date:20130124

Dear Gromacs Users!


In the gromacs-4.6 version I have some problems with the trp files
obtained after reduction of atom subset via

tpbconv -f initial.tpr -n index -o reduced.tpr

where in index file reduced atom sub set was defined ( e.g c-alpha
atoms from the protein only )

then I'm using g_Covar to calculate covariance matrix from my
trajectory also with reduced atom subset and obtain error
g_covar -f xz.xtc  -s reduced.tpr -o EDA_eigenval.xvg -v
EDA_eigenvec.trr -av EDA_average.pdb  -tu ps

Program g_covar, VERSION 4.6
Source code file:
/home/own/Documents/distr/gromacs-4.6/src/gmxlib/mtop_util.c, line:
932

Software inconsistency error:
Position restraint coordinates are missing

the same error was obtained with other commands wich also require tpr
file as the input

How it could be filed?



James
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Re: [gmx-users] Problem with gromacs-4.6 compilation on Debian

After switching to gcc-4.6 I've obtained that error on the first step
of gromacs compilation

[  0%] Building NVCC (Device) object
src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o
gcc: error trying to exec 'cc1plus': execvp: No such file or directory
CMake Error at gpu_utils_generated_gpu_utils.cu.o.cmake:198 (message):
  Error generating
  
/home/own/distr/gromacs-4.6/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o


make[2]: *** 
[src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/./gpu_utils_generated_gpu_utils.cu.o]
Error 1
make[1]: *** [src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/all] Error 2
make: *** [all] Error 2


2013/1/24, Szilárd Páll szilard.p...@cbr.su.se:
 Hi all,

 Let me clarify one thing: I highly doubt that the *gcc version* upgrade is
 what fixes your the issue, but rather the standard C++ library's version,
 as you can see the undefined symbols refer to GLIBCXX_3.4.15.

 Of course, updating the compiler is a perfectly fine solution if you get
 the new (enough version of the) standard C++ library by doing so.

 Just wanted to clarify this for users bumping into this issue later.

 Cheers,

 --
 Szilárd


 On Wed, Jan 23, 2013 at 5:47 PM, Ricardo rsoa...@fcfrp.usp.br wrote:

 On 01/22/2013 06:02 PM, Christoph Junghans wrote:

 Message: 5
 Date: Tue, 22 Jan 2013 19:42:01 +0100
 From: Szil?rd P?llszilard.p...@cbr.su.se
 Subject: Re: [gmx-users] Problem with gromacs-4.6 compilation on
  Debian
 To: Discussion list for GROMACS usersgmx-users@gromacs.org
 Message-ID:
  CANnYEw5=t=25hnZPfHpdJot7=3YN**CU1AeGv7HCAc3mut_75w8Q@mail.**
 gmail.com 3yncu1aegv7hcac3mut_75...@mail.gmail.com
 Content-Type: text/plain; charset=ISO-8859-1

 On Tue, Jan 22, 2013 at 12:45 PM, James Starlightjmsstarlight@gmail.**
 com jmsstarli...@gmail.comwrote:

  Szilárd,

 Today I've tried to re-install cuda+gromacs and do apt-get
 distr-upgrade but the same error was obtained during gromacs

  I'm don't see how does the distribution upgrade relate to the issues
 you
 had (except if you have updated glibs to a newer version which is
 *still*
 incompatible with libcuda. You should probably try getting a more
 recent
 glibc and GCC version, one that libcuda is linked against. However, I'm
 not
 sure what the source of your problem is, so I can't suggest a certain
 solution.

 I had a similar problem on Gentoo Linux
 (https://bugs.gentoo.org/show_**bug.cgi?id=452386https://bugs.gentoo.org/show_bug.cgi?id=452386),
 it helped to use a
 newer version of gcc (=4.6).

 Cheers,

 Christoph




 I also had this problem, and found that (manually) updating GCC to
 version
 4.6 or higher has fully solved some installation issues with GROMACS 4.6.
 Please note that, for older linux dists, updating via console 'apt-get
 update' does not assure that you'd get newer versions of GCC, therefore,
 in
 this case, it should be downloaded and installed manually.

 Cheers


  compilation. By the way where I could provide --add-needed option ?

 CMAKE_EXE_LINKER_FLAGS=-wl,--**add-needed

 Cheers,
 Szilárd



 James


 2013/1/21 Szilárd Pállszilard.p...@cbr.su.se:

 Szilárd

 --
 gmx-users mailing listgmx-users@gromacs.org
 http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users
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 http://fisbio.fcfrp.usp.br/**joomla/ http://fisbio.fcfrp.usp.br/joomla/

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Re: [gmx-users] Hydrogen bonding differences

2013-01-24 Thread Erik Marklund


Hi. What version was this? Have you tried with -nomerge?

Erik

On Jan 21, 2013, at 10:55 AM, Kavyashree M wrote:


Dear users,

While calculating hydrogen bonds for a simulation, it
was found that the average number of intra protein
hbonds was not equal to sum of MM, MS and SS
hydrogen bonds. (MM - main chain - main chain,
MS - main chain - side chain and side chain - side
chain hydrogen bonds). There was a difference of 5
or so hbonds between intra-protein and MM+MS+SS
hbonds. why is this so?
I selected the options 7 7 for MM, 7 8 for MS and 8 8
for SS hydrogen bonds.

One clarification. nhbdist option gives 0, 1, 2, 3 and
total hydrogen bonds per hydrogen. Does this mean
that a single hydrogen involving in forming hbond with
2 different acceptors/donors at different points of time
in the trajectory.

Thanks
kavya
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Re: [gmx-users] how can I make statics for Z-axis?

2013-01-24 Thread Erik Marklund


g_traj -nox -noy if I recall correctly.

On Jan 21, 2013, at 4:10 PM, Albert wrote:


hello:

 I would like to make statics for an atom along Z-axis. I am just  
wondering how can I to do this in Gromacs?


thank you very much
best
Albert
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Re: [gmx-users] RMSD

2013-01-24 Thread FLOR MARTINI

The values are OK, you obtain a value of RMSD of 0.2510229 . The value -1 
refers time, and it is because you do not have a trajectory. You are comparing 
only two .pdb structures, so it is consistent that you obtain only one value, 
as you do not have more than one frame to compare.
Regards
Flor
 
Dra.M.Florencia Martini
Cátedra de Farmacotecnia II
Facultad de Farmacia y Bioquímica
Universidad de Buenos Aires
Junín 956 6º (1113)
TE: 54 011 4964-8273



 De: Shima Arasteh shima_arasteh2...@yahoo.com
Para: Discussion list for GROMACS users gmx-users@gromacs.org 
Enviado: miércoles, 23 de enero de 2013 16:14
Asunto: Re: [gmx-users] RMSD
 
What I see in xvg file is as below:

# g_rms -s 1.pdb -f 2.pdb -o rmsd1.xvg 
#
# g_rms is part of G R O M A C S:
#
# Gromacs Runs On Most of All Computer Systems
#
@    title RMSD
@    xaxis  label Time (ps)
@    yaxis  label RMSD (nm)
@TYPE xy
@ subtitle Protein after lsq fit to Protein
  -1.000    0.2510229


I though that -1 is the ref value and the other is the relative RMSD for 2.pdb. 
Is this -1 should be positive? What is this -1? Would you give me any 
suggestions   please?

 
Sincerely,
Shima


- Original Message -
From: Justin Lemkul jalem...@vt.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
Cc: 
Sent: Wednesday, January 23, 2013 9:36 PM
Subject: Re: [gmx-users] RMSD



On 1/23/13 12:48 PM, Shima Arasteh wrote:
 I want to find the structure with the lowest RMSD, so I think it does not 
 make different to set any of pdb files as the ref structure.
 I made an attempt and got the RMSD regarding the first pdb file. The RMSD 
 relative to -1 for the ref structure, is written in xvg file. Is my approach 
 logically correct?
 

The RMSD value should be positive, so I don't know how you get -1.  Your 
approach does not seem very sound - a structure does not have an absolute RMSD 
value; it has an RMSD value relative to a reference structure, which must be 
some sort of meaningful comparison or else you're not really measuring anything 
useful.

-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


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Re: [gmx-users] Problem with tpr files




On 1/24/13 7:21 AM, James Starlight wrote:

Dear Gromacs Users!


In the gromacs-4.6 version I have some problems with the trp files
obtained after reduction of atom subset via

tpbconv -f initial.tpr -n index -o reduced.tpr

where in index file reduced atom sub set was defined ( e.g c-alpha
atoms from the protein only )

then I'm using g_Covar to calculate covariance matrix from my
trajectory also with reduced atom subset and obtain error
g_covar -f xz.xtc  -s reduced.tpr -o EDA_eigenval.xvg -v
EDA_eigenvec.trr -av EDA_average.pdb  -tu ps

Program g_covar, VERSION 4.6
Source code file:
/home/own/Documents/distr/gromacs-4.6/src/gmxlib/mtop_util.c, line:
932

Software inconsistency error:
Position restraint coordinates are missing

the same error was obtained with other commands wich also require tpr
file as the input

How it could be filed?



Create a .tpr file that doesn't use position restraints.

-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


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Re: [gmx-users] Problem with gromacs-4.6 compilation on Debian

oh that was simply solved by upgrading of G++ :)

the only problem which remains is the missing of support of mu GPU :(
That time I've tried to start simulation on simply 2 cores CPU + geforce 9500

From md run I've obtained

NOTE: Error occurred during GPU detection:
  CUDA driver version is insufficient for CUDA runtime version
  Can not use GPU acceleration, will fall back to CPU kernels.

ED sampling will be performed!
ED: Reading edi file new_a2a_pca_biased.edi
ED: Note: Reference and average structure are composed of the same atom indices.
ED: Found 1 ED group.
Using 1 MPI thread
Using 2 OpenMP threads

No GPUs detected


I've installed cuda-5.0 with driver
NVRM version: NVIDIA UNIX x86_64 Kernel Module  304.54  Sat Sep 29
00:05:49 PDT 2012

that system works fine with the recent nvidia GPU's but has no support
for GeForce 9500.

James

2013/1/24, James Starlight jmsstarli...@gmail.com:
 After switching to gcc-4.6 I've obtained that error on the first step
 of gromacs compilation

 [  0%] Building NVCC (Device) object
 src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o
 gcc: error trying to exec 'cc1plus': execvp: No such file or directory
 CMake Error at gpu_utils_generated_gpu_utils.cu.o.cmake:198 (message):
   Error generating

 /home/own/distr/gromacs-4.6/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o


 make[2]: ***
 [src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/./gpu_utils_generated_gpu_utils.cu.o]
 Error 1
 make[1]: *** [src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/all] Error 2
 make: *** [all] Error 2


 2013/1/24, Szilárd Páll szilard.p...@cbr.su.se:
 Hi all,

 Let me clarify one thing: I highly doubt that the *gcc version* upgrade
 is
 what fixes your the issue, but rather the standard C++ library's version,
 as you can see the undefined symbols refer to GLIBCXX_3.4.15.

 Of course, updating the compiler is a perfectly fine solution if you get
 the new (enough version of the) standard C++ library by doing so.

 Just wanted to clarify this for users bumping into this issue later.

 Cheers,

 --
 Szilárd


 On Wed, Jan 23, 2013 at 5:47 PM, Ricardo rsoa...@fcfrp.usp.br wrote:

 On 01/22/2013 06:02 PM, Christoph Junghans wrote:

 Message: 5
 Date: Tue, 22 Jan 2013 19:42:01 +0100
 From: Szil?rd P?llszilard.p...@cbr.su.se
 Subject: Re: [gmx-users] Problem with gromacs-4.6 compilation on
  Debian
 To: Discussion list for GROMACS usersgmx-users@gromacs.org
 Message-ID:

 CANnYEw5=t=25hnZPfHpdJot7=3YN**CU1AeGv7HCAc3mut_75w8Q@mail.**
 gmail.com 3yncu1aegv7hcac3mut_75...@mail.gmail.com
 Content-Type: text/plain; charset=ISO-8859-1

 On Tue, Jan 22, 2013 at 12:45 PM, James
 Starlightjmsstarlight@gmail.**
 com jmsstarli...@gmail.comwrote:

  Szilárd,

 Today I've tried to re-install cuda+gromacs and do apt-get
 distr-upgrade but the same error was obtained during gromacs

  I'm don't see how does the distribution upgrade relate to the issues
 you
 had (except if you have updated glibs to a newer version which is
 *still*
 incompatible with libcuda. You should probably try getting a more
 recent
 glibc and GCC version, one that libcuda is linked against. However,
 I'm
 not
 sure what the source of your problem is, so I can't suggest a certain
 solution.

 I had a similar problem on Gentoo Linux
 (https://bugs.gentoo.org/show_**bug.cgi?id=452386https://bugs.gentoo.org/show_bug.cgi?id=452386),
 it helped to use a
 newer version of gcc (=4.6).

 Cheers,

 Christoph




 I also had this problem, and found that (manually) updating GCC to
 version
 4.6 or higher has fully solved some installation issues with GROMACS
 4.6.
 Please note that, for older linux dists, updating via console 'apt-get
 update' does not assure that you'd get newer versions of GCC, therefore,
 in
 this case, it should be downloaded and installed manually.

 Cheers


  compilation. By the way where I could provide --add-needed option ?

 CMAKE_EXE_LINKER_FLAGS=-wl,--**add-needed

 Cheers,
 Szilárd



 James


 2013/1/21 Szilárd Pállszilard.p...@cbr.su.se:

 Szilárd

 --
 gmx-users mailing listgmx-users@gromacs.org
 http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users
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 http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore
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  --
 Christoph Junghans
 Web: http://www.compphys.de


 Ricardo O S Soares
 http://fisbio.fcfrp.usp.br/**joomla/
 http://fisbio.fcfrp.usp.br/joomla/

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 http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users
 * Please search the archive at

Re: [gmx-users] Problem with gromacs-4.6 compilation on Debian




On 1/24/13 9:23 AM, James Starlight wrote:

oh that was simply solved by upgrading of G++ :)

the only problem which remains is the missing of support of mu GPU :(
That time I've tried to start simulation on simply 2 cores CPU + geforce 9500


From md run I've obtained


NOTE: Error occurred during GPU detection:
   CUDA driver version is insufficient for CUDA runtime version
   Can not use GPU acceleration, will fall back to CPU kernels.

ED sampling will be performed!
ED: Reading edi file new_a2a_pca_biased.edi
ED: Note: Reference and average structure are composed of the same atom indices.
ED: Found 1 ED group.
Using 1 MPI thread
Using 2 OpenMP threads

No GPUs detected


I've installed cuda-5.0 with driver
NVRM version: NVIDIA UNIX x86_64 Kernel Module  304.54  Sat Sep 29
00:05:49 PDT 2012

that system works fine with the recent nvidia GPU's but has no support
for GeForce 9500.



GeForce 9500 cards have a compute capability of 1.1.  The minimum required for 
Gromacs is 2.0 (noted in the installation instructions).


-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


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Re: [gmx-users] Problem with tpr files

Justin,

thanks. I've not known that posres were defined in the tpr file as well.

By the way could you make your suggestion in my another topic which
I've posted some days ago about problem with the g_anaeig  ( below I
coppy that issue).

There is some bug  with g_anaeig the souce of which I could not fully
understand.   I have problems when I perform PCA of X-ray data set.
Below you can my workflow.


g_covar -f b2ar_xray_coors.pdb  -s ref.pdb  -o PCA_eigenval.xvg -v
PCA_eigenvec.trr -av PCA_average.pdb -last 8
g_anaeig -v PCA_eigenvec.trr -s ref.pdb  -f b2ar_xray_coors.pdb -rmsf
eigrmsfPCA.xvg -filt


here b2ar_xray_coors.pdb  is the trajectory made from 10 X-ray
structures of my protein (only main chain atoms are included)
ref_pdb is the first frame of that trajectory


As the result I've obtained reasonable eigenvalues and aigenvectors
from g_covar BUT when I check filter trajectory ( produced by
g_anaeig) fitted it to the ref.pdb or to the averaged structure in
both cases I've obtained very distorted geometry of the  protein in
thefiltered trajectory. I have no such problems in case of PCA of MD
trajectory ( when  -f trajectory.trr is from the md snapshots not from
x-ray structures)


How it could be fixed ?

2013/1/24 Justin Lemkul jalem...@vt.edu:


 On 1/24/13 7:21 AM, James Starlight wrote:

 Dear Gromacs Users!


 In the gromacs-4.6 version I have some problems with the trp files
 obtained after reduction of atom subset via

 tpbconv -f initial.tpr -n index -o reduced.tpr

 where in index file reduced atom sub set was defined ( e.g c-alpha
 atoms from the protein only )

 then I'm using g_Covar to calculate covariance matrix from my
 trajectory also with reduced atom subset and obtain error
 g_covar -f xz.xtc  -s reduced.tpr -o EDA_eigenval.xvg -v
 EDA_eigenvec.trr -av EDA_average.pdb  -tu ps

 Program g_covar, VERSION 4.6
 Source code file:
 /home/own/Documents/distr/gromacs-4.6/src/gmxlib/mtop_util.c, line:
 932

 Software inconsistency error:
 Position restraint coordinates are missing

 the same error was obtained with other commands wich also require tpr
 file as the input

 How it could be filed?


 Create a .tpr file that doesn't use position restraints.

 -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
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Re: [gmx-users] Problem with gromacs-4.6 compilation on Debian

On Thu, Jan 24, 2013 at 3:28 PM, Justin Lemkul jalem...@vt.edu wrote:

On 1/24/13 9:23 AM, James Starlight wrote:

oh that was simply solved by upgrading of G++ :)

the only problem which remains is the missing of support of mu GPU :(
That time I've tried to start simulation on simply 2 cores CPU + geforce
9500

From md run I've obtained

NOTE: Error occurred during GPU detection:
CUDA driver version is insufficient for CUDA runtime version
Can not use GPU acceleration, will fall back to CPU kernels.

ED sampling will be performed!
ED: Reading edi file new_a2a_pca_biased.edi
ED: Note: Reference and average structure are composed of the same atom
indices.
ED: Found 1 ED group.
Using 1 MPI thread
Using 2 OpenMP threads

No GPUs detected

I've installed cuda-5.0 with driver
NVRM version: NVIDIA UNIX x86_64 Kernel Module 304.54 Sat Sep 29
00:05:49 PDT 2012

that system works fine with the recent nvidia GPU's but has no support
for GeForce 9500.

GeForce 9500 cards have a compute capability of 1.1. The minimum required
for Gromacs is 2.0 (noted in the installation instructions).

Exactly! Anything below CC 2.0 lacks certain features that make those
devices rather slow for our algorithms and therefore pretty much
impractical.

Cheers,
--
Szilárd

-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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

==**==

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Re: [gmx-users] Problem with gromacs-4.6 compilation on Debian

Let me add two more things.

Note that we *always* compare performance and acceleration to our
super-tuned state-of-the-art CPU code, which I can confidently say that is
among the fastest if not the fastest to date, and never to some slow (CPU)
implementation. Therefore, while other codes might be able to get 10-20x
with GPUs and many x-es even with pre-Fermi (CC 2.0) cards, for obvious
reasons we simply can't.

Still you'll get high *absolute performance* regardless whether you can use
CPU only or CPU+GPU, so this should be a decent deal, right?

If anybody volunteers to add software-based floating point atomic
operations for CC 2.0 and try running the current kernels on earlier
hardware, I'm willing to give pointers, but I simply had no time to try it
myself. This would enable using earlier cards, with a considerable
performance penalty of emulated atomic ops (plus these cards are anyway
slower), but it *might* be worth a try!

Feel free to drop me a mail if anybody is interested.

Cheers,

--
Szilárd

On Thu, Jan 24, 2013 at 3:48 PM, Szilárd Páll szilard.p...@cbr.su.sewrote:

On Thu, Jan 24, 2013 at 3:28 PM, Justin Lemkul jalem...@vt.edu wrote:

On 1/24/13 9:23 AM, James Starlight wrote:

oh that was simply solved by upgrading of G++ :)

the only problem which remains is the missing of support of mu GPU :(
That time I've tried to start simulation on simply 2 cores CPU + geforce
9500

From md run I've obtained

NOTE: Error occurred during GPU detection:
CUDA driver version is insufficient for CUDA runtime version
Can not use GPU acceleration, will fall back to CPU kernels.

No GPUs detected

I've installed cuda-5.0 with driver
NVRM version: NVIDIA UNIX x86_64 Kernel Module 304.54 Sat Sep 29
00:05:49 PDT 2012

that system works fine with the recent nvidia GPU's but has no support
for GeForce 9500.

GeForce 9500 cards have a compute capability of 1.1. The minimum
required for Gromacs is 2.0 (noted in the installation instructions).

Exactly! Anything below CC 2.0 lacks certain features that make those
devices rather slow for our algorithms and therefore pretty much
impractical.

Cheers,
--
Szilárd

-Justin

--
==**==

==**==

Re: [gmx-users] Hydrogen bonding differences

2013-01-24 Thread Kavyashree M

Dear Sir,

This is 4.5.3. I have not tried nomerge. I did not use
nomerge option in any of them, So if it has counted
it (Hbond b/w same donor and acceptor but with
different hydrogen) twice in one calculation then it will
be counted twice in another, So wont the result with/without
nomerge be the same?

The difference is 4-5 Hbonds..

Thank you
Kavya

On Thu, Jan 24, 2013 at 7:30 PM, Erik Marklund er...@xray.bmc.uu.se wrote:

Hi. What version was this? Have you tried with -nomerge?

Erik

On Jan 21, 2013, at 10:55 AM, Kavyashree M wrote:

Dear users,

While calculating hydrogen bonds for a simulation, it
was found that the average number of intra protein
hbonds was not equal to sum of MM, MS and SS
hydrogen bonds. (MM - main chain - main chain,
MS - main chain - side chain and side chain - side
chain hydrogen bonds). There was a difference of 5
or so hbonds between intra-protein and MM+MS+SS
hbonds. why is this so?
I selected the options 7 7 for MM, 7 8 for MS and 8 8
for SS hydrogen bonds.

One clarification. nhbdist option gives 0, 1, 2, 3 and
total hydrogen bonds per hydrogen. Does this mean
that a single hydrogen involving in forming hbond with
2 different acceptors/donors at different points of time
in the trajectory.

Thanks
kavya
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Re: [gmx-users] how can I make statics for Z-axis?

2013-01-24 Thread Albert


HI Erik:

thanks a lot for kind advices, I will try it.

best
Albert

On 01/24/2013 03:00 PM, Erik Marklund wrote:

g_traj -nox -noy if I recall correctly.

On Jan 21, 2013, at 4:10 PM, Albert wrote:


hello:

 I would like to make statics for an atom along Z-axis. I am just 
wondering how can I to do this in Gromacs?


thank you very much
best
Albert
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[gmx-users] Need Help on Simulated annealing (Implicit Solvation)

2013-01-24 Thread Raghuvir R. S. Pissurlenkar

Hi
I have tried to write a grompp.mdp file for simulated annealing of a peptide 
(~30 aa) in implicit solvent.

Please someone could tell me if the parameters set are fine for the same.

-
; Preprocessing
define = -DFLEXIBLE

; Run control
integrator = md
dt = 0.002
nsteps = 50; 1 ns
comm-mode = angular
nstcomm = 1000
comm-grps = system

; Langevin dynamics
bd-fric = 0
ld-seed = 1993

; Output control
nstxout = 1000
nstvout = 1000
nstfout = 1000
nstlog = 1000
nstenergy = 1000
nstxtcout = 1000

; Neighbor searching
cutoff-scheme = group
nstlist = 10
ns-type = simple
pbc = no
rlist = 0

; Electrostatics
coulombtype = cut-off
rcoulomb = 0

; VdW
vdwtype = cut-off
rvdw = 0

; Temperature coupling
tcoupl = v-rescale
tc-grps = Protein
tau-t = 0.5
ref-t = 300.0

; Pressure coupling
pcoupl = no

; Simulated annealing
annealing = single
annealing-npoints = 1
annealing-npoints = 0 10 20 30 40 50
annealing-temp = 300 320 340 360 380 400

; Velocity generation
gen-vel = yes
gen-temp = 300.0
gen-seed = 173529

; Bonds
constraints = all-bonds
constraint-algorithm = P-LINCS
lincs-order = 4
lincs-iter = 1

; Implicit solvent
implicit-solvent = GBSA
gb-algorithm = OBC
nstgbradii = 1.0
rgbradii = 1.0
gb-epsilon-solvent = 80
gb-saltconc = 0
gb-obc-alpha = 1
gb-obc-beta = 0.8
gb-obc-gamma = 4.85
gb-dielectric-offset = 0.009
sa-algorithm = Ace-approximation
sa-surface-tension = –1

---

Thanks and Regards


Raghuvir-- 
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[gmx-users] g_hbond existence matrix

2013-01-24 Thread Kavyashree M

Dear users,

I have a little confusion -
The hbmap.xpm file gives the existence of each hydrogen bond.
The file mentions -
   c #FF  /* None */,
o  c #FF  /* Present */,
Meaning -
character space in white colour means Hbond not present
character o in red colour means Hbond is present.

In addition, the file also contains white coloured o what is
this?

Thank you
Kavya
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Re: [gmx-users] error about pbc

2013-01-24 Thread Tsjerk Wassenaar

Hi KT,

This is caused by another problem. Your system blew up. Check messages
before this one, and check the log for LINCS warnings.

Cheers,

Tsjerk

On Thu, Jan 24, 2013 at 9:11 AM, Kieu Thu Nguyen kieuthu2...@gmail.comwrote:

 Dear All,

 My MD simulation  has an error

 Warning: Only triclinic boxes with the first vector parallel to the x-axis
 and the second vector in the xy-plane are supported.
  Box (3x3):
 Box[0]={ nan,  nan,  nan}
 Box[1]={ nan,  nan,  nan}
 Box[2]={ nan,  nan,  nan}
  Can not fix pbc.

 I searched on Gromacs-errors web, but i did not see this error.
 How can i fix it ?

 Thanks and regards,
 KT
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Biocomputing Group
Department of Biological Sciences
2500 University Drive NW
Calgary, AB T2N 1N4
Canada
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Re: [gmx-users] RMSD

2013-01-24 Thread Leandro Bortot

 you can make a simple script which calculates all the pairwise RMSD
values with g_rms. By doing this you can make a RMSD matrix.

 The usefulness of this depends on what you are trying to see, which
wasn't clearly stated to us. I did it once because I wanted to know how
similar the 20 conformers from a NMR PDB actually were.



2013/1/24 FLOR MARTINI flormart...@yahoo.com.ar

 The values are OK, you obtain a value of RMSD of 0.2510229 . The value -1
 refers time, and it is because you do not have a trajectory. You are
 comparing only two .pdb structures, so it is consistent that you obtain
 only one value, as you do not have more than one frame to compare.
 Regards
 Flor

 Dra.M.Florencia Martini
 Cátedra de Farmacotecnia II
 Facultad de Farmacia y Bioquímica
 Universidad de Buenos Aires
 Junín 956 6º (1113)
 TE: 54 011 4964-8273


 
  De: Shima Arasteh shima_arasteh2...@yahoo.com
 Para: Discussion list for GROMACS users gmx-users@gromacs.org
 Enviado: miércoles, 23 de enero de 2013 16:14
 Asunto: Re: [gmx-users] RMSD

 What I see in xvg file is as below:

 # g_rms -s 1.pdb -f 2.pdb -o rmsd1.xvg
 #
 # g_rms is part of G R O M A C S:
 #
 # Gromacs Runs On Most of All Computer Systems
 #
 @title RMSD
 @xaxis  label Time (ps)
 @yaxis  label RMSD (nm)
 @TYPE xy
 @ subtitle Protein after lsq fit to Protein
   -1.0000.2510229


 I though that -1 is the ref value and the other is the relative RMSD for
 2.pdb. Is this -1 should be positive? What is this -1? Would you give me
 any suggestions   please?


 Sincerely,
 Shima


 - Original Message -
 From: Justin Lemkul jalem...@vt.edu
 To: Discussion list for GROMACS users gmx-users@gromacs.org
 Cc:
 Sent: Wednesday, January 23, 2013 9:36 PM
 Subject: Re: [gmx-users] RMSD



 On 1/23/13 12:48 PM, Shima Arasteh wrote:
  I want to find the structure with the lowest RMSD, so I think it does
 not make different to set any of pdb files as the ref structure.
  I made an attempt and got the RMSD regarding the first pdb file. The
 RMSD relative to -1 for the ref structure, is written in xvg file. Is my
 approach logically correct?
 

 The RMSD value should be positive, so I don't know how you get -1.  Your
 approach does not seem very sound - a structure does not have an absolute
 RMSD value; it has an RMSD value relative to a reference structure, which
 must be some sort of meaningful comparison or else you're not really
 measuring anything useful.

 -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

 
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Re: [gmx-users] Problem with gromacs-4.6 compilation on Debian

Justin, Szilárd, thanks for suggestion!

It will be easily for me to found a better card :)

By the way in other topics some developments told me that the Plumed
plugin for methadynamics will be realised in gromacs 4.6. I've checked
for it in manual but could not find any notions about it . Have it
been included in newest Gromacs?

James

2013/1/24 Szilárd Páll szilard.p...@cbr.su.se:
Let me add two more things.

Still you'll get high *absolute performance* regardless whether you can use
CPU only or CPU+GPU, so this should be a decent deal, right?

Feel free to drop me a mail if anybody is interested.

Cheers,

--
Szilárd

On Thu, Jan 24, 2013 at 3:48 PM, Szilárd Páll szilard.p...@cbr.su.sewrote:

On Thu, Jan 24, 2013 at 3:28 PM, Justin Lemkul jalem...@vt.edu wrote:

On 1/24/13 9:23 AM, James Starlight wrote:

oh that was simply solved by upgrading of G++ :)

the only problem which remains is the missing of support of mu GPU :(
That time I've tried to start simulation on simply 2 cores CPU + geforce
9500

From md run I've obtained

NOTE: Error occurred during GPU detection:
CUDA driver version is insufficient for CUDA runtime version
Can not use GPU acceleration, will fall back to CPU kernels.

No GPUs detected

I've installed cuda-5.0 with driver
NVRM version: NVIDIA UNIX x86_64 Kernel Module 304.54 Sat Sep 29
00:05:49 PDT 2012

that system works fine with the recent nvidia GPU's but has no support
for GeForce 9500.

GeForce 9500 cards have a compute capability of 1.1. The minimum
required for Gromacs is 2.0 (noted in the installation instructions).

Exactly! Anything below CC 2.0 lacks certain features that make those
devices rather slow for our algorithms and therefore pretty much
impractical.

Cheers,
--
Szilárd

-Justin

--
==**==

==**==

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Re: [gmx-users] Problem with gromacs-4.6 compilation on Debian

2013-01-24 Thread Christoph Junghans

 Date: Thu, 24 Jan 2013 01:07:04 +0100
 From: Szil?rd P?ll szilard.p...@cbr.su.se
 Subject: Re: [gmx-users] Problem with gromacs-4.6 compilation on
 Debian
 To: Discussion list for GROMACS users gmx-users@gromacs.org
 Message-ID:
 CANnYEw522dfPw5ELOr=xwqyn3xwoeujjpubh4bfc1r7ynhs...@mail.gmail.com
 Content-Type: text/plain; charset=ISO-8859-1

 Hi all,

 Let me clarify one thing: I highly doubt that the *gcc version* upgrade is
 what fixes your the issue, but rather the standard C++ library's version,
 as you can see the undefined symbols refer to GLIBCXX_3.4.15.
Usually that is the case but for std::, the symbols are defined in
libstdc++, which is part of the gcc package.

$ strings /usr/lib/gcc/i686-pc-linux-gnu/4.6.3/libstdc++.so | grep _M_hook
_ZNSt6__norm15_List_node_base7_M_hookEPS0_
_ZNSt15_List_node_base7_M_hookEPS_
_ZNSt8__detail15_List_node_base7_M_hookEPS0_
_ZNSt9__cxx199815_List_node_base7_M_hookEPS0_

Christoph

 Of course, updating the compiler is a perfectly fine solution if you get
 the new (enough version of the) standard C++ library by doing so.

 Just wanted to clarify this for users bumping into this issue later.

 Cheers,

 --
 Szilárd

--
Christoph Junghans
Web: http://www.compphys.de
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Re: [gmx-users] Buckingham potential

On Thu, Jan 24, 2013 at 5:08 PM, Ali Alizadeh ali.alizadehmoja...@gmail.com
 wrote:

 Dear All users

 How can i use only Buckingham potential(non bonded interaction) for my
 system? Is it possible?


Yes. First you need a force field that implements it, and then you need to
look in chapters 4 and 5 of the manual for the details on how it would work.

Mark
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Re: [gmx-users] Problem with gromacs-4.6 compilation on Debian

On Thu, Jan 24, 2013 at 6:48 PM, James Starlight jmsstarli...@gmail.comwrote:

 Justin, Szilárd, thanks for suggestion!

 It will be easily for me to found a better card :)

 By the way in other topics some developments told me that the Plumed
 plugin for methadynamics will be realised in gromacs 4.6. I've checked
 for it in manual but could not find any notions about it . Have it
 been included in newest Gromacs?


I said in that thread there would not be such a feature. Something being a
plug-in means it is not standard. There's never been any mention of PLUMED
(or any other plug-in) in the GROMACS manual, which documents the standard
features. That's because the authors of GROMACS don't write PLUMED. Other
people write plug-ins and document them :-) One of the PLUMED authors wrote
that it would be implemented *for* GROMACS 4.6, not *in* GROMACS 4.6.

Mark



 James

 2013/1/24 Szilárd Páll szilard.p...@cbr.su.se:
  Let me add two more things.
 
  Note that we *always* compare performance and acceleration to our
  super-tuned state-of-the-art CPU code, which I can confidently say that
 is
  among the fastest if not the fastest to date, and never to some slow
 (CPU)
  implementation. Therefore, while other codes might be able to get 10-20x
  with GPUs and many x-es even with pre-Fermi (CC 2.0) cards, for obvious
  reasons we simply can't.
 
  Still you'll get high *absolute performance* regardless whether you can
 use
  CPU only or CPU+GPU, so this should be a decent deal, right?
 
  If anybody volunteers to add software-based floating point atomic
  operations for CC 2.0 and try running the current kernels on earlier
  hardware, I'm willing to give pointers, but I simply had no time to try
 it
  myself. This would enable using earlier cards, with a considerable
  performance penalty of emulated atomic ops (plus these cards are anyway
  slower), but it *might* be worth a try!
 
  Feel free to drop me a mail if anybody is interested.
 
  Cheers,
 
  --
  Szilárd
 
 
  On Thu, Jan 24, 2013 at 3:48 PM, Szilárd Páll szilard.p...@cbr.su.se
 wrote:
 
  On Thu, Jan 24, 2013 at 3:28 PM, Justin Lemkul jalem...@vt.edu wrote:
 
 
 
  On 1/24/13 9:23 AM, James Starlight wrote:
 
  oh that was simply solved by upgrading of G++ :)
 
  the only problem which remains is the missing of support of mu GPU :(
  That time I've tried to start simulation on simply 2 cores CPU +
 geforce
  9500
 
   From md run I've obtained
 
 
  NOTE: Error occurred during GPU detection:
 CUDA driver version is insufficient for CUDA runtime version
 Can not use GPU acceleration, will fall back to CPU kernels.
 
  ED sampling will be performed!
  ED: Reading edi file new_a2a_pca_biased.edi
  ED: Note: Reference and average structure are composed of the same
 atom
  indices.
  ED: Found 1 ED group.
  Using 1 MPI thread
  Using 2 OpenMP threads
 
  No GPUs detected
 
 
  I've installed cuda-5.0 with driver
  NVRM version: NVIDIA UNIX x86_64 Kernel Module  304.54  Sat Sep 29
  00:05:49 PDT 2012
 
  that system works fine with the recent nvidia GPU's but has no support
  for GeForce 9500.
 
 
  GeForce 9500 cards have a compute capability of 1.1.  The minimum
  required for Gromacs is 2.0 (noted in the installation instructions).
 
 
  Exactly! Anything below CC 2.0 lacks certain features that make those
  devices rather  slow for our algorithms and therefore pretty much
  impractical.
 
  Cheers,
  --
  Szilárd
 
 
 
 
 
 
 
  -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
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
 
  ==**==
 
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Re: Re: [gmx-users] Problem with gromacs-4.6 compilation on Debian

2013-01-24 Thread Christoph Junghans

 Date: Thu, 24 Jan 2013 15:55:13 +0100
 From: Szil?rd P?ll szilard.p...@cbr.su.se
 Subject: Re: [gmx-users] Problem with gromacs-4.6 compilation on
 Debian
 To: Discussion list for GROMACS users gmx-users@gromacs.org
 Message-ID:
 CANnYEw7Q3U_8aMyY=bzds0vveb_dg7fvc+pbkacoph8jzm4...@mail.gmail.com
 Content-Type: text/plain; charset=ISO-8859-1

 Let me add two more things.

 Note that we *always* compare performance and acceleration to our
 super-tuned state-of-the-art CPU code, which I can confidently say that is
 among the fastest if not the fastest to date, and never to some slow (CPU)
 implementation. Therefore, while other codes might be able to get 10-20x
 with GPUs and many x-es even with pre-Fermi (CC 2.0) cards, for obvious
 reasons we simply can't.
Always check the following 10 points before believing the speed-up of any code:
http://www.hpcwire.com/hpcwire/2011-12-13/ten_ways_to_fool_the_masses_when_giving_performance_results_on_gpus.html

And Gromacs does a pretty fair comparison.

 Still you'll get high *absolute performance* regardless whether you can use
 CPU only or CPU+GPU, so this should be a decent deal, right?

 If anybody volunteers to add software-based floating point atomic
 operations for CC 2.0 and try running the current kernels on earlier
 hardware, I'm willing to give pointers, but I simply had no time to try it
 myself. This would enable using earlier cards, with a considerable
 performance penalty of emulated atomic ops (plus these cards are anyway
 slower), but it *might* be worth a try!

 Feel free to drop me a mail if anybody is interested.

 Cheers,

 --
 Szilárd

 On Thu, Jan 24, 2013 at 3:48 PM, Szilárd Páll szilard.p...@cbr.su.sewrote:

 On Thu, Jan 24, 2013 at 3:28 PM, Justin Lemkul jalem...@vt.edu wrote:

 On 1/24/13 9:23 AM, James Starlight wrote:

 oh that was simply solved by upgrading of G++ :)

 the only problem which remains is the missing of support of mu GPU :(
 That time I've tried to start simulation on simply 2 cores CPU + geforce
 9500

  From md run I've obtained

 NOTE: Error occurred during GPU detection:
CUDA driver version is insufficient for CUDA runtime version
Can not use GPU acceleration, will fall back to CPU kernels.

 ED sampling will be performed!
 ED: Reading edi file new_a2a_pca_biased.edi
 ED: Note: Reference and average structure are composed of the same atom
 indices.
 ED: Found 1 ED group.
 Using 1 MPI thread
 Using 2 OpenMP threads

 No GPUs detected

 I've installed cuda-5.0 with driver
 NVRM version: NVIDIA UNIX x86_64 Kernel Module  304.54  Sat Sep 29
 00:05:49 PDT 2012

 that system works fine with the recent nvidia GPU's but has no support
 for GeForce 9500.

 GeForce 9500 cards have a compute capability of 1.1.  The minimum
 required for Gromacs is 2.0 (noted in the installation instructions).

 Exactly! Anything below CC 2.0 lacks certain features that make those
 devices rather  slow for our algorithms and therefore pretty much
 impractical.

 Cheers,
 --
 Szilárd

 -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 ==**==

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 ***

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Web: http://www.compphys.de
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Re: [gmx-users] g_hbond existence matrix




On 1/24/13 11:03 AM, Kavyashree M wrote:

Dear users,

I have a little confusion -
The hbmap.xpm file gives the existence of each hydrogen bond.
The file mentions -
   c #FF  /* None */,
o  c #FF  /* Present */,
Meaning -
character space in white colour means Hbond not present
character o in red colour means Hbond is present.

In addition, the file also contains white coloured o what is
this?



There are only two characters in the .xpm file, a space and an 'o' as you noted 
above.  The font color that appears in your terminal is whatever you have set it 
to be; there is no significance of different colored letters in the .xpm file. 
There either is a hydrogen bond in a frame (in which case you see 'o') or there 
is not (and thus a blank space).


-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


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Re: [gmx-users] Need Help on Simulated annealing (Implicit Solvation)




On 1/24/13 10:26 AM, Raghuvir R. S. Pissurlenkar wrote:

Hi
I have tried to write a grompp.mdp file for simulated annealing of a peptide 
(~30 aa) in implicit solvent.

Please someone could tell me if the parameters set are fine for the same.

-
; Preprocessing
define = -DFLEXIBLE



Irrelevant if there is no explicit water, and shouldn't be used for MD anyway 
(only EM).



; Run control
integrator = md
dt = 0.002
nsteps = 50; 1 ns
comm-mode = angular
nstcomm = 1000


grompp will complain about this.  nstcomm should be equal to nstcalcenergy.


comm-grps = system

; Langevin dynamics
bd-fric = 0
ld-seed = 1993

; Output control
nstxout = 1000
nstvout = 1000
nstfout = 1000
nstlog = 1000
nstenergy = 1000
nstxtcout = 1000

; Neighbor searching
cutoff-scheme = group
nstlist = 10


Better to use a fixed neighbor list (nstlist = 0) to use the all-vs-all kernels. 
 You're using infinite cutoffs anyway, so all interactions are calculated. 
There's no point in updating a neighbor list that contains every atom in it.



ns-type = simple
pbc = no
rlist = 0

; Electrostatics
coulombtype = cut-off
rcoulomb = 0

; VdW
vdwtype = cut-off
rvdw = 0

; Temperature coupling
tcoupl = v-rescale
tc-grps = Protein
tau-t = 0.5
ref-t = 300.0

; Pressure coupling
pcoupl = no

; Simulated annealing
annealing = single
annealing-npoints = 1
annealing-npoints = 0 10 20 30 40 50


You've got the same keyword twice.  The first instance (annealing-npoints = 1) 
is correct; there is only one group specified in tc-grps.


Presumably what you want here is annealing-time rather than annealing-npoints.


annealing-temp = 300 320 340 360 380 400



Simulated annealing is a linear increase in temperature, and thus all you need 
to do to warm from 300K to 400K over 50 ps is:


annealing-time = 0 50
annealing-temp = 300 400


; Velocity generation
gen-vel = yes
gen-temp = 300.0
gen-seed = 173529

; Bonds
constraints = all-bonds
constraint-algorithm = P-LINCS


P-LINCS is not a valid setting.  If running in parallel, LINCS automatically 
uses P-LINCS.



lincs-order = 4
lincs-iter = 1

; Implicit solvent
implicit-solvent = GBSA
gb-algorithm = OBC
nstgbradii = 1.0
rgbradii = 1.0


Set both nstgbradii and rgbradii to zero when using infinite cutoffs.

-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


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Re: [gmx-users] Problem with tpr files




On 1/24/13 9:44 AM, James Starlight wrote:

Justin,

thanks. I've not known that posres were defined in the tpr file as well.



Sure, how else would mdrun know what to do? :)


By the way could you make your suggestion in my another topic which
I've posted some days ago about problem with the g_anaeig  ( below I
coppy that issue).



If I had any insight into that issue, I would have posted before.  Let's not 
pollute threads with unrelated stuff, but it doesn't sound like a bug to me at 
all; average structures need not have any physical significance.


-Justin


There is some bug  with g_anaeig the souce of which I could not fully
understand.   I have problems when I perform PCA of X-ray data set.
Below you can my workflow.


g_covar -f b2ar_xray_coors.pdb  -s ref.pdb  -o PCA_eigenval.xvg -v
PCA_eigenvec.trr -av PCA_average.pdb -last 8
g_anaeig -v PCA_eigenvec.trr -s ref.pdb  -f b2ar_xray_coors.pdb -rmsf
eigrmsfPCA.xvg -filt


here b2ar_xray_coors.pdb  is the trajectory made from 10 X-ray
structures of my protein (only main chain atoms are included)
ref_pdb is the first frame of that trajectory


As the result I've obtained reasonable eigenvalues and aigenvectors
from g_covar BUT when I check filter trajectory ( produced by
g_anaeig) fitted it to the ref.pdb or to the averaged structure in
both cases I've obtained very distorted geometry of the  protein in
thefiltered trajectory. I have no such problems in case of PCA of MD
trajectory ( when  -f trajectory.trr is from the md snapshots not from
x-ray structures)


How it could be fixed ?

2013/1/24 Justin Lemkul jalem...@vt.edu:



On 1/24/13 7:21 AM, James Starlight wrote:


Dear Gromacs Users!


In the gromacs-4.6 version I have some problems with the trp files
obtained after reduction of atom subset via

tpbconv -f initial.tpr -n index -o reduced.tpr

where in index file reduced atom sub set was defined ( e.g c-alpha
atoms from the protein only )

then I'm using g_Covar to calculate covariance matrix from my
trajectory also with reduced atom subset and obtain error
g_covar -f xz.xtc  -s reduced.tpr -o EDA_eigenval.xvg -v
EDA_eigenvec.trr -av EDA_average.pdb  -tu ps

Program g_covar, VERSION 4.6
Source code file:
/home/own/Documents/distr/gromacs-4.6/src/gmxlib/mtop_util.c, line:
932

Software inconsistency error:
Position restraint coordinates are missing

the same error was obtained with other commands wich also require tpr
file as the input

How it could be filed?



Create a .tpr file that doesn't use position restraints.

-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


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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


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Re: [gmx-users] Problem with gromacs-4.6 compilation on Debian

On Thu, Jan 24, 2013 at 7:09 PM, Christoph Junghans jungh...@votca.orgwrote:

  Date: Thu, 24 Jan 2013 01:07:04 +0100
  From: Szil?rd P?ll szilard.p...@cbr.su.se
  Subject: Re: [gmx-users] Problem with gromacs-4.6 compilation on
  Debian
  To: Discussion list for GROMACS users gmx-users@gromacs.org
  Message-ID:
  CANnYEw522dfPw5ELOr=
 xwqyn3xwoeujjpubh4bfc1r7ynhs...@mail.gmail.com
  Content-Type: text/plain; charset=ISO-8859-1

  Hi all,

  Let me clarify one thing: I highly doubt that the *gcc version* upgrade
 is
  what fixes your the issue, but rather the standard C++ library's version,
  as you can see the undefined symbols refer to GLIBCXX_3.4.15.
 Usually that is the case but for std::, the symbols are defined in
 libstdc++, which is part of the gcc package.

 $ strings /usr/lib/gcc/i686-pc-linux-gnu/4.6.3/libstdc++.so | grep _M_hook
 _ZNSt6__norm15_List_node_base7_M_hookEPS0_
 _ZNSt15_List_node_base7_M_hookEPS_
 _ZNSt8__detail15_List_node_base7_M_hookEPS0_
 _ZNSt9__cxx199815_List_node_base7_M_hookEPS0_

Christoph, you're right I was just looking at the Ubuntu setup where
libstdc++ comes as a separate package - although it is in a similar
location as the one you suggest and it is a hard dependency for g++.

So folks  fellow gglers: the conclusion is that if you see the
initially reported errors, you should update your g++ (which will get you
new libstdc++).

Cheers,
--
Szilárd

 Christoph

  Of course, updating the compiler is a perfectly fine solution if you get
  the new (enough version of the) standard C++ library by doing so.

  Just wanted to clarify this for users bumping into this issue later.

  Cheers,

  --
  Szilárd

 --
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Re: [gmx-users] Re: g_msd additional information




On 1/24/13 6:12 AM, dakoenig wrote:

Hi Justin,

thank you so far. Now I got some more specific questions regarding g_msd
I got my trajectory from 0-30ns. So far it should to be correct.

I was analyzing this trajectory with g_msd and the following command:

g_msd -f mdrun.xtc -s mdrun.tpr -nice 0 -b 0 -e 3 -beginfit 15000
-endfit 16000 -o D_coeff
g_msd -f mdrun.xtc -s mdrun.tpr -nice 0 -b 0 -e 3 -beginfit 15000
-endfit 17000 -o D_coeff
g_msd -f mdrun.xtc -s mdrun.tpr -nice 0 -b 0 -e 3 -beginfit 15000
-endfit 18000 -o D_coeff
and so on

I observed an slight linear decreasing diffusion coefficient. The error bars
instead were increasing (starting at -beginfit 15000 -endfit 23000)
dramatically. Why do I observe such a behavior?


I don't have a direct answer, but the quality of the resulting calculation 
depends on the quality of the fit.  I don't know how parsing out random parts of 
the MSD curve necessarily helps you.  It should be a fairly straight line with 
default values of -beginfit and -endfit doing a decent job unless the ends are 
really weird.



Is this the reason:
http://gromacs.5086.n6.nabble.com/MSD-and-self-diffusion-td4411869.html



I don't see how that's related.


In addition to that I analyzed the trajectory every 1 ns:


Careful, you're not analyzing every ns, you're fitting over every ns and doing 
the calculation over 30 ns of data.



g_msd -f mdrun.xtc -s mdrun.tpr -nice 0 -b 0 -e 3 -beginfit 1000 -endfit
2000 -o D_coeff
g_msd -f mdrun.xtc -s mdrun.tpr -nice 0 -b 0 -e 3 -beginfit 2000 -endfit
3000 -o D_coeff
g_msd -f mdrun.xtc -s mdrun.tpr -nice 0 -b 0 -e 3 -beginfit 3000 -endfit
4000 -o D_coeff

Here I observed extreme fluctuations starting at 25ns. The errors bars
starting at 27ns were huge. Why do I observe these extreme error bars and
fluctuation for the last 3/5 ns?



You're using less and less data and getting wider error bars, likely.


I checked my whole trajectory (g_msd -f mdrun.xtc -s mdrun.tpr -nice 0 -b 0
-e 3) as well, but it is a straight line, without any observable curves.



That's the expected outcome.  If you zoom into the very beginning of the data 
(first few hundred ps or less), there is likely a small curvature that then 
leads into a long period of linear data.


-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


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Re: [gmx-users] Estimation of the trajectory sampling from Covariance analysis

If your trajectory halves were fully converged then you would observe no
difference in their PCs. Since differences exist, your simulations cannot
possibly have converged. Convergence implies the same covariance matrix,
but unfortunately even if you had the same PCs, it's still a leap in the
dark to assume convergence. (For example, in a deep double-well potential,
each of two simulations could be trapped in a different well, and produce
the same covariance matrix, despite their temporal ensembles not being
identical, nor those ensembles resembling the thermodynamic ensemble.)

Mark

On Sat, Jan 19, 2013 at 8:44 PM, James Starlight jmsstarli...@gmail.comwrote:

 Dear Gromacs users!


 In the gromacs manual I found that A good way to check the relevance
 of the first few principal modes is to calculate the overlap of the
 sampling between the first and second half of the simulation.
 Below you can see results of such overlap (inner product) between 2
 sub-spaces calculated from first and second part of my trajectory ( in
 the lowest frequency regime- only first 5 principal modes from both
 trajectories)


 MD Second Half of
 simulation
   #1 #2 #3
 #4 #5
 MD first Half of simulation #1   +0.21  +0.68  +0.36  -0.33  -0.37
 MD first Half of simulation #2   -0.07  +0.13  +0.57  +0.30  +0.02
 MD first Half of simulation #3   +0.16  -0.22  +0.31  +0.20  -0.28
 MD first Half of simulation #4   +0.85  +0.22  -0.07  +0.02  -0.14
 MD first Half of simulation #5   +0.14  +0.40  -0.37  +0.49  -0.13


 Here you can see that 4rd PC from the first half of simulation
 correspond to the 1st PC from second half of simulation (+0.85). On
 the contrary 2nd mode from second half of simulation correspond to the
 1st mode of first part of simulation (+0.68 ). Finally 3rd mode from
 second half of simulation corresponds to the second mode of the first
 mode. So it seems that during simulation there is some 'dynamics' in
 the lowest frequency regime (e.g I noticed that SEVERAL high frequency
 modes in the shorter trajectory during evolution of the system  join
 together forming ONE more slower mode in the longest trajectory). How
 this can be described from the physic points of view? And how exactly
 I can estimate the sampling quality of my complete trajectory ?

 Thanks for help,
 James
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Re: [gmx-users] Problems with g_anaeig

On Tue, Jan 22, 2013 at 8:22 PM, James Starlight jmsstarli...@gmail.comwrote:

 Dear Gromacs users!


 There is some bug  with g_anaeig the souce of which I could not fully
 understand.


Good Advice: until you can almost write a code patch to fix it, be very
hesitant in suggesting any software has a bug. The best people to help
solve the issue are often those who wrote the code, and you don't want them
annoyed with you :-)

  I have problems when I perform PCA of X-ray data set.
 Below you can my workflow.


 g_covar -f b2ar_xray_coors.pdb  -s ref.pdb  -o PCA_eigenval.xvg -v
 PCA_eigenvec.trr -av PCA_average.pdb -last 8
 g_anaeig -v PCA_eigenvec.trr -s ref.pdb  -f b2ar_xray_coors.pdb -rmsf
 eigrmsfPCA.xvg -filt


 here b2ar_xray_coors.pdb  is the trajectory made from 10 X-ray
 structures of my protein (only main chain atoms are included)
 ref_pdb is the first frame of that trajectory


 As the result I've obtained reasonable eigenvalues and aigenvectors
 from g_covar BUT when I check filter trajectory ( produced by
 g_anaeig) fitted it to the ref.pdb or to the averaged structure in
 both cases I've obtained very distorted geometry of the  protein in
 thefiltered trajectory. I have no such problems in case of PCA of MD
 trajectory ( when  -f trajectory.trr is from the md snapshots not from
 x-ray structures)


 How it could be fixed ?


How have you excluded the hypotheses that your reference structure is not a
valid representative of the middle of the range of variation? Or even that
the X-ray structural ensemble really is one?

Mark
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[gmx-users] switching and shifting in GMX 4.6 on GPUs

2013-01-24 Thread Jesper Sørensen

Dear GMX developers,

Thanks so much for the GMX 4.6 release. Testing on GPUs has shown impressive 
speed-ups.

I have a question however, regarding the missing switching and shifting for 
non-bonded interactions.
I looked at the developer zone website and saw this comment below:

http://www.gromacs.org/Developer_Zone/Roadmap/GROMACS_4.6
* Features currently not supported by the new GPU and SSE kernels:
** Switch and shift interactions (but those are not important, as there is an 
exact cut-off)

While the statement maybe true that they are not important, some force fields 
are very particular about the use of switching and shifting, as it is integral 
to the FF development.
So to my question, is there a timeframe for these features being implemented?

I realized things like this take time, so I am merely asking out of curiosity. 

Best regards,
Jesper


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RE: [gmx-users] switching and shifting in GMX 4.6 on GPUs

2013-01-24 Thread Berk Hess


Hi,

I am not a fan of especially switching the potential, as that produces 
artifacts.
Shifting is less harmful, but unnecessary in nearly all cases.
But I do realize some force fields require this (although you can probably find 
a cut-off
setting at which results would be very similar).
Another reason for not implementing everything right away, is that it would 
increase the number
of CPU and GPU kernels by a factor 3.

What type(s) of LJ cut-off treatments would you consider most important?
I know that CHARMM uses a switch function and Martini uses shift.

Cheers,

Berk


 From: jesoren...@ucsd.edu
 Date: Thu, 24 Jan 2013 12:43:30 -0800
 To: gmx-users@gromacs.org
 Subject: [gmx-users] switching and shifting in GMX 4.6 on GPUs

 Dear GMX developers,

 Thanks so much for the GMX 4.6 release. Testing on GPUs has shown impressive 
 speed-ups.

 I have a question however, regarding the missing switching and shifting for 
 non-bonded interactions.
 I looked at the developer zone website and saw this comment below:

 http://www.gromacs.org/Developer_Zone/Roadmap/GROMACS_4.6
 * Features currently not supported by the new GPU and SSE kernels:
 ** Switch and shift interactions (but those are not important, as there is an 
 exact cut-off)

 While the statement maybe true that they are not important, some force 
 fields are very particular about the use of switching and shifting, as it is 
 integral to the FF development.
 So to my question, is there a timeframe for these features being implemented?

 I realized things like this take time, so I am merely asking out of curiosity.

 Best regards,
 Jesper


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Re: [gmx-users] switching and shifting in GMX 4.6 on GPUs

2013-01-24 Thread Jesper Sørensen

Hi Berk,

I am running membrane simulations using both the CHARMM36 and MARTINI v. 2.1 
parameters.
So both those cut-off treatments are important to me, but if there are ways 
around it I'd be happy to explore them to be able to use the GPUs. The place it 
would be most effective would probably be for the all-atom simulations, as the 
number of particles is much higher in general, so switching would be the most 
important at this stage.

On a similar note the switching done in gromacs is by the energy - correct? 
This has been mentioned as an issue for the CHARMM36 lipid parameters as it is 
the forces that are normally switched off in both CHARMM and NAMD, although 
both options are available there. The difference I am told results in a smaller 
area/lipid for the bilayers. 

Best,
Jesper

On Jan 24, 2013, at 1:09 PM, Berk Hess g...@hotmail.com wrote:

 
 Hi,
 
 I am not a fan of especially switching the potential, as that produces 
 artifacts.
 Shifting is less harmful, but unnecessary in nearly all cases.
 But I do realize some force fields require this (although you can probably 
 find a cut-off
 setting at which results would be very similar).
 Another reason for not implementing everything right away, is that it would 
 increase the number
 of CPU and GPU kernels by a factor 3.
 
 What type(s) of LJ cut-off treatments would you consider most important?
 I know that CHARMM uses a switch function and Martini uses shift.
 
 Cheers,
 
 Berk
 
 
 From: jesoren...@ucsd.edu
 Date: Thu, 24 Jan 2013 12:43:30 -0800
 To: gmx-users@gromacs.org
 Subject: [gmx-users] switching and shifting in GMX 4.6 on GPUs
 
 Dear GMX developers,
 
 Thanks so much for the GMX 4.6 release. Testing on GPUs has shown impressive 
 speed-ups.
 
 I have a question however, regarding the missing switching and shifting 
 for non-bonded interactions.
 I looked at the developer zone website and saw this comment below:
 
 http://www.gromacs.org/Developer_Zone/Roadmap/GROMACS_4.6
 * Features currently not supported by the new GPU and SSE kernels:
 ** Switch and shift interactions (but those are not important, as there is 
 an exact cut-off)
 
 While the statement maybe true that they are not important, some force 
 fields are very particular about the use of switching and shifting, as it is 
 integral to the FF development.
 So to my question, is there a timeframe for these features being implemented?
 
 I realized things like this take time, so I am merely asking out of 
 curiosity.
 
 Best regards,
 Jesper
 
 
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Re: [gmx-users] On the choosing of GPU for MD runs

Hi,

Typically, the fastest the GPU the better. On a more detailed level, less
multiprocessors (that's not cores!) with faster clock speeds help in
achieving higher performance with small systems. As GPUs are highly
parallel processors, 20-30k atoms/GPU can be considered small-ish -
especially with Kepler GPUs.

Our algorithms neither require large amount of memory nor are affected very
much by the speed of the on-board GPU main memory. For this reason ECC,
which is available on Tesla compute cards, has a negligible effect on the
performance.

The ideal CPU and GPU depends on the type of simulation and the amount/mix
of force computational work determined by system and settings.  With PME is
used, the bonded force and long-range electrostatics is calculated on the
CPU while the GPU computes non-bonded forces (see the wiki for more
details). Therefore, the longer the cut-off you provide in the mdp file
(which will result in coarser the PME grid) the relatively higher the GPU
non-bonded workload compared to the CPU PME workload will be. mdrun does
automated particle-particle - PME load balancing but I will not get into
those details now. The point is that if for a given cut-off the GPU is not
fast enough to finish before the CPU, the CPU will have to wait and
therefore idle; the opposite case will be handled by the PP-PME load
balancing. Therefore, for a modern desktop CPU, as the GROMACS CPU code is
also highly tuned, you will typically need a mid to high-end desktop
GeForce card or a Tesla GPU. If you use long cut-offs (1.2 nm), my guess
is that you might need a faster GPU for the pretty fast Intel CPU you have,
but that you can see by looking at the amount of Wait for GPU time in the
log file.

For reference, on an Intel i7-3930K and a GTX 680 with a 134k solvated
protein system with PME, rc=1.0, dt=5fs (with virtual sites) I get 33
ns/day (15 ns/day with dt=0.2 without virtual sites) with pretty good
CPU-GPU balance (only a few % waiting for GPU). If I increase the cut-off
to 1.2 nm, the performance drops to 26.8 ns/day caused by GPU taking much
more time to compute due to the larger cut off (the force-only kernel takes
30% more time) and the CPU ends up waiting for 35% of the total time.

Cheers,

--
Szilárd


On Mon, Jan 14, 2013 at 9:00 AM, James Starlight jmsstarli...@gmail.comwrote:

 Dear Gromacs Users!


 I wounder to know some detailes about choosing of the gpu for md with
 gromacs. In particular on what properties of the videoadapter should I
 pay most attention ? What modern gpu nvidia-series might give best
 performance (gtx 6xx, tesla or quadro series) ? Could you provide me
 with some bechmarks besides the information present on the Gromacs web
 ?

 For instance with the gpu Geforce GTX 670 + core i5 (4 cores) I have
 performance 10ns\day for explicit system with 67000 atoms ( protein in
 tip3p water). Have someone better results with common home-like
 desktop? :)


 James
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Re: [gmx-users] Re: On the choosing of GPU for MD runs

On Mon, Jan 14, 2013 at 7:20 PM, James Starlight jmsstarli...@gmail.comwrote:

 1)As I understood from nvidia site at present time GPU's from the
 tesla serie are the best for the calculations like md. For instasnce
 NVIDIA Tesla C2075 have performance ~ 1 TFLOPS in the
 single-precission calculations. I wounder to know how many 8-core CPU
 must have typical cluster to obtain such performance ? Have someone
 tried to use tesla GPU with gromacs ? What real performance in ns\day
 have been obtained with the explicit solvent systems?


 2) Today I performed test gpu-based calculation with 2 different gpu's
 ( GTX 670 vs GT 640). Both of that gpu's have the same GPU frequency
 but GTX 670 has 256 bit memory interface width with ddr5 ram worked on
 higher frequency. As the result I've obtained 50% more perfomance with
 the GTX 670. Does the memory interface width as well as ram frequency
 affect on total GPU performance in addition to GPU frequency?


As mentioned before, the memory does not matter as much as the number of
processing cores on the GPUs and their frequency.
- GTX 670: 1344 CUDA cores (7 multiprocessors * 192 cores) running at 915
Mhz.
- GTX 640: 384 CUDA cores (2 multiprocessors * 192 cores) running at 900
Mhz.

The raw GPU performance with our current algorithms has a roughly linear
relationship with the number of cores and frequency, so the raw GPU kernel
performance difference between 670 and 640 should be around 3.5x. It is a
bit surprising that you've only got 50% higher total performance with the
670.

--
Szilárd



 James



 2013/1/14 James Starlight jmsstarli...@gmail.com:
  Dear Gromacs Users!
 
 
  I wounder to know some detailes about choosing of the gpu for md with
  gromacs. In particular on what properties of the videoadapter should I
  pay most attention ? What modern gpu nvidia-series might give best
  performance (gtx 6xx, tesla or quadro series) ? Could you provide me
  with some bechmarks besides the information present on the Gromacs web
  ?
 
  For instance with the gpu Geforce GTX 670 + core i5 (4 cores) I have
  performance 10ns\day for explicit system with 67000 atoms ( protein in
  tip3p water). Have someone better results with common home-like
  desktop? :)
 
 
  James
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Re: [gmx-users] g_hbond existence matrix

2013-01-24 Thread Kavyashree M

Thank you for the clarification.

On Fri, Jan 25, 2013 at 12:40 AM, Justin Lemkul jalem...@vt.edu wrote:



 On 1/24/13 11:03 AM, Kavyashree M wrote:

 Dear users,

 I have a little confusion -
 The hbmap.xpm file gives the existence of each hydrogen bond.
 The file mentions -
c #FF  /* None */,
 o  c #FF  /* Present */,
 Meaning -
 character space in white colour means Hbond not present
 character o in red colour means Hbond is present.

 In addition, the file also contains white coloured o what is
 this?


 There are only two characters in the .xpm file, a space and an 'o' as you
 noted above.  The font color that appears in your terminal is whatever you
 have set it to be; there is no significance of different colored letters in
 the .xpm file. There either is a hydrogen bond in a frame (in which case
 you see 'o') or there is not (and thus a blank space).

 -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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Re: [gmx-users] RMSD

2013-01-24 Thread Shima Arasteh



Thanks for your reply.
I want to chose one of the 5 conformers from a NMR PDB. As I studied in 
literature, the average structure could be selected regarding RMSD values and 
the go on with selected one to simulate in in water, lipid bilayer.
All right, I may make a matrix, but how would I chose my purposed conformers?


 Thanks for all your suggestions.

Sincerely,
Shima



From: Leandro Bortot leandro@gmail.com
To: Discussion list for GROMACS users gmx-users@gromacs.org 
Sent: Thursday, January 24, 2013 8:54 PM
Subject: Re: [gmx-users] RMSD

     you can make a simple script which calculates all the pairwise RMSD
values with g_rms. By doing this you can make a RMSD matrix.

     The usefulness of this depends on what you are trying to see, which
wasn't clearly stated to us. I did it once because I wanted to know how
similar the 20 conformers from a NMR PDB actually were.



2013/1/24 FLOR MARTINI flormart...@yahoo.com.ar

 The values are OK, you obtain a value of RMSD of 0.2510229 . The value -1
 refers time, and it is because you do not have a trajectory. You are
 comparing only two .pdb structures, so it is consistent that you obtain
 only one value, as you do not have more than one frame to compare.
 Regards
 Flor

 Dra.M.Florencia Martini
 Cátedra de Farmacotecnia II
 Facultad de Farmacia y Bioquímica
 Universidad de Buenos Aires
 Junín 956 6º (1113)
 TE: 54 011 4964-8273


 
  De: Shima Arasteh shima_arasteh2...@yahoo.com
 Para: Discussion list for GROMACS users gmx-users@gromacs.org
 Enviado: miércoles, 23 de enero de 2013 16:14
 Asunto: Re: [gmx-users] RMSD

 What I see in xvg file is as below:

 # g_rms -s 1.pdb -f 2.pdb -o rmsd1.xvg
 #
 # g_rms is part of G R O M A C S:
 #
 # Gromacs Runs On Most of All Computer Systems
 #
 @    title RMSD
 @    xaxis  label Time (ps)
 @    yaxis  label RMSD (nm)
 @TYPE xy
 @ subtitle Protein after lsq fit to Protein
   -1.000    0.2510229


 I though that -1 is the ref value and the other is the relative RMSD for
 2.pdb. Is this -1 should be positive? What is this -1? Would you give me
 any suggestions   please?


 Sincerely,
 Shima


 - Original Message -
 From: Justin Lemkul jalem...@vt.edu
 To: Discussion list for GROMACS users gmx-users@gromacs.org
 Cc:
 Sent: Wednesday, January 23, 2013 9:36 PM
 Subject: Re: [gmx-users] RMSD



 On 1/23/13 12:48 PM, Shima Arasteh wrote:
  I want to find the structure with the lowest RMSD, so I think it does
 not make different to set any of pdb files as the ref structure.
  I made an attempt and got the RMSD regarding the first pdb file. The
 RMSD relative to -1 for the ref structure, is written in xvg file. Is my
 approach logically correct?
 

 The RMSD value should be positive, so I don't know how you get -1.  Your
 approach does not seem very sound - a structure does not have an absolute
 RMSD value; it has an RMSD value relative to a reference structure, which
 must be some sort of meaningful comparison or else you're not really
 measuring anything useful.

 -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

 
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Re: [gmx-users] Problem with tpr files

Justin,

the problem is not in the average structure (it looks fine) but in the
filter.xtc trajectory produced by g_anaeig. When I load that xtc to
any structure in vmd I obtained dynamics picture of my protein with
broken geometry (its look loke my protein was shrunken). But when I
compared eigenvectors ( produced by g__covar) with the the results of
the same cov.analysis where there were no such problems in filter.xtc
I obtained full coverage in the same modes ( so g_covar in both cases
produce apropriate cov.matrix and the problem only in g_anaeig .


James


2013/1/24 Justin Lemkul jalem...@vt.edu:


 On 1/24/13 9:44 AM, James Starlight wrote:

 Justin,

 thanks. I've not known that posres were defined in the tpr file as well.


 Sure, how else would mdrun know what to do? :)


 By the way could you make your suggestion in my another topic which
 I've posted some days ago about problem with the g_anaeig  ( below I
 coppy that issue).


 If I had any insight into that issue, I would have posted before.  Let's not
 pollute threads with unrelated stuff, but it doesn't sound like a bug to me
 at all; average structures need not have any physical significance.

 -Justin


 There is some bug  with g_anaeig the souce of which I could not fully
 understand.   I have problems when I perform PCA of X-ray data set.
 Below you can my workflow.


 g_covar -f b2ar_xray_coors.pdb  -s ref.pdb  -o PCA_eigenval.xvg -v
 PCA_eigenvec.trr -av PCA_average.pdb -last 8
 g_anaeig -v PCA_eigenvec.trr -s ref.pdb  -f b2ar_xray_coors.pdb -rmsf
 eigrmsfPCA.xvg -filt


 here b2ar_xray_coors.pdb  is the trajectory made from 10 X-ray
 structures of my protein (only main chain atoms are included)
 ref_pdb is the first frame of that trajectory


 As the result I've obtained reasonable eigenvalues and aigenvectors
 from g_covar BUT when I check filter trajectory ( produced by
 g_anaeig) fitted it to the ref.pdb or to the averaged structure in
 both cases I've obtained very distorted geometry of the  protein in
 thefiltered trajectory. I have no such problems in case of PCA of MD
 trajectory ( when  -f trajectory.trr is from the md snapshots not from
 x-ray structures)


 How it could be fixed ?

 2013/1/24 Justin Lemkul jalem...@vt.edu:



 On 1/24/13 7:21 AM, James Starlight wrote:


 Dear Gromacs Users!


 In the gromacs-4.6 version I have some problems with the trp files
 obtained after reduction of atom subset via

 tpbconv -f initial.tpr -n index -o reduced.tpr

 where in index file reduced atom sub set was defined ( e.g c-alpha
 atoms from the protein only )

 then I'm using g_Covar to calculate covariance matrix from my
 trajectory also with reduced atom subset and obtain error
 g_covar -f xz.xtc  -s reduced.tpr -o EDA_eigenval.xvg -v
 EDA_eigenvec.trr -av EDA_average.pdb  -tu ps

 Program g_covar, VERSION 4.6
 Source code file:
 /home/own/Documents/distr/gromacs-4.6/src/gmxlib/mtop_util.c, line:
 932

 Software inconsistency error:
 Position restraint coordinates are missing

 the same error was obtained with other commands wich also require tpr
 file as the input

 How it could be filed?


 Create a .tpr file that doesn't use position restraints.

 -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

 
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 --
 

 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

 
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[gmx-users] aligning problem

2013-01-24 Thread 申昊

Dear GMX users,

   I have a question about aligning my molecules along specific coordinate axis 
,such as Z-axis.
   Does anyone know the codes?

 
 Best regards,
 Hao
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Re: [gmx-users] Re: On the choosing of GPU for MD runs

Szilárd,


thanks for suggestions.

IT's only not quite understand for me in what GPU ( gtx or tesla) I'll
get best performance with the typical ssystem consisted of 50-80k
atoms with explicit solvent and PME ( assuming that I'm using small
cut-offs as you told). For example on the 400$  gtx 670 I have
performance similar to your at the GTX 680. I't intresting to me is
there any reason to buy modern tesla card ( which prise is  2000$ )


James

2013/1/25 Szilárd Páll szilard.p...@cbr.su.se:
 On Mon, Jan 14, 2013 at 7:20 PM, James Starlight 
 jmsstarli...@gmail.comwrote:

 1)As I understood from nvidia site at present time GPU's from the
 tesla serie are the best for the calculations like md. For instasnce
 NVIDIA Tesla C2075 have performance ~ 1 TFLOPS in the
 single-precission calculations. I wounder to know how many 8-core CPU
 must have typical cluster to obtain such performance ? Have someone
 tried to use tesla GPU with gromacs ? What real performance in ns\day
 have been obtained with the explicit solvent systems?


 2) Today I performed test gpu-based calculation with 2 different gpu's
 ( GTX 670 vs GT 640). Both of that gpu's have the same GPU frequency
 but GTX 670 has 256 bit memory interface width with ddr5 ram worked on
 higher frequency. As the result I've obtained 50% more perfomance with
 the GTX 670. Does the memory interface width as well as ram frequency
 affect on total GPU performance in addition to GPU frequency?


 As mentioned before, the memory does not matter as much as the number of
 processing cores on the GPUs and their frequency.
 - GTX 670: 1344 CUDA cores (7 multiprocessors * 192 cores) running at 915
 Mhz.
 - GTX 640: 384 CUDA cores (2 multiprocessors * 192 cores) running at 900
 Mhz.

 The raw GPU performance with our current algorithms has a roughly linear
 relationship with the number of cores and frequency, so the raw GPU kernel
 performance difference between 670 and 640 should be around 3.5x. It is a
 bit surprising that you've only got 50% higher total performance with the
 670.

 --
 Szilárd



 James



 2013/1/14 James Starlight jmsstarli...@gmail.com:
  Dear Gromacs Users!
 
 
  I wounder to know some detailes about choosing of the gpu for md with
  gromacs. In particular on what properties of the videoadapter should I
  pay most attention ? What modern gpu nvidia-series might give best
  performance (gtx 6xx, tesla or quadro series) ? Could you provide me
  with some bechmarks besides the information present on the Gromacs web
  ?
 
  For instance with the gpu Geforce GTX 670 + core i5 (4 cores) I have
  performance 10ns\day for explicit system with 67000 atoms ( protein in
  tip3p water). Have someone better results with common home-like
  desktop? :)
 
 
  James
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Re: [gmx-users] Problems with g_anaeig