk
Date: Tue, 5 Feb 2013 14:27:44 +0100
Subject: Re: [gmx-users] MPI oversubscription
From: hypo...@googlemail.com
To: gmx-users@gromacs.org
None of the variables referenced here are set on my system, the
print
statements are never executed.
What I did:
printf(Checking which processor variable is set);
#if defined(_SC_NPROCESSORS_ONLN)
ret = sysconf(_SC_NPROCESSORS_ONLN);
printf(case 1 ret = %d\n,ret);
#elif defined(_SC_NPROC_ONLN)
ret = sysconf(_SC_NPROC_ONLN);
printf(case 2 ret = %d\n,ret);
#elif defined(_SC_NPROCESSORS_CONF)
ret = sysconf(_SC_NPROCESSORS_CONF);
printf(case 3 ret = %d\n,ret);
#elif defined(_SC_NPROC_CONF)
ret = sysconf(_SC_NPROC_CONF);
printf(case 4 ret = %d\n,ret);
#endif /* End of check for sysconf argument values */
From /etc/issue:
Welcome to openSUSE 12.2 Mantis - Kernel \r (\l)
From uname -a:
Linux kafka 3.4.11-2.16-desktop #1 SMP PREEMPT Wed Sep 26
17:05:00
UTC
2012
(259fc87) x86_64 x86_64 x86_64 GNU/Linux
RE: [gmx-users] MPI oversubscription
Hi,
I am not an expert on cmake, make etc.
But it seems you include search path is not setup properly.
make can't find io.h, which I assume is located in /usr/include/sys/io.h, like
on my opensuse installation.
It might be that your MPI installation doesn't properly interface with your gcc
installation(s).
But the cmake error log doesn't provide much information.
I hope someone else on the list can help to track down the source of this
problem.
Does the problem disappear when you run cmake without MPI?
PS If you are running on a single physical node, you don't need openmpi, as you
can use the Gromacs
built-in thread-MPI library.
Cheers,
Berk
Date: Wed, 6 Feb 2013 09:38:09 +0100
Subject: Re: [gmx-users] MPI oversubscription
From: hypo...@googlemail.com
To: gmx-users@gromacs.org
And if the zip file did not get through: http://de.pastebin.ca/2311103
2013/2/6 Christian H. hypo...@googlemail.com
Seems like my last message got lost because the CMakeError.log was too
big, I attached that as a zip file.
If i call sysconf() without any arguments it returns 1.
Sysconf(_SC_NPROCESSOR_ONLN) complains that _SC_NPROCESSOR_ONLN is not
defined.
Also this comes up during make, which looks like trouble:
src/gromacs/gmxlib/gmx_detect_
hardware.c: In function ‘get_nthreads_hw_avail’:
src/gromacs/gmxlib/gmx_detect_hardware.c:414:1: warning: implicit
declaration of function ‘sysconf’ [-Wimplicit-function-declaration]
I built gromacs as described in:
http://www.gromacs.org/Documentation/Installation_Instructions/Cmake#MPI_build
with
cmake -DGMX_MPI=ON ../gromacs-src
make -j 8
I did not set anything else.
2013/2/5 Roland Schulz rol...@utk.edu
On Tue, Feb 5, 2013 at 8:58 AM, Berk Hess g...@hotmail.com wrote:
One last thing:
Maybe a macro is not set, but we can actually query the number of
processors.
Could you replace the conditional that gets triggered on my machine:
#if defined(_SC_NPROCESSORS_ONLN)
to
#if 1
So we can check if the actual sysconf call works or not?
My workaround won't work without OpenMP.
Did you disable that manually?
Also large file support is not turned on.
It seems like your build setup is somehow messed up and lot of features
are not found.
Could you post your CMakeFiles/CMakeError.log? That should show why those
features are disabled.
Roland
Cheers,
Berk
Date: Tue, 5 Feb 2013 14:52:17 +0100
Subject: Re: [gmx-users] MPI oversubscription
From: hypo...@googlemail.com
To: gmx-users@gromacs.org
Head of .log:
Gromacs version: VERSION 5.0-dev-20121213-e1fcb0a-dirty
GIT SHA1 hash: e1fcb0a3d2768a8bb28c2e4e8012123ce773e18c (dirty)
Precision: single
MPI library: MPI
OpenMP support: disabled
GPU support: disabled
invsqrt routine: gmx_software_invsqrt(x)
CPU acceleration: AVX_256
FFT library: fftw-3.3.2-sse2
Large file support: disabled
RDTSCP usage: enabled
Built on: Tue Feb 5 10:58:32 CET 2013
Built by: christian@k [CMAKE]
Build OS/arch: Linux 3.4.11-2.16-desktop x86_64
Build CPU vendor: GenuineIntel
Build CPU brand: Intel(R) Core(TM) i7-2600K CPU @ 3.40GHz
Build CPU family: 6 Model: 42 Stepping: 7
Build CPU features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx
msr
nonstop_tsc pcid pclmuldq pdcm popcnt pse rdtscp sse2 sse3 sse4.1
sse4.2
ssse3 tdt
C compiler: /home/christian/opt/bin/mpicc GNU gcc (GCC) 4.8.0
20120618 (experimental)
C compiler flags: -mavx -Wextra -Wno-missing-field-initializers
-Wno-sign-compare -Wall -Wno-unused -Wunused-value
-Wno-unknown-pragmas
-fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -O3
-DNDEBUG
C++ compiler: /home/christian/opt/bin/mpiCC GNU g++ (GCC) 4.8.0
20120618 (experimental)
C++ compiler flags: -mavx -std=c++0x -Wextra
-Wno-missing-field-initializers -Wnon-virtual-dtor -Wall -Wno-unused
-Wunused-value -Wno-unknown-pragmas -fomit-frame-pointer
-funroll-all-loops -fexcess-precision=fast -O3 -DNDEBUG
I will try your workaround, thanks!
2013/2/5 Berk Hess g...@hotmail.com
OK, then this is an unhandled case.
Strange, because I am also running OpenSUSE 12.2 with the same
CPU, but
use gcc 4.7.1.
I will file a bug report on redmine.
Could you also post the header of md.log which gives all
configuration
information?
To make it work for now, you can insert immediately after #ifdef
GMX_OMPENMP:
if (ret = 0)
{
ret = gmx_omp_get_num_procs();
}
Cheers,
Berk
Date: Tue, 5 Feb 2013 14:27:44 +0100
Subject: Re: [gmx-users] MPI oversubscription
From: hypo...@googlemail.com
To:
[gmx-users] Regarding mean square displacement
Dear users, I have a very basic question in MSD calculation. g_msd calculation on a protein dimer (~237 aa each) trajectory gave a plot of msd, with the values ranging between 1 to 14nm^2. But is this a sensible MSD? As the values given in a paper i was referring was in Ang^2 J. Chem. Theory Comput. 2012, 8, 1129-1142 Command that i used - echo 3 3 |g_msd -f a.xtc -s a.tpr -o a.xvg -n a.ndx -trestart 10 -b 4000 -e 5 -rmcomm Is the range of diffusion coefficient of proteins of in water l in the range of x e-5 cm^2/s? (hemoglobin is 0.1 e-5 cm^2/s) Thank you kavya -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Lipid topologies generated by ATB
Dear all, Are the topologies generated for lipids by ATB accurate enough? (I have mentioned the molecule type as *Lipid* prior to submission to ATB) Thanks for your valuable time With best wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] a question on rerun MD after computer crash
On 2/6/13 2:40 AM, Acoot Brett wrote: Dear All, For the MD extension purpose by mdrun -s OUT_PUT.tpr -cpi md-0-1_prev.cpt as discussed in the following e-mail, will you please tell me the difference between md-0-1_prev.cpt and md-0-1.cpt? I want to know the difference enven minor. I am looking forward to getting your reply. Please read the following, particularly the last line in this section: http://www.gromacs.org/Documentation/How-tos/Doing_Restarts#Version_4.x You can always find out exactly what's in a file using gmxcheck. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] reg minimization problem
On 2/6/13 2:41 AM, Subramaniam Boopathi wrote: Dear sir, i have running new molecules add in standard protein that new is morin molecules unfortunetly 102 error occur which is no defualt angle found , etc. i overcome this problem but one more new appear which is shown below could you help me to overcome these following errror 26 atoms are not part of any of the T-Coupling groups can you tell what is the necessary steps carry to overcome this mistake Make sure whatever your tc-grps are cover all the molecules in the system. You haven't shown us what you're doing, so no one can suggest an actual fix. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Using AMBER FF with GROMACS
Hello Apologies if this topic has been already discussed; I didn't manage to find something relevant on the list. How safe is to use the AMBER FF with GROMACS? I am aware of the validation for the ffamber ports here http://ffamber.cnsm.csulb.edu/#validation and here Sorin Pande (2005), Biophysical Journal, 88, 2472-2493. The new GROMACS distributions have integrated the ffamber ports and there are quite a few papers where GROMACS is used in conjunction with AMBER FF. I just wanted to double-check. Many thanks in advance. Dr. George Patargias Postdoctoral Researcher Biomedical Research Foundation Academy of Athens 4, Soranou Ephessiou 115 27 Athens Greece Office: +302106597568 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Using AMBER FF with GROMACS
On 2/6/13 6:48 AM, George Patargias wrote: Hello Apologies if this topic has been already discussed; I didn't manage to find something relevant on the list. How safe is to use the AMBER FF with GROMACS? I am aware of the validation for the ffamber ports here http://ffamber.cnsm.csulb.edu/#validation and here Sorin Pande (2005), Biophysical Journal, 88, 2472-2493. The new GROMACS distributions have integrated the ffamber ports and there are quite a few papers where GROMACS is used in conjunction with AMBER FF. I just wanted to double-check. We have used several Amber force fields for diverse systems and have never had any problems. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Using AMBER FF with GROMACS
Hi, All AMBER force fields in Gromacs which are also available in AMBER have been validated against energies from the AMBER package. Cheers, Berk Date: Wed, 6 Feb 2013 13:48:13 +0200 From: g...@bioacademy.gr To: gmx-users@gromacs.org Subject: [gmx-users] Using AMBER FF with GROMACS Hello Apologies if this topic has been already discussed; I didn't manage to find something relevant on the list. How safe is to use the AMBER FF with GROMACS? I am aware of the validation for the ffamber ports here http://ffamber.cnsm.csulb.edu/#validation and here Sorin Pande (2005), Biophysical Journal, 88, 2472-2493. The new GROMACS distributions have integrated the ffamber ports and there are quite a few papers where GROMACS is used in conjunction with AMBER FF. I just wanted to double-check. Many thanks in advance. Dr. George Patargias Postdoctoral Researcher Biomedical Research Foundation Academy of Athens 4, Soranou Ephessiou 115 27 Athens Greece Office: +302106597568 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Using AMBER FF with GROMACS
On 02/06/2013 01:15 PM, Berk Hess wrote: Hi, All AMBER force fields in Gromacs which are also available in AMBER have been validated against energies from the AMBER package. Cheers, Berk How about the latest Amber 12 SB FF? When will it be available in Gromacs? And also the latest CHARMM36 FF for protein? Currently, there is only CHARMM36 FF for lipids. It seems that the CHARMM36 FF for protein introduced the nbfix term which is absent in any previous version of CHARMM. probably this would take sometime to be introduced to Gromacs. regards Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_membed deprecated?
hello: I am trying to build membrane system with g_menbed, but it said: Back Off! I just backed up membed.dat to ./#membed.dat.2# You can membed your protein now by: mdrun -s input.tpr -membed membed.dat -o traj.trr -c membed.pdb -e ener.edr -nt 1 -cpt -1 -mn index.ndx -mp merged.top -v -stepout 100 Please cite: Wolf et al, J Comp Chem 31 (2010) 2169-2174. does it means that g_membed deprecated from Gromacs-4.6 and we must use mdrun instead? THX Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Error- Simulation box resizes during mdrun
Hi everyone, Today, I was attempting a simulation of a system with a lipid bilayer, and the size of my simulation box, obtained from a previous simulation, was 15 nm x 7.5 nm x 7.5 nm (15 nm being the direction perpendicular to the plane of the bilayer). The bilayer consisted of 128 DOPC lipids and was located at the centre of the box. I used periodic boundary conditions in all three directions. I then resized the box to 7.5 nm in all directions, using the editconf -box option. After doing the requisite energy minimization steps, I ran the simulation using mdrun. However, running the simulation caused the box to gradually shrink in the y-direction (parallel to the plane of the bilayer!) during the simulation, ultimately settling at around half the original dimension. Is there anything I may have done that could cause this effect? I'm thoroughly baffled. Thanks! Regards Bharath -- Bharath K Srikanth IV Year B.Tech Dept. of Chemical Engineering Indian Institute of Technology, Guwahati Ph: (+91) 88762 03224 E.mail: s.bhar...@iitg.ernet.in -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Adsorption layer of water molecules
I'm working with a protein in water and I used periodic boundary conditions in three dimension. At first the initial system was minimized, then I followed Justin's protocol. The system was equilibrated in a first stage nvt for 1 ns and in a second stage npt for 1 ns (with restraints). Then the production stage had been done with 100ns. When I visualize the trajectory results in vmd, I have a problem with the adsorption layer. During the production trajectory, water molecules had spread very much and actually no adsorption happened. The size of the box increases a lot in the beginning of the pvt equilibrated stage (it was 341 nm³ and it becomes 351nm³) and I can't understand that. Why are the water molecules spreading so much? Why don't they constitute an adsorption layer? Any help would be appreciated. Thanks. -- *Yara Pereira Cerceau Alves* Graduanda em Engenharia de Alimentos Bolsista PIBIC/CNPq Universidade Federal de Viçosa - UFV/MG (32)99751550 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_membed deprecated?
On 02/06/2013 05:37 PM, Namita Dube wrote: Hi, There must be some kind of problem with your system. have you tried using : mdrun -s input.tpr -membed membed.dat -o traj.trr -c membed.pdb -e ener.edr -nt 1 -cpt -1 -mn index.ndx -mp merged.top -v -stepout 100 what it says? Thanks. it stopped with errors. not eough space for XTC? However, when I run it in gromacs-4.5.6 by g_membed, it finished well. best Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] compiling on different architecture than the compute nodes architecture
Dear All, I would like to compile gromacs 4.6 to run with the correct acceleration on the compute nodes on our local cluster. Some of the nodes have intel sandy-bridge whilst others only have sse4.1 and some (including the login and single core job nodes) are still stuck on ssse3 (gmx would use sse2 acceleration here). Installing several versions is not a problem however, I'm not sure how to make cmake build a version of the code that is not using the acceleration for the system on which the code is being compiled. Restrictions on job sizes makes running the compilation on the sandy-bridge nodes almost impossible. Can anyone let me know which flags cmake needs to enable avx-256 acceleration? my standard cmake line is: $ CC=mpiicc CXX=mpiicpc ; cmake -DGMX_OPENMP=ON -DGMX_MPI=ON -DGMX_DOUBLE=ON -DGMX_GPU=OFF -DGMX_PREFER_STATIC_LIBS=ON -DGMX_FFT_LIBRARY=mkl -DMKL_INCLUDE_DIR=$MKLROOT/include -DMKL_LIBRARIES=$MKLROOT/lib/intel64/libmkl_core.so;$MKLROOT/lib/intel64/libmkl_intel_lp64.so;$MKLROOT/lib/intel64/libmkl_sequential.so -DCMAKE_INSTALL_PREFIX=$HOME/libs/gromacs ../ Thanks, Richard -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] MPI oversubscription
http://pastebin.com/6t0y5mTX So it's the same problem with io.h etc. if I just run cmake without any mpi flags in my build directory. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] compiling on different architecture than the compute nodes architecture
Hi, On Feb 6, 2013, at 6:03 PM, Richard Broadbent richard.broadben...@imperial.ac.uk wrote: Dear All, I would like to compile gromacs 4.6 to run with the correct acceleration on the compute nodes on our local cluster. Some of the nodes have intel sandy-bridge whilst others only have sse4.1 and some (including the login and single core job nodes) are still stuck on ssse3 (gmx would use sse2 acceleration here). Installing several versions is not a problem however, I'm not sure how to make cmake build a version of the code that is not using the acceleration for the system on which the code is being compiled. Restrictions on job sizes makes running the compilation on the sandy-bridge nodes almost impossible. Can anyone let me know which flags cmake needs to enable avx-256 acceleration? Use -DGMX_CPU_ACCELERATION=AVX_256 Try ccmake to have a look at the variables you can define and what values they can be set to. Carsten my standard cmake line is: $ CC=mpiicc CXX=mpiicpc ; cmake -DGMX_OPENMP=ON -DGMX_MPI=ON -DGMX_DOUBLE=ON -DGMX_GPU=OFF -DGMX_PREFER_STATIC_LIBS=ON -DGMX_FFT_LIBRARY=mkl -DMKL_INCLUDE_DIR=$MKLROOT/include -DMKL_LIBRARIES=$MKLROOT/lib/intel64/libmkl_core.so;$MKLROOT/lib/intel64/libmkl_intel_lp64.so;$MKLROOT/lib/intel64/libmkl_sequential.so -DCMAKE_INSTALL_PREFIX=$HOME/libs/gromacs ../ Thanks, Richard -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] MPI oversubscription
On Tue, Feb 5, 2013 at 8:52 AM, Christian H. hypo...@googlemail.com wrote:
Head of .log:
Gromacs version:VERSION 5.0-dev-20121213-e1fcb0a-dirty
Is it on purpose that you use version 5.0 and not 4.6? Unless you plan
development I suggest to use 4.6 (git checkout release-4-6)
I can reproduce your problem with 5.0. We haven't tested 5.0 much lately
because we were so busy with 4.6.
C compiler: /home/christian/opt/bin/mpicc GNU gcc (GCC) 4.8.0
It seems you are not using 4.7.x as you said
Roland
2013/2/5 Berk Hess g...@hotmail.com
OK, then this is an unhandled case.
Strange, because I am also running OpenSUSE 12.2 with the same CPU, but
use gcc 4.7.1.
I will file a bug report on redmine.
Could you also post the header of md.log which gives all configuration
information?
To make it work for now, you can insert immediately after #ifdef
GMX_OMPENMP:
if (ret = 0)
{
ret = gmx_omp_get_num_procs();
}
Cheers,
Berk
Date: Tue, 5 Feb 2013 14:27:44 +0100
Subject: Re: [gmx-users] MPI oversubscription
From: hypo...@googlemail.com
To: gmx-users@gromacs.org
None of the variables referenced here are set on my system, the print
statements are never executed.
What I did:
printf(Checking which processor variable is set);
#if defined(_SC_NPROCESSORS_ONLN)
ret = sysconf(_SC_NPROCESSORS_ONLN);
printf(case 1 ret = %d\n,ret);
#elif defined(_SC_NPROC_ONLN)
ret = sysconf(_SC_NPROC_ONLN);
printf(case 2 ret = %d\n,ret);
#elif defined(_SC_NPROCESSORS_CONF)
ret = sysconf(_SC_NPROCESSORS_CONF);
printf(case 3 ret = %d\n,ret);
#elif defined(_SC_NPROC_CONF)
ret = sysconf(_SC_NPROC_CONF);
printf(case 4 ret = %d\n,ret);
#endif /* End of check for sysconf argument values */
From /etc/issue:
Welcome to openSUSE 12.2 Mantis - Kernel \r (\l)
From uname -a:
Linux kafka 3.4.11-2.16-desktop #1 SMP PREEMPT Wed Sep 26 17:05:00 UTC
2012
(259fc87) x86_64 x86_64 x86_64 GNU/Linux
2013/2/5 Berk Hess g...@hotmail.com
Hi,
This is the same cpu I have in my workstation and this case should
not
cause any problems.
Which operating system and version are you using?
If you know a bit about programming, could you check what goes wrong
in
get_nthreads_hw_avail
in src/gmxlib/gmx_detect_hardware.c ?
Add after the four ret = at line 434, 436, 438 and 440:
printf(case 1 ret = %d\n,ret);
and replace 1 by different numbers.
Thus you can check if one of the 4 cases returns 0 or none of the
cases
is called.
Cheers,
Berk
Date: Tue, 5 Feb 2013 13:45:02 +0100
Subject: Re: [gmx-users] MPI oversubscription
From: hypo...@googlemail.com
To: gmx-users@gromacs.org
From the .log file:
Present hardware specification:
Vendor: GenuineIntel
Brand: Intel(R) Core(TM) i7-2600K CPU @ 3.40GHz
Family: 6 Model: 42 Stepping: 7
Features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr
nonstop_tsc
pcid pclmuldq pdcm popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3
tdt
Acceleration most likely to fit this hardware: AVX_256
Acceleration selected at GROMACS compile time: AVX_256
Table routines are used for coulomb: FALSE
Table routines are used for vdw: FALSE
From /proc/cpuinfo (8 entries like this in total):
processor : 0
vendor_id : GenuineIntel
cpu family : 6
model : 42
model name : Intel(R) Core(TM) i7-2600K CPU @ 3.40GHz
stepping : 7
microcode : 0x28
cpu MHz : 1600.000
cache size : 8192 KB
physical id : 0
siblings : 8
core id : 0
cpu cores : 4
apicid : 0
initial apicid : 0
fpu : yes
fpu_exception : yes
cpuid level : 13
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca
cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe
syscall nx
rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl
xtopology
nonstop_tsc aperfmper
f pni pclmulqdq dtes64 monitor ds_cpl vmx est tm2 ssse3 cx16 xtpr
pdcm
pcid
sse4_1 sse4_2 popcnt tsc_deadline_timer aes xsave avx lahf_lm ida
arat
epb
xsaveopt pln pts dtherm tpr_shadow vnmi flexpriority ept vpid
bogomips : 6784.04
clflush size : 64
cache_alignment : 64
address sizes : 36 bits physical, 48 bits virtual
power management:
It also does not work on the local cluster, the output in the .log
file
is:
Detecting CPU-specific acceleration.
Present hardware specification:
Vendor: AuthenticAMD
Brand: AMD Opteron(TM) Processor 6220
Family: 21 Model: 1 Stepping: 2
Features: aes apic avx clfsh cmov cx8 cx16 fma4 htt lahf_lm
misalignsse
[gmx-users] Re: protein-ligand interactions in charmm force field
by the way could someone provide me with some simple tutorial of the usage of the CGenFF for construction ITP topology for charmm f.f ? Also I still could not found any simple way to monitor dynamics of the non-covalent interactions between ligand and ligand binding pocket. E.g I select manually in the ndx file all residues which could be involved in such interactions (including formation of possible h.bonds, salt bridges as well as stacking interactions ) in one group and ligand inthe second group. Should I use combination of g_hbond and g_saltbr tools for such identification? How stacking interactions could be monitored? James 2013/2/5, James Starlight jmsstarli...@gmail.com: Dear Gromacs users! At present time I'm simulating protein-ligand complexes parametrized in Charmm force field. In particular I'm not quite sure aboout correctness of params made for my ligands by SwissParams. So I wounder to know the suggestions from the people which already prepared their systems including ligands parametrized by swiss-param (About possible corrections in that topologies) for example this is the topology of small drug-like mollecule isoprenaline which I simulate with membrane receptor [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 CB 1 LIG C9 1 0.0825 12.0110 2 CB 1 LIG C11 2 0.0825 12.0110 3 CB 1 LIG C10 3 -0.1500 12.0110 4 CB 1 LIG C7 4 -0.1500 12.0110 5 CB 1 LIG C4 5 -0.1435 12.0110 6 CB 1 LIG C8 6 -0.1500 12.0110 7 CR 1 LIG C5 7 0. 12.0110 8 CR 1 LIG C2 8 0.5030 12.0110 9 NRP 1 LIG N1 9 -0.9060 14.0067 10 HNRP 1 LIG H4 10 0.4500 1.0079 11 HNRP 1 LIG H5 11 0.4500 1.0079 12 CR 1 LIG C3 12 0.5030 12.0110 13 OR 1 LIG O3 13 -0.5325 15.9994 14 HOCC 1 LIG H3 14 0.4500 1.0079 15 OR 1 LIG O2 15 -0.5325 15.9994 16 HOCC 1 LIG H2 16 0.4500 1.0079 17 HCMM 1 LIG H1817 0.1500 1.0079 18 HCMM 1 LIG H1618 0.1500 1.0079 19 CR 1 LIG C1 19 0.4235 12.0110 20 OR 1 LIG O1 20 -0.6800 15.9994 21 HOR 1 LIG H1 21 0.4000 1.0079 22 HCMM 1 LIG H1722 0.1500 1.0079 23 CR 1 LIG C6 23 0. 12.0110 24 HCMM 1 LIG HC224 0. 1.0079 25 HCMM 1 LIG HC325 0. 1.0079 26 HCMM 1 LIG HC 26 0. 1.0079 27 HCMM 1 LIG HC127 0. 1.0079 28 HCMM 1 LIG HC428 0. 1.0079 29 HCMM 1 LIG HC529 0. 1.0079 30 HCMM 1 LIG HC630 0. 1.0079 31 HCMM 1 LIG HC731 0. 1.0079 32 HCMM 1 LIG HC832 0. 1.0079 33 HCMM 1 LIG HC933 0. 1.0079 from that atom set two polar OH groups are crusial for establishment of the polar interaction with some side-chains of my proteins within its ligand-binding pocket. 13 OR 1 LIG O3 13 -0.5325 15.9994 14 HOCC 1 LIG H3 14 0.4500 1.0079 15 OR 1 LIG O2 15 -0.5325 15.9994 16 HOCC 1 LIG H2 16 0.4500 1.0079 Im not sure about correctness of charge distribution of that residues but in fact of my md trajectory I've observed only very rarely h-bond establishment between that OH and some Ser residues (which are seen in the X-ray structures of that protein). By the way does it possible to obtain some XVG graphs for H_bond distances (using g_hbond tool) between separate ligand functional groups and protein polar side chains (in a manner of graphs which are produced by g_saltbr )? Thanks for help, James -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] MPI oversubscription
On Wed, Feb 6, 2013 at 2:35 PM, Roland Schulz rol...@utk.edu wrote:
On Tue, Feb 5, 2013 at 8:52 AM, Christian H. hypo...@googlemail.comwrote:
Head of .log:
Gromacs version:VERSION 5.0-dev-20121213-e1fcb0a-dirty
Is it on purpose that you use version 5.0 and not 4.6? Unless you plan
development I suggest to use 4.6 (git checkout release-4-6)
I can reproduce your problem with 5.0. We haven't tested 5.0 much lately
because we were so busy with 4.6.
If you want to use 5.0 you can take the version from here:
https://gerrit.gromacs.org/#/c/2132/. This fixes the problems.
Roland
2013/2/5 Berk Hess g...@hotmail.com
OK, then this is an unhandled case.
Strange, because I am also running OpenSUSE 12.2 with the same CPU, but
use gcc 4.7.1.
I will file a bug report on redmine.
Could you also post the header of md.log which gives all configuration
information?
To make it work for now, you can insert immediately after #ifdef
GMX_OMPENMP:
if (ret = 0)
{
ret = gmx_omp_get_num_procs();
}
Cheers,
Berk
Date: Tue, 5 Feb 2013 14:27:44 +0100
Subject: Re: [gmx-users] MPI oversubscription
From: hypo...@googlemail.com
To: gmx-users@gromacs.org
None of the variables referenced here are set on my system, the print
statements are never executed.
What I did:
printf(Checking which processor variable is set);
#if defined(_SC_NPROCESSORS_ONLN)
ret = sysconf(_SC_NPROCESSORS_ONLN);
printf(case 1 ret = %d\n,ret);
#elif defined(_SC_NPROC_ONLN)
ret = sysconf(_SC_NPROC_ONLN);
printf(case 2 ret = %d\n,ret);
#elif defined(_SC_NPROCESSORS_CONF)
ret = sysconf(_SC_NPROCESSORS_CONF);
printf(case 3 ret = %d\n,ret);
#elif defined(_SC_NPROC_CONF)
ret = sysconf(_SC_NPROC_CONF);
printf(case 4 ret = %d\n,ret);
#endif /* End of check for sysconf argument values */
From /etc/issue:
Welcome to openSUSE 12.2 Mantis - Kernel \r (\l)
From uname -a:
Linux kafka 3.4.11-2.16-desktop #1 SMP PREEMPT Wed Sep 26 17:05:00 UTC
2012
(259fc87) x86_64 x86_64 x86_64 GNU/Linux
2013/2/5 Berk Hess g...@hotmail.com
Hi,
This is the same cpu I have in my workstation and this case should
not
cause any problems.
Which operating system and version are you using?
If you know a bit about programming, could you check what goes
wrong in
get_nthreads_hw_avail
in src/gmxlib/gmx_detect_hardware.c ?
Add after the four ret = at line 434, 436, 438 and 440:
printf(case 1 ret = %d\n,ret);
and replace 1 by different numbers.
Thus you can check if one of the 4 cases returns 0 or none of the
cases
is called.
Cheers,
Berk
Date: Tue, 5 Feb 2013 13:45:02 +0100
Subject: Re: [gmx-users] MPI oversubscription
From: hypo...@googlemail.com
To: gmx-users@gromacs.org
From the .log file:
Present hardware specification:
Vendor: GenuineIntel
Brand: Intel(R) Core(TM) i7-2600K CPU @ 3.40GHz
Family: 6 Model: 42 Stepping: 7
Features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr
nonstop_tsc
pcid pclmuldq pdcm popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3
tdt
Acceleration most likely to fit this hardware: AVX_256
Acceleration selected at GROMACS compile time: AVX_256
Table routines are used for coulomb: FALSE
Table routines are used for vdw: FALSE
From /proc/cpuinfo (8 entries like this in total):
processor : 0
vendor_id : GenuineIntel
cpu family : 6
model : 42
model name : Intel(R) Core(TM) i7-2600K CPU @ 3.40GHz
stepping : 7
microcode : 0x28
cpu MHz : 1600.000
cache size : 8192 KB
physical id : 0
siblings : 8
core id : 0
cpu cores : 4
apicid : 0
initial apicid : 0
fpu : yes
fpu_exception : yes
cpuid level : 13
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca
cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe
syscall nx
rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl
xtopology
nonstop_tsc aperfmper
f pni pclmulqdq dtes64 monitor ds_cpl vmx est tm2 ssse3 cx16 xtpr
pdcm
pcid
sse4_1 sse4_2 popcnt tsc_deadline_timer aes xsave avx lahf_lm ida
arat
epb
xsaveopt pln pts dtherm tpr_shadow vnmi flexpriority ept vpid
bogomips : 6784.04
clflush size : 64
cache_alignment : 64
address sizes : 36 bits physical, 48 bits virtual
power management:
It also does not work on the local cluster, the output in the .log
file
is:
Detecting CPU-specific acceleration.
Present hardware specification:
Vendor: AuthenticAMD
Brand: AMD Opteron(TM) Processor 6220
Family: 21 Model: 1 Stepping: 2
[gmx-users] The time for the temperature and pressure coupling
Dear Gromacs Team, I have a small question related to the scheme of the MD in Gromacs. When are the temperature and pressure constrains are enforced, before the update of the velocity and position or after? Thank you very much. Best Regards, Kai -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] The time for the temperature and pressure coupling
The coordinates and velocities that are printed (and that are used to calculate the properties like energy, virial, etc) are always consistent with the constraints. The exact order of how things are done often depends on the integrator. For example, velocity scaling can be done before or after constraints, because there are no velocities parallel to the bond vector, so after velocity scaling, the constraints are still obeyed. On Wed, Feb 6, 2013 at 5:28 PM, Bao Kai paeanb...@gmail.com wrote: Dear Gromacs Team, I have a small question related to the scheme of the MD in Gromacs. When are the temperature and pressure constrains are enforced, before the update of the velocity and position or after? Thank you very much. Best Regards, Kai -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] configure gromacs 4.6
On Wed, Feb 6, 2013 at 6:05 PM, jeela keel jeel...@gmail.com wrote: cmake .. -DGMX_BUILD_OWN_FFTW=ON Because you already build fftw yourself you don't need GMX_BUILD_OWN_FFTW. The option means that gromacs builds fftw for you. Instead simply specify where you installed fftw with CMAKE_PREFIX_PATH Roland -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Error- Simulation box resizes during mdrun
On 2/6/13 11:52 AM, Bharath K. Srikanth wrote: Hi everyone, Today, I was attempting a simulation of a system with a lipid bilayer, and the size of my simulation box, obtained from a previous simulation, was 15 nm x 7.5 nm x 7.5 nm (15 nm being the direction perpendicular to the plane of the bilayer). The bilayer consisted of 128 DOPC lipids and was located at the centre of the box. I used periodic boundary conditions in all three directions. I then resized the box to 7.5 nm in all directions, using the editconf -box option. After doing the requisite energy minimization steps, I ran the simulation using mdrun. However, running the simulation caused the box to gradually shrink in the y-direction (parallel to the plane of the bilayer!) during the simulation, ultimately settling at around half the original dimension. Is there anything I may have done that could cause this effect? I'm thoroughly baffled. What do you mean by resized the box? Did you strip out water, adjust box vectors, re-solvate, equilibrate, etc? What you're describing is very weird; pictures, plots, etc would help a lot here. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Adsorption layer of water molecules
On 2/6/13 11:56 AM, Yara Alves wrote: I'm working with a protein in water and I used periodic boundary conditions in three dimension. At first the initial system was minimized, then I followed Justin's protocol. The system was equilibrated in a first stage nvt for 1 ns and in a second stage npt for 1 ns (with restraints). Then the production stage had been done with 100ns. When I visualize the trajectory results in vmd, I have a problem with the adsorption layer. During the production trajectory, water molecules had spread very much and actually no adsorption happened. The size of the box increases a lot in the beginning of the pvt equilibrated stage (it was 341 nm³ and it becomes 351nm³) and I can't understand that. This represents a rather small change (something like 3%). What does your analysis of the pressure of the system indicate? Why are the water molecules spreading so much? Why don't they constitute an adsorption layer? Please define what you mean by spreading. Can you post links to images? Why would expect discrete adsorption layers in a protein surrounded by water. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: protein-ligand interactions in charmm force field
On 2/6/13 2:54 PM, James Starlight wrote: by the way could someone provide me with some simple tutorial of the usage of the CGenFF for construction ITP topology for charmm f.f ? Also I still could not found any simple way to monitor dynamics of the non-covalent interactions between ligand and ligand binding pocket. E.g I select manually in the ndx file all residues which could be involved in such interactions (including formation of possible h.bonds, salt bridges as well as stacking interactions ) in one group and ligand inthe second group. Should I use combination of g_hbond and g_saltbr tools for such identification? How stacking interactions could be monitored? g_hbond, g_dist, and g_mindist -on with clever use of index groups can address all of these. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Translating my system using editconf causes my run to crash!
On 2/6/13 3:03 PM, S. Alireza Bagherzadeh wrote: Dear Mark, Today's Topics: 4. Translating my system using editconf causes my run to crash! (S. Alireza Bagherzadeh) 5. Re: Translating my system using editconf causes my run to crash! (Mark Abraham) -- Message: 5 Date: Tue, 5 Feb 2013 22:21:05 +0100 From: Mark Abraham mark.j.abra...@gmail.com Subject: Re: [gmx-users] Translating my system using editconf causes my run to crash! To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: CAMNuMAT6ofqGeJGGGNJ6KEhM++e5XKBf_w4kfPEfmcOJL= v...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 On Tue, Feb 5, 2013 at 10:05 PM, S. Alireza Bagherzadeh s.a.bagherzade...@gmail.com wrote: Hi everyone, I am using editconf to translate my system along the z-axis. Why? mdrun doesn't care. Because I want to preserve the geometry of my system for the purpose of visualization as well as some post-analysis code that I write. I noticed that mdrun as an output gives an image of the simulation box that sits on the origin and extends along the positive direction of the coordinate axises. This might clarify what I mean: My initial configuration looks like this: GAS | WATER | ICE | WATER | GAS (center of system at z-axis: z = 35 nm) My final configuration looks like this: TER | ICE | WATER | GAS GAS | WA(center of system at z-axis: z = dZ/2 = 14.32431) dZ is the simulation box length along the z-axis. This all looks like a rather normal product of PBC. It sounds like you're just repositioning the elements within the unit cell for visualization and post-processing; where does a new simulation come into play? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] compiling on different architecture than the compute nodes architecture
On Wed, Feb 6, 2013 at 6:03 PM, Richard Broadbent richard.broadben...@imperial.ac.uk wrote: Dear All, I would like to compile gromacs 4.6 to run with the correct acceleration on the compute nodes on our local cluster. Some of the nodes have intel sandy-bridge whilst others only have sse4.1 and some (including the login and single core job nodes) are still stuck on ssse3 (gmx would use sse2 acceleration here). Installing several versions is not a problem however, I'm not sure how to make cmake build a version of the code that is not using the acceleration for the system on which the code is being compiled. Restrictions on job sizes makes running the compilation on the sandy-bridge nodes almost impossible. Can anyone let me know which flags cmake needs to enable avx-256 acceleration? my standard cmake line is: $ CC=mpiicc CXX=mpiicpc ; cmake -DGMX_OPENMP=ON -DGMX_MPI=ON -DGMX_DOUBLE=ON -DGMX_GPU=OFF -DGMX_PREFER_STATIC_LIBS=ON -DGMX_FFT_LIBRARY=mkl -DMKL_INCLUDE_DIR=$MKLROOT/**include -DMKL_LIBRARIES=$MKLROOT/lib/**intel64/libmkl_core.so;$** MKLROOT/lib/intel64/libmkl_**intel_lp64.so;$MKLROOT/lib/**intel64/libmkl_sequential.so -DCMAKE_INSTALL_PREFIX=$HOME/**libs/gromacs ../ Note that MKL (without the fftw wrappers) is known to not work out of the box. Making it work requires a fairly simple workaround described here: http://redmine.gromacs.org/issues/1110#note-3 Additionally, note that FFTW is in most cases faster than MKL (but if you find the contrary do let us know). -- Szilárd Thanks, Richard -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] RNA MD
Dear experts, Hello! Is it possible to run RNA md with GBSA? Thank you. bestKim. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Regarding mean square displacement
Dear users, Since I am getting the mean square displacements in terms of several nm^2. I doubt it is wrong. Could anyone please explain me the solution for this. I checked the structure it is not denatured, In addition I used -rmcomm in order to remove the COM movements. Kindly reply Thank you Kavya On Wed, Feb 6, 2013 at 3:35 PM, Kavyashree M hmkv...@gmail.com wrote: Dear users, I have a very basic question in MSD calculation. g_msd calculation on a protein dimer (~237 aa each) trajectory gave a plot of msd, with the values ranging between 1 to 14nm^2. But is this a sensible MSD? As the values given in a paper i was referring was in Ang^2 J. Chem. Theory Comput. 2012, 8, 1129-1142 Command that i used - echo 3 3 |g_msd -f a.xtc -s a.tpr -o a.xvg -n a.ndx -trestart 10 -b 4000 -e 5 -rmcomm Is the range of diffusion coefficient of proteins of in water l in the range of x e-5 cm^2/s? (hemoglobin is 0.1 e-5 cm^2/s) Thank you kavya -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Superimposed trajectory
trjconv -fit rot+trans Cheers, Tsjerk On Thu, Feb 7, 2013 at 6:19 AM, Kavyashree M hmkv...@gmail.com wrote: Dear users, Which tool can be used to create a trajectory of structures (from each frame) superimposed on the first frame using the original traj.xtc file? Thank you kavya -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Superimposed trajectory
Thank you Sir! Kavya On Thu, Feb 7, 2013 at 11:18 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: trjconv -fit rot+trans Cheers, Tsjerk On Thu, Feb 7, 2013 at 6:19 AM, Kavyashree M hmkv...@gmail.com wrote: Dear users, Which tool can be used to create a trajectory of structures (from each frame) superimposed on the first frame using the original traj.xtc file? Thank you kavya -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
