Re: [gmx-users] Re: eigenvectors in readable format

[Tsjerk Wassenaar]

Hi Rama,

You can convert the .trr file to readable .gro/.g96 with trjconv.
Frames with positive times will correspond to eigenvectors; the time
indicates the eigenvector index. Make sure not to use any options like
pbc/fitting :p

Cheers,

Tsjerk

On Sat, Oct 16, 2010 at 7:00 AM, Ramachandran G  wrote:
> Hi,
> Can anyone help to get the eigen vector in ascii format. I have with me the
> trajectory file 'eigenvec.trr'.
>
> On using g_covar_d, i got the the ascii format file 'covar.dat'  and it has
> covariance matrix of 3(NxN) number. But i am not interested in that.
>
> I am interested in getting the ascii(readable) format of eigenvector and
> hessian.mtx .
> Your help is highly appreciated. Thank you.
>
> with regards,
> Rama
>
> On Fri, Oct 15, 2010 at 2:29 PM, Ramachandran G  wrote:
>>
>> Hi gmx users:
>>     I did normal mode analysis and got the hessian.mtx . Using the command
>> g_nmeig_d on the hessian.mtx
>> i got the eigenfreq.xvg, eigenval.xvg, eigenvec.trr.
>>
>> I need the complete eigenvector in the readable format. How i can get it?
>> Thank you.
>>
>> with regards,
>> Rama
>>
>> --
>> Postdoctoral Research Scholar,
>> Department of Chemistry,
>> University of Nevada, Reno.
>
>
>
>
>
> --
> gmx-users mailing list    gmx-us...@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
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>



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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[gmx-users] Re: eigenvectors in readable format

[Ramachandran G]

Hi,
Can anyone help to get the eigen vector in ascii format. I have with me the
trajectory file 'eigenvec.trr'.

On using g_covar_d, i got the the ascii format file 'covar.dat'  and it has
covariance matrix of 3(NxN) number. But i am not interested in that.

I am interested in getting the ascii(readable) format of eigenvector and
hessian.mtx .
Your help is highly appreciated. Thank you.

with regards,
Rama

On Fri, Oct 15, 2010 at 2:29 PM, Ramachandran G  wrote:

> Hi gmx users:
> I did normal mode analysis and got the hessian.mtx . Using the command
> g_nmeig_d on the hessian.mtx
> i got the eigenfreq.xvg, eigenval.xvg, eigenvec.trr.
>
> I need the complete eigenvector in the readable format. How i can get it?
> Thank you.
>
> with regards,
> Rama
>
> --
> Postdoctoral Research Scholar,
> Department of Chemistry,
> University of Nevada, Reno.
>
-- 
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[gmx-users] How does g_msd calculates MSD?

[Julian]

Hi everybody,

We're trying to understand how gromacs g_msd calculates MSD (without reading 
through the C code, I really don't know much about it, and there are hundreds 
of 
lines).
(What we want to do is to calculate MSD properly in our supercooled water 
simulations, i.e., to choose correctly the values for -b, -e  and -trestart in 
order to get the longest, reliable MSD data)


We found a mail from Gaurav Goel (quoted below) which gives a reasonable 
explanation on the topic.

If we understand this correctly, then the output of

g_msd -b 50 -e 100 -trestart 50

should be the same as the second half (with the proper shifting) of  
the output of

g_msd -b 0 -e 100 -trestart 50

But it is not, as anyone can verify with any simulation.
.. what are we missing?

Thanks in advance,
Julian

--
Julian Gelman Constantin 
Department of Inorganic, Analytic and Chemical Physics (DQIAQF) 
School of Exact and Natural Sciences 
University of Buenos Aires, Argentina


---
Gaurav Goel gauravgoeluta at gmail.com
Tue Jul 13 00:56:02 CEST 2010

On Mon, Jul 12, 2010 at 5:22 PM, Ricardo Cuya Guizado
 wrote:
> Dear gromacs users
> I make a MD of 20 ns of a solute in water
> With the g_msd program the msd vs the time was obtained
> In the plot, I observed a linear behaviour of the MSD from 0 to 15 ns and a
> plateau with no linear tendence at the last 5 ns arpoximately.
> In order to know if the observed plateau was due to the data or is due to
> the way as the algorithm process the data, I divided the MD in two
> trajectories and obtained the msd for each one.
> From 0-10ns, the plot observed shows a linear tendence en the begining
and a
> plateau with no linear tendence from 9 to 10 ns.
> From 10-20 ns the plot observed was linear from 10 to 18 ns and not linear
> at the last, the same plateau was observed.
> Comparing the plots there are not equivalent,.
> Why g_msd produces a non linear plot at the last of the calculation and the
> plateau is ever produces.
> Somebody will explain the way as the g_msd algorithm work? and why the plot
> are no equivalent or why there must be equivalent?

I will explain how the g_msd algorithm works and hopefully that will
answer all your questions above. What you see in the output file is
average-MSD versus time. This average is done over all the particles
in the group you selected and over multiple time origins (this last
option can be selected with the -trestart parameter). Also, time in
column 1 is time difference from the start of your trajectory to
current time.

E.g., let's say you collected a trajectory over 5 time units and
choose -trestart=1 time unit and -dt=1 time unit.

dt=1 means you'll have 6 configurations for your analysis (including
the configuration at t=0).

trestart=1 means you'll have 5 distinct trajectories for your analysis:
Trajectory 1: 0-5
T2: 1-5
T3: 2-5
T4: 3-5
T5: 4-5

Now you can notice that all 5 trajectories contribute to the average
MSD after 1 time unit (T1-T5), 4 trajectories contribute to the
average MSD after 2 time units (T1-T4),  3 trajectories to the average
MSD after 3 time units (T1-T3), , and only one trajectory to the
MSD after 5 time units (T1). Of course, this assumes that trestart is
large enough that all all these trajectories are uncorrelated.

So, it's clear that longer the time interval at which you want to
evaluate the MSD lesser the number of trajectories used to evaluate
it...and hence, higher error in MSD values at longer times. That might
explain deviation from linear behaviour at long times.

However, you must be careful in interpreting the MSD data and I
recommend reading some literature on the subject. A plateau in MSD
versus time data might also signify what is called cage motion, in
which a particle or atom is trapped by the surrounding particles and
is not able to move out of that hole on the simulation time scale. If
you want you can send me your MSD versus time data along with some
information on your system (such as potentials, density, temperature
etc.) and I can let you know my comments.

Few words of caution:
Make sure that the center of mass of your particle (or atom or
molecule) is diffusing several particle diameters. Also, make sure
that you're calculating the self-diffusion coefficient  by fitting a
straight line to the linear region of MSD versus time data. You can
either modify the -beginfit and -endfit options... or calculate the
slope of the MSD versus time data using some other software (e.g.,
gnuplot, excel, etc.). If you're doing the latter you'll need to take
a look at the code in gmx_msd.c to know how the diffusion coefficent
is calculated from the slope of MSD versus time data (tog et correct
units, use proper scaling factors, etc.).

I hope that helped.

-Gaurav
>
>
>
>
> Regards
> Ricardo Cuya



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[gmx-users] eigenvectors in readable format

[Ramachandran G]

Hi gmx users:
I did normal mode analysis and got the hessian.mtx . Using the command
g_nmeig_d on the hessian.mtx
i got the eigenfreq.xvg, eigenval.xvg, eigenvec.trr.

I need the complete eigenvector in the readable format. How i can get it?
Thank you.

with regards,
Rama

-- 
Postdoctoral Research Scholar,
Department of Chemistry,
University of Nevada, Reno.
-- 
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Re: [gmx-users] Memory allocation - xpm2ps

[Justin A. Lemkul]

Maurício Menegatti Rigo wrote:
Hi, 

I copy the file gmx_xpm2ps from the repository to my gromacs folder 
/usl/local/gromacs/src/tools (i.e. I substitute the old file by the new 
one). After that, I run xpm2ps and the problem persisted. 

Any ideas? 



As I said before, you have to actually re-compile and install the git version of 
Gromacs to see any effect.  Further, simply replacing a file likely will not 
work due to a multitude of code changes that have taken place in other source files.


PS: I run the same job in another i7, but with gromacs version 4.0.7 
installed, and everything occured well. 



Yes, there was a bug introduced in version 4.5.  Please either install the git 
version properly, use xpm2ps included in version 4.0.7, or wait for the release 
of version 4.5.2.


-Justin



2010/10/15 Justin A. Lemkul mailto:jalem...@vt.edu>>



Maurício Menegatti Rigo wrote:


Hi,

Thank you for your answer. Unfortunately, I can't fix my problem.
I dont know if I'm doing this right, but first I type the line
"/git clone git://git.gromacs.org/gromacs.git

/" in the command line.
After all the outputs, I tried to run xpm2ps again, but occured
the same error.


Simply downloading the source code won't fix the problem.  You have
to install (and then use) the resulting binaries.

-Justin



2010/10/15 Justin A. Lemkul mailto:jalem...@vt.edu> >>




   Maurício Menegatti Rigo wrote:

   Hi,
   I found the following error when I tried to run xpm2ps.


   *** glibc detected *** xpm2ps: realloc(): invalid pointer:
   0x00dd0541 ***
   === Backtrace: =
   /lib/libc.so.6[0x7f20a53b0dd6]
   /lib/libc.so.6(realloc+0x2e1)[0x7f20a53b67e1]
   xpm2ps(save_realloc+0x5e)[0x43741e]
   xpm2ps[0x42cf24]
   xpm2ps(read_xpm_entry+0x2fe)[0x42d88e]
   xpm2ps(read_xpm_matrix+0xb2)[0x42eaf2]
   xpm2ps(gmx_xpm2ps+0x7a0)[0x41d000]
   /lib/libc.so.6(__libc_start_main+0xfd)[0x7f20a5359abd]
   xpm2ps[0x412949]
   === Memory map: 
   0040-005e3000 r-xp  fc:03 7799252
  /usr/local/gromacs/bin/xpm2ps
   007e2000-007e3000 r-xp 001e2000 fc:03 7799252
  /usr/local/gromacs/bin/xpm2ps
   007e3000-007e9000 rwxp 001e3000 fc:03 7799252
  /usr/local/gromacs/bin/xpm2ps

   007e9000-007ea000 rwxp  00:00 0 00dce000-00def000
rwxp
    00:00 0  [heap]
   7f20a5124000-7f20a513a000 r-xp  fc:03 17400029  
   /lib/libgcc_s.so.1
   7f20a513a000-7f20a5339000 ---p 00016000 fc:03 17400029  
   /lib/libgcc_s.so.1
   7f20a5339000-7f20a533a000 r-xp 00015000 fc:03 17400029  
   /lib/libgcc_s.so.1
   7f20a533a000-7f20a533b000 rwxp 00016000 fc:03 17400029  
   /lib/libgcc_s.so.1
   7f20a533b000-7f20a54a1000 r-xp  fc:03 17400032  
   /lib/libc-2.10.1.so

 
   
   7f20a54a1000-7f20a56a ---p 00166000 fc:03 17400032  
   /lib/libc-2.10.1.so

 
   
   7f20a56a-7f20a56a4000 r-xp 00165000 fc:03 17400032  
   /lib/libc-2.10.1.so

 
   
   7f20a56a4000-7f20a56a5000 rwxp 00169000 fc:03 17400032  
   /lib/libc-2.10.1.so

 
   
   7f20a56a5000-7f20a56aa000 rwxp  00:00 0
   7f20a56aa000-7f20a56c1000 r-xp  fc:03 17400305  
   /lib/libpthread-2.10.1.so

 
   
   7f20a56c1000-7f20a58c ---p 00017000 fc:03 17400305  
   /lib/libpthread-2.10.1.so

 
   
   7f20a58c-7f20a58c1000 r-xp 00016000 fc:03 17400305  
   /lib/libpthread-2.10.1.so

Re: [gmx-users] Memory allocation - xpm2ps

[Maurício Menegatti Rigo]

Hi,

I copy the file gmx_xpm2ps from the repository to my gromacs folder
/usl/local/gromacs/src/tools (i.e. I substitute the old file by the new
one). After that, I run xpm2ps and the problem persisted.

Any ideas?

PS: I run the same job in another i7, but with gromacs version 4.0.7
installed, and everything occured well.


2010/10/15 Justin A. Lemkul 

>
>
> Maurício Menegatti Rigo wrote:
>
>>
>> Hi,
>>
>> Thank you for your answer. Unfortunately, I can't fix my problem.
>> I dont know if I'm doing this right, but first I type the line "/git clone
>> git://git.gromacs.org/gromacs.git /"
>> in the command line. After all the outputs, I tried to run xpm2ps again, but
>> occured the same error.
>>
>
> Simply downloading the source code won't fix the problem.  You have to
> install (and then use) the resulting binaries.
>
> -Justin
>
>
>>
>> 2010/10/15 Justin A. Lemkul mailto:jalem...@vt.edu>>
>>
>>
>>
>>
>>Maurício Menegatti Rigo wrote:
>>
>>Hi,
>>I found the following error when I tried to run xpm2ps.
>>
>>
>>*** glibc detected *** xpm2ps: realloc(): invalid pointer:
>>0x00dd0541 ***
>>=== Backtrace: =
>>/lib/libc.so.6[0x7f20a53b0dd6]
>>/lib/libc.so.6(realloc+0x2e1)[0x7f20a53b67e1]
>>xpm2ps(save_realloc+0x5e)[0x43741e]
>>xpm2ps[0x42cf24]
>>xpm2ps(read_xpm_entry+0x2fe)[0x42d88e]
>>xpm2ps(read_xpm_matrix+0xb2)[0x42eaf2]
>>xpm2ps(gmx_xpm2ps+0x7a0)[0x41d000]
>>/lib/libc.so.6(__libc_start_main+0xfd)[0x7f20a5359abd]
>>xpm2ps[0x412949]
>>=== Memory map: 
>>0040-005e3000 r-xp  fc:03 7799252
>> /usr/local/gromacs/bin/xpm2ps
>>007e2000-007e3000 r-xp 001e2000 fc:03 7799252
>> /usr/local/gromacs/bin/xpm2ps
>>007e3000-007e9000 rwxp 001e3000 fc:03 7799252
>> /usr/local/gromacs/bin/xpm2ps
>>007e9000-007ea000 rwxp  00:00 0 00dce000-00def000 rwxp
>> 00:00 0  [heap]
>>7f20a5124000-7f20a513a000 r-xp  fc:03 17400029
>>  /lib/libgcc_s.so.1
>>7f20a513a000-7f20a5339000 ---p 00016000 fc:03 17400029
>>  /lib/libgcc_s.so.1
>>7f20a5339000-7f20a533a000 r-xp 00015000 fc:03 17400029
>>  /lib/libgcc_s.so.1
>>7f20a533a000-7f20a533b000 rwxp 00016000 fc:03 17400029
>>  /lib/libgcc_s.so.1
>>7f20a533b000-7f20a54a1000 r-xp  fc:03 17400032
>>  /lib/libc-2.10.1.so 
>>
>>7f20a54a1000-7f20a56a ---p 00166000 fc:03 17400032
>>  /lib/libc-2.10.1.so 
>>
>>7f20a56a-7f20a56a4000 r-xp 00165000 fc:03 17400032
>>  /lib/libc-2.10.1.so 
>>
>>7f20a56a4000-7f20a56a5000 rwxp 00169000 fc:03 17400032
>>  /lib/libc-2.10.1.so 
>>
>>7f20a56a5000-7f20a56aa000 rwxp  00:00 0
>>7f20a56aa000-7f20a56c1000 r-xp  fc:03 17400305
>>  /lib/libpthread-2.10.1.so 
>>
>>7f20a56c1000-7f20a58c ---p 00017000 fc:03 17400305
>>  /lib/libpthread-2.10.1.so 
>>
>>7f20a58c-7f20a58c1000 r-xp 00016000 fc:03 17400305
>>  /lib/libpthread-2.10.1.so 
>>
>>7f20a58c1000-7f20a58c2000 rwxp 00017000 fc:03 17400305
>>  /lib/libpthread-2.10.1.so 
>>
>>7f20a58c2000-7f20a58c6000 rwxp  00:00 0
>>7f20a58c6000-7f20a58c8000 r-xp  fc:03 17401201
>>  /lib/libutil-2.10.1.so 
>>
>>7f20a58c8000-7f20a5ac7000 ---p 2000 fc:03 17401201
>>  /lib/libutil-2.10.1.so 
>>
>>7f20a5ac7000-7f20a5ac8000 r-xp 1000 fc:03 17401201
>>  /lib/libutil-2.10.1.so 
>>
>>7f20a5ac8000-7f20a5ac9000 rwxp 2000 fc:03 17401201
>>  /lib/libutil-2.10.1.so 
>>
>>7f20a5ac9000-7f20a5acb000 r-xp  fc:03 17400035
>>  /lib/libdl-2.10.1.so 
>>
>>7f20a5acb000-7f20a5ccb000 ---p 2000 fc:03 17400035
>>  /lib/libdl-2.10.1.so 
>>
>>7f20a5ccb000-7f20a5ccc000 

RE: [gmx-users] mdrun-gpu error

[Osmair Oliveira]

Hi Renato,
 >Fatal error:
> reading tpx file (md.tpr) version 73 with version 71 program

This error occur because you are using different version of the gromacs.
Are you sure that the version of the grompp is the same of the mdrun

I hope this help.

Prof. Dr. Osmair V. Oliveira
Federal Institute of Espirito Santo
Brazil

> Date: Fri, 15 Oct 2010 17:16:00 -0300
> From: renato...@gmail.com
> To: gmx-users@gromacs.org
> Subject: [gmx-users] mdrun-gpu error
> 
> Hi there,
> I have installed the gromacs-4.5.1 and it was running without
> problems. Also I installed the GPU version of GROMACS
> (gromacs-4.5-GPU-beta2). I have a GTX 480, and the CUDA libraries and
> NVIDIA driver are installed. Then I tried to run the test provided by
> Alan with the mdrun-gpu and I got an error.
> 
> # To test mdrun-gpu
> 
> cat << EOF >| em.mdp
> define   = -DFLEXIBLE
> integrator   = cg ; steep
> nsteps   = 200
> constraints  = none
> emtol= 1000.0
> nstcgsteep   = 10 ; do a steep every 10 steps of cg
> emstep   = 0.01 ; used with steep
> nstcomm  = 1
> coulombtype  = PME
> ns_type  = grid
> rlist= 1.0
> rcoulomb = 1.0
> rvdw = 1.4
> Tcoupl   = no
> Pcoupl   = no
> gen_vel  = no
> nstxout  = 0 ; write coords every # step
> optimize_fft = yes
> EOF
> 
> cat << EOF >| md.mdp
> integrator   = md-vv
> nsteps   = 1000
> dt   = 0.002
> constraints  = all-bonds
> constraint-algorithm = shake
> nstcomm  = 1
> nstcalcenergy= 1
> ns_type  = grid
> rlist= 1.3
> rcoulomb = 1.3
> rvdw = 1.3
> vdwtype  = cut-off
> coulombtype  = PME
> Tcoupl   = Andersen
> nsttcouple   = 1
> tau_t= 0.1
> tc-grps  = system
> ref_t= 300
> Pcoupl   = mttk
> Pcoupltype   = isotropic
> nstpcouple   = 1
> tau_p= 0.5
> compressibility  = 4.5e-5
> ref_p= 1.0
> gen_vel  = yes
> nstxout  = 2 ; write coords every # step
> lincs-iter   = 2
> DispCorr = EnerPres
> optimize_fft = yes
> EOF
> 
> wget -c "http://www.pdbe.org/download/1brv";; -O 1brv.pdb
> 
> pdb2gmx -ff amber99sb -f 1brv.pdb -o Prot.pdb -p Prot.top -water spce -ignh
> 
> editconf -bt triclinic -f Prot.pdb -o Prot.pdb -d 1.0
> 
> genbox -cp Prot.pdb -o Prot.pdb -p Prot.top -cs
> 
> grompp -f em.mdp -c Prot.pdb -p Prot.top -o Prot.tpr
> 
> echo 13 | genion -s Prot.tpr -o Prot.pdb -neutral -conc 0.15 -p
> Prot.top -norandom
> 
> grompp -f em.mdp -c Prot.pdb -p Prot.top -o em.tpr
> 
> mdrun -v -deffnm em
> 
> grompp -f md.mdp -c em.gro -p Prot.top -o md.tpr
> 
> mdrun-gpu -v -deffnm md -device
> "OpenMM:platform=Cuda,memtest=15,deviceid=0,force-device=yes"
> 
> ---
> Getting Loaded...
> Reading file md.tpr, VERSION 4.5 (single precision)
> 
> ---
> Program mdrun-gpu, VERSION 4.5-GPU-beta2
> Source code file:
> /home/rossen/Research/Projects/Gromacs-dev/gromacs/src/gmxlib/tpxio.c,
> line: 1971
> 
> Fatal error:
> reading tpx file (md.tpr) version 73 with version 71 program
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
> 
> I also have tried to use my own system to test the mdrun-gpu and I got
> the same error.
> Any ideas?
> 
> Thanks,
> 
> Renato
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
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Re: [gmx-users] mdrun-gpu error

[Roland Schulz]

You should use the latest GROMACS version also for the GPU. Thus compile the
4.5.1 for the GPU and run this.

On Fri, Oct 15, 2010 at 4:16 PM, Renato Freitas  wrote:

> Hi there,
> I have installed the gromacs-4.5.1 and it was running without
> problems. Also I installed the GPU version of GROMACS
> (gromacs-4.5-GPU-beta2). I have a GTX 480, and the CUDA libraries and
> NVIDIA driver are installed. Then I tried to run the test provided by
> Alan with the mdrun-gpu and I got an error.
>
> # To test mdrun-gpu
>
> cat << EOF >| em.mdp
> define   = -DFLEXIBLE
> integrator   = cg ; steep
> nsteps   = 200
> constraints  = none
> emtol= 1000.0
> nstcgsteep   = 10 ; do a steep every 10 steps of cg
> emstep   = 0.01 ; used with steep
> nstcomm  = 1
> coulombtype  = PME
> ns_type  = grid
> rlist= 1.0
> rcoulomb = 1.0
> rvdw = 1.4
> Tcoupl   = no
> Pcoupl   = no
> gen_vel  = no
> nstxout  = 0 ; write coords every # step
> optimize_fft = yes
> EOF
>
> cat << EOF >| md.mdp
> integrator   = md-vv
> nsteps   = 1000
> dt   = 0.002
> constraints  = all-bonds
> constraint-algorithm = shake
> nstcomm  = 1
> nstcalcenergy= 1
> ns_type  = grid
> rlist= 1.3
> rcoulomb = 1.3
> rvdw = 1.3
> vdwtype  = cut-off
> coulombtype  = PME
> Tcoupl   = Andersen
> nsttcouple   = 1
> tau_t= 0.1
> tc-grps  = system
> ref_t= 300
> Pcoupl   = mttk
> Pcoupltype   = isotropic
> nstpcouple   = 1
> tau_p= 0.5
> compressibility  = 4.5e-5
> ref_p= 1.0
> gen_vel  = yes
> nstxout  = 2 ; write coords every # step
> lincs-iter   = 2
> DispCorr = EnerPres
> optimize_fft = yes
> EOF
>
> wget -c "http://www.pdbe.org/download/1brv";; -O 1brv.pdb
>
> pdb2gmx -ff amber99sb -f 1brv.pdb -o Prot.pdb -p Prot.top -water spce -ignh
>
> editconf -bt triclinic -f Prot.pdb -o Prot.pdb -d 1.0
>
> genbox -cp Prot.pdb -o Prot.pdb -p Prot.top -cs
>
> grompp -f em.mdp -c Prot.pdb -p Prot.top -o Prot.tpr
>
> echo 13 | genion -s Prot.tpr -o Prot.pdb -neutral -conc 0.15 -p
> Prot.top -norandom
>
> grompp -f em.mdp -c Prot.pdb -p Prot.top -o em.tpr
>
> mdrun -v -deffnm em
>
> grompp -f md.mdp -c em.gro -p Prot.top -o md.tpr
>
> mdrun-gpu -v -deffnm md -device
> "OpenMM:platform=Cuda,memtest=15,deviceid=0,force-device=yes"
>
> ---
> Getting Loaded...
> Reading file md.tpr, VERSION 4.5 (single precision)
>
> ---
> Program mdrun-gpu, VERSION 4.5-GPU-beta2
> Source code file:
> /home/rossen/Research/Projects/Gromacs-dev/gromacs/src/gmxlib/tpxio.c,
> line: 1971
>
> Fatal error:
> reading tpx file (md.tpr) version 73 with version 71 program
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>
> I also have tried to use my own system to test the mdrun-gpu and I got
> the same error.
> Any ideas?
>
> Thanks,
>
> Renato
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
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Re: [gmx-users] Memory allocation - xpm2ps

[Justin A. Lemkul]

Maurício Menegatti Rigo wrote:


Hi,

Thank you for your answer. Unfortunately, I can't fix my problem. 

I dont know if I'm doing this right, but first I type the line "/git 
clone git://git.gromacs.org/gromacs.git 
/" in the command line. After all 
the outputs, I tried to run xpm2ps again, but occured the same error. 



Simply downloading the source code won't fix the problem.  You have to install 
(and then use) the resulting binaries.


-Justin




2010/10/15 Justin A. Lemkul mailto:jalem...@vt.edu>>



Maurício Menegatti Rigo wrote:

Hi,
I found the following error when I tried to run xpm2ps.


*** glibc detected *** xpm2ps: realloc(): invalid pointer:
0x00dd0541 ***
=== Backtrace: =
/lib/libc.so.6[0x7f20a53b0dd6]
/lib/libc.so.6(realloc+0x2e1)[0x7f20a53b67e1]
xpm2ps(save_realloc+0x5e)[0x43741e]
xpm2ps[0x42cf24]
xpm2ps(read_xpm_entry+0x2fe)[0x42d88e]
xpm2ps(read_xpm_matrix+0xb2)[0x42eaf2]
xpm2ps(gmx_xpm2ps+0x7a0)[0x41d000]
/lib/libc.so.6(__libc_start_main+0xfd)[0x7f20a5359abd]
xpm2ps[0x412949]
=== Memory map: 
0040-005e3000 r-xp  fc:03 7799252  
 /usr/local/gromacs/bin/xpm2ps
007e2000-007e3000 r-xp 001e2000 fc:03 7799252  
 /usr/local/gromacs/bin/xpm2ps
007e3000-007e9000 rwxp 001e3000 fc:03 7799252  
 /usr/local/gromacs/bin/xpm2ps

007e9000-007ea000 rwxp  00:00 0 00dce000-00def000 rwxp
 00:00 0  [heap]
7f20a5124000-7f20a513a000 r-xp  fc:03 17400029  
/lib/libgcc_s.so.1
7f20a513a000-7f20a5339000 ---p 00016000 fc:03 17400029  
/lib/libgcc_s.so.1
7f20a5339000-7f20a533a000 r-xp 00015000 fc:03 17400029  
/lib/libgcc_s.so.1
7f20a533a000-7f20a533b000 rwxp 00016000 fc:03 17400029  
/lib/libgcc_s.so.1
7f20a533b000-7f20a54a1000 r-xp  fc:03 17400032  
/lib/libc-2.10.1.so 


7f20a54a1000-7f20a56a ---p 00166000 fc:03 17400032  
/lib/libc-2.10.1.so 


7f20a56a-7f20a56a4000 r-xp 00165000 fc:03 17400032  
/lib/libc-2.10.1.so 


7f20a56a4000-7f20a56a5000 rwxp 00169000 fc:03 17400032  
/lib/libc-2.10.1.so 


7f20a56a5000-7f20a56aa000 rwxp  00:00 0
7f20a56aa000-7f20a56c1000 r-xp  fc:03 17400305  
/lib/libpthread-2.10.1.so 


7f20a56c1000-7f20a58c ---p 00017000 fc:03 17400305  
/lib/libpthread-2.10.1.so 


7f20a58c-7f20a58c1000 r-xp 00016000 fc:03 17400305  
/lib/libpthread-2.10.1.so 


7f20a58c1000-7f20a58c2000 rwxp 00017000 fc:03 17400305  
/lib/libpthread-2.10.1.so 


7f20a58c2000-7f20a58c6000 rwxp  00:00 0
7f20a58c6000-7f20a58c8000 r-xp  fc:03 17401201  
/lib/libutil-2.10.1.so 


7f20a58c8000-7f20a5ac7000 ---p 2000 fc:03 17401201  
/lib/libutil-2.10.1.so 


7f20a5ac7000-7f20a5ac8000 r-xp 1000 fc:03 17401201  
/lib/libutil-2.10.1.so 


7f20a5ac8000-7f20a5ac9000 rwxp 2000 fc:03 17401201  
/lib/libutil-2.10.1.so 


7f20a5ac9000-7f20a5acb000 r-xp  fc:03 17400035  
/lib/libdl-2.10.1.so 


7f20a5acb000-7f20a5ccb000 ---p 2000 fc:03 17400035  
/lib/libdl-2.10.1.so 


7f20a5ccb000-7f20a5ccc000 r-xp 2000 fc:03 17400035  
/lib/libdl-2.10.1.so 


7f20a5ccc000-7f20a5ccd000 rwxp 3000 fc:03 17400035  
/lib/libdl-2.10.1.so 

Re: [gmx-users] Memory allocation - xpm2ps

[Maurício Menegatti Rigo]

Hi,

Thank you for your answer. Unfortunately, I can't fix my problem.

I dont know if I'm doing this right, but first I type the line "*git clone
git://git.gromacs.org/gromacs.git*" in the command line. After all the
outputs, I tried to run xpm2ps again, but occured the same error.



2010/10/15 Justin A. Lemkul 

>
>
> Maurício Menegatti Rigo wrote:
>
>> Hi,
>> I found the following error when I tried to run xpm2ps.
>>
>>
>> *** glibc detected *** xpm2ps: realloc(): invalid pointer:
>> 0x00dd0541 ***
>> === Backtrace: =
>> /lib/libc.so.6[0x7f20a53b0dd6]
>> /lib/libc.so.6(realloc+0x2e1)[0x7f20a53b67e1]
>> xpm2ps(save_realloc+0x5e)[0x43741e]
>> xpm2ps[0x42cf24]
>> xpm2ps(read_xpm_entry+0x2fe)[0x42d88e]
>> xpm2ps(read_xpm_matrix+0xb2)[0x42eaf2]
>> xpm2ps(gmx_xpm2ps+0x7a0)[0x41d000]
>> /lib/libc.so.6(__libc_start_main+0xfd)[0x7f20a5359abd]
>> xpm2ps[0x412949]
>> === Memory map: 
>> 0040-005e3000 r-xp  fc:03 7799252
>>  /usr/local/gromacs/bin/xpm2ps
>> 007e2000-007e3000 r-xp 001e2000 fc:03 7799252
>>  /usr/local/gromacs/bin/xpm2ps
>> 007e3000-007e9000 rwxp 001e3000 fc:03 7799252
>>  /usr/local/gromacs/bin/xpm2ps
>> 007e9000-007ea000 rwxp  00:00 0 00dce000-00def000 rwxp 
>> 00:00 0  [heap]
>> 7f20a5124000-7f20a513a000 r-xp  fc:03 17400029
>> /lib/libgcc_s.so.1
>> 7f20a513a000-7f20a5339000 ---p 00016000 fc:03 17400029
>> /lib/libgcc_s.so.1
>> 7f20a5339000-7f20a533a000 r-xp 00015000 fc:03 17400029
>> /lib/libgcc_s.so.1
>> 7f20a533a000-7f20a533b000 rwxp 00016000 fc:03 17400029
>> /lib/libgcc_s.so.1
>> 7f20a533b000-7f20a54a1000 r-xp  fc:03 17400032
>> /lib/libc-2.10.1.so 
>> 7f20a54a1000-7f20a56a ---p 00166000 fc:03 17400032
>> /lib/libc-2.10.1.so 
>> 7f20a56a-7f20a56a4000 r-xp 00165000 fc:03 17400032
>> /lib/libc-2.10.1.so 
>> 7f20a56a4000-7f20a56a5000 rwxp 00169000 fc:03 17400032
>> /lib/libc-2.10.1.so 
>> 7f20a56a5000-7f20a56aa000 rwxp  00:00 0 7f20a56aa000-7f20a56c1000
>> r-xp  fc:03 17400305   /lib/libpthread-2.10.1.so<
>> http://libpthread-2.10.1.so>
>> 7f20a56c1000-7f20a58c ---p 00017000 fc:03 17400305
>> /lib/libpthread-2.10.1.so 
>> 7f20a58c-7f20a58c1000 r-xp 00016000 fc:03 17400305
>> /lib/libpthread-2.10.1.so 
>> 7f20a58c1000-7f20a58c2000 rwxp 00017000 fc:03 17400305
>> /lib/libpthread-2.10.1.so 
>> 7f20a58c2000-7f20a58c6000 rwxp  00:00 0 7f20a58c6000-7f20a58c8000
>> r-xp  fc:03 17401201   /lib/libutil-2.10.1.so <
>> http://libutil-2.10.1.so>
>> 7f20a58c8000-7f20a5ac7000 ---p 2000 fc:03 17401201
>> /lib/libutil-2.10.1.so 
>> 7f20a5ac7000-7f20a5ac8000 r-xp 1000 fc:03 17401201
>> /lib/libutil-2.10.1.so 
>> 7f20a5ac8000-7f20a5ac9000 rwxp 2000 fc:03 17401201
>> /lib/libutil-2.10.1.so 
>> 7f20a5ac9000-7f20a5acb000 r-xp  fc:03 17400035
>> /lib/libdl-2.10.1.so 
>> 7f20a5acb000-7f20a5ccb000 ---p 2000 fc:03 17400035
>> /lib/libdl-2.10.1.so 
>> 7f20a5ccb000-7f20a5ccc000 r-xp 2000 fc:03 17400035
>> /lib/libdl-2.10.1.so 
>> 7f20a5ccc000-7f20a5ccd000 rwxp 3000 fc:03 17400035
>> /lib/libdl-2.10.1.so 
>>
>> 7f20a5ccd000-7f20a5d1b000 r-xp  fc:03 7921041
>>  /usr/local/lib/libopen-pal.so.0.0.0
>> 7f20a5d1b000-7f20a5f1b000 ---p 0004e000 fc:03 7921041
>>  /usr/local/lib/libopen-pal.so.0.0.0
>> 7f20a5f1b000-7f20a5f1c000 r-xp 0004e000 fc:03 7921041
>>  /usr/local/lib/libopen-pal.so.0.0.0
>> 7f20a5f1c000-7f20a5f1e000 rwxp 0004f000 fc:03 7921041
>>  /usr/local/lib/libopen-pal.so.0.0.0
>> 7f20a5f1e000-7f20a5f41000 rwxp  00:00 0 7f20a5f41000-7f20a5f89000
>> r-xp  fc:03 7921099
>>  /usr/local/lib/libopen-rte.so.0.0.0
>> Aborted
>>
>>
>> I note that someone already had the same problem. Could someone tell me if
>> this was fixed?
>>
>
> There have been several fixes to xpm2ps that are available in the
> development code.  Try the latest git version to see if you still have the
> same problem.
>
> -Justin
>
>
>  I'm using the gromacs version 4.5.1, in an i7 processor.
>>
>> Thanks in advance,
>>
>> --
>> Maurício M. Rigo
>>
>>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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/Sea

[gmx-users] mdrun-gpu error

[Renato Freitas]

Hi there,
I have installed the gromacs-4.5.1 and it was running without
problems. Also I installed the GPU version of GROMACS
(gromacs-4.5-GPU-beta2). I have a GTX 480, and the CUDA libraries and
NVIDIA driver are installed. Then I tried to run the test provided by
Alan with the mdrun-gpu and I got an error.

# To test mdrun-gpu

cat << EOF >| em.mdp
define   = -DFLEXIBLE
integrator   = cg ; steep
nsteps   = 200
constraints  = none
emtol= 1000.0
nstcgsteep   = 10 ; do a steep every 10 steps of cg
emstep   = 0.01 ; used with steep
nstcomm  = 1
coulombtype  = PME
ns_type  = grid
rlist= 1.0
rcoulomb = 1.0
rvdw = 1.4
Tcoupl   = no
Pcoupl   = no
gen_vel  = no
nstxout  = 0 ; write coords every # step
optimize_fft = yes
EOF

cat << EOF >| md.mdp
integrator   = md-vv
nsteps   = 1000
dt   = 0.002
constraints  = all-bonds
constraint-algorithm = shake
nstcomm  = 1
nstcalcenergy= 1
ns_type  = grid
rlist= 1.3
rcoulomb = 1.3
rvdw = 1.3
vdwtype  = cut-off
coulombtype  = PME
Tcoupl   = Andersen
nsttcouple   = 1
tau_t= 0.1
tc-grps  = system
ref_t= 300
Pcoupl   = mttk
Pcoupltype   = isotropic
nstpcouple   = 1
tau_p= 0.5
compressibility  = 4.5e-5
ref_p= 1.0
gen_vel  = yes
nstxout  = 2 ; write coords every # step
lincs-iter   = 2
DispCorr = EnerPres
optimize_fft = yes
EOF

wget -c "http://www.pdbe.org/download/1brv";; -O 1brv.pdb

pdb2gmx -ff amber99sb -f 1brv.pdb -o Prot.pdb -p Prot.top -water spce -ignh

editconf -bt triclinic -f Prot.pdb -o Prot.pdb -d 1.0

genbox -cp Prot.pdb -o Prot.pdb -p Prot.top -cs

grompp -f em.mdp -c Prot.pdb -p Prot.top -o Prot.tpr

echo 13 | genion -s Prot.tpr -o Prot.pdb -neutral -conc 0.15 -p
Prot.top -norandom

grompp -f em.mdp -c Prot.pdb -p Prot.top -o em.tpr

mdrun -v -deffnm em

grompp -f md.mdp -c em.gro -p Prot.top -o md.tpr

mdrun-gpu -v -deffnm md -device
"OpenMM:platform=Cuda,memtest=15,deviceid=0,force-device=yes"

---
Getting Loaded...
Reading file md.tpr, VERSION 4.5 (single precision)

---
Program mdrun-gpu, VERSION 4.5-GPU-beta2
Source code file:
/home/rossen/Research/Projects/Gromacs-dev/gromacs/src/gmxlib/tpxio.c,
line: 1971

Fatal error:
reading tpx file (md.tpr) version 73 with version 71 program
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

I also have tried to use my own system to test the mdrun-gpu and I got
the same error.
Any ideas?

Thanks,

Renato
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Re: [gmx-users] Memory allocation - xpm2ps

[Justin A. Lemkul]

Maurício Menegatti Rigo wrote:
Hi, 


I found the following error when I tried to run xpm2ps.


*** glibc detected *** xpm2ps: realloc(): invalid pointer: 
0x00dd0541 ***

=== Backtrace: =
/lib/libc.so.6[0x7f20a53b0dd6]
/lib/libc.so.6(realloc+0x2e1)[0x7f20a53b67e1]
xpm2ps(save_realloc+0x5e)[0x43741e]
xpm2ps[0x42cf24]
xpm2ps(read_xpm_entry+0x2fe)[0x42d88e]
xpm2ps(read_xpm_matrix+0xb2)[0x42eaf2]
xpm2ps(gmx_xpm2ps+0x7a0)[0x41d000]
/lib/libc.so.6(__libc_start_main+0xfd)[0x7f20a5359abd]
xpm2ps[0x412949]
=== Memory map: 
0040-005e3000 r-xp  fc:03 7799252   
 /usr/local/gromacs/bin/xpm2ps
007e2000-007e3000 r-xp 001e2000 fc:03 7799252   
 /usr/local/gromacs/bin/xpm2ps
007e3000-007e9000 rwxp 001e3000 fc:03 7799252   
 /usr/local/gromacs/bin/xpm2ps
007e9000-007ea000 rwxp  00:00 0 
00dce000-00def000 rwxp  00:00 0 
 [heap]
7f20a5124000-7f20a513a000 r-xp  fc:03 17400029   
/lib/libgcc_s.so.1
7f20a513a000-7f20a5339000 ---p 00016000 fc:03 17400029   
/lib/libgcc_s.so.1
7f20a5339000-7f20a533a000 r-xp 00015000 fc:03 17400029   
/lib/libgcc_s.so.1
7f20a533a000-7f20a533b000 rwxp 00016000 fc:03 17400029   
/lib/libgcc_s.so.1
7f20a533b000-7f20a54a1000 r-xp  fc:03 17400032   
/lib/libc-2.10.1.so 
7f20a54a1000-7f20a56a ---p 00166000 fc:03 17400032   
/lib/libc-2.10.1.so 
7f20a56a-7f20a56a4000 r-xp 00165000 fc:03 17400032   
/lib/libc-2.10.1.so 
7f20a56a4000-7f20a56a5000 rwxp 00169000 fc:03 17400032   
/lib/libc-2.10.1.so 
7f20a56a5000-7f20a56aa000 rwxp  00:00 0 
7f20a56aa000-7f20a56c1000 r-xp  fc:03 17400305   
/lib/libpthread-2.10.1.so 
7f20a56c1000-7f20a58c ---p 00017000 fc:03 17400305   
/lib/libpthread-2.10.1.so 
7f20a58c-7f20a58c1000 r-xp 00016000 fc:03 17400305   
/lib/libpthread-2.10.1.so 
7f20a58c1000-7f20a58c2000 rwxp 00017000 fc:03 17400305   
/lib/libpthread-2.10.1.so 
7f20a58c2000-7f20a58c6000 rwxp  00:00 0 
7f20a58c6000-7f20a58c8000 r-xp  fc:03 17401201   
/lib/libutil-2.10.1.so 
7f20a58c8000-7f20a5ac7000 ---p 2000 fc:03 17401201   
/lib/libutil-2.10.1.so 
7f20a5ac7000-7f20a5ac8000 r-xp 1000 fc:03 17401201   
/lib/libutil-2.10.1.so 
7f20a5ac8000-7f20a5ac9000 rwxp 2000 fc:03 17401201   
/lib/libutil-2.10.1.so 
7f20a5ac9000-7f20a5acb000 r-xp  fc:03 17400035   
/lib/libdl-2.10.1.so 
7f20a5acb000-7f20a5ccb000 ---p 2000 fc:03 17400035   
/lib/libdl-2.10.1.so 
7f20a5ccb000-7f20a5ccc000 r-xp 2000 fc:03 17400035   
/lib/libdl-2.10.1.so 
7f20a5ccc000-7f20a5ccd000 rwxp 3000 fc:03 17400035   
/lib/libdl-2.10.1.so 
7f20a5ccd000-7f20a5d1b000 r-xp  fc:03 7921041   
 /usr/local/lib/libopen-pal.so.0.0.0
7f20a5d1b000-7f20a5f1b000 ---p 0004e000 fc:03 7921041   
 /usr/local/lib/libopen-pal.so.0.0.0
7f20a5f1b000-7f20a5f1c000 r-xp 0004e000 fc:03 7921041   
 /usr/local/lib/libopen-pal.so.0.0.0
7f20a5f1c000-7f20a5f1e000 rwxp 0004f000 fc:03 7921041   
 /usr/local/lib/libopen-pal.so.0.0.0
7f20a5f1e000-7f20a5f41000 rwxp  00:00 0 
7f20a5f41000-7f20a5f89000 r-xp  fc:03 7921099   
 /usr/local/lib/libopen-rte.so.0.0.0

Aborted


I note that someone already had the same problem. Could someone tell me 
if this was fixed? 



There have been several fixes to xpm2ps that are available in the development 
code.  Try the latest git version to see if you still have the same problem.


-Justin


I'm using the gromacs version 4.5.1, in an i7 processor.

Thanks in advance,

--
Maurício M. Rigo



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] Memory allocation - xpm2ps

[Maurício Menegatti Rigo]

Hi,

I found the following error when I tried to run xpm2ps.


*** glibc detected *** xpm2ps: realloc(): invalid pointer:
0x00dd0541 ***
=== Backtrace: =
/lib/libc.so.6[0x7f20a53b0dd6]
/lib/libc.so.6(realloc+0x2e1)[0x7f20a53b67e1]
xpm2ps(save_realloc+0x5e)[0x43741e]
xpm2ps[0x42cf24]
xpm2ps(read_xpm_entry+0x2fe)[0x42d88e]
xpm2ps(read_xpm_matrix+0xb2)[0x42eaf2]
xpm2ps(gmx_xpm2ps+0x7a0)[0x41d000]
/lib/libc.so.6(__libc_start_main+0xfd)[0x7f20a5359abd]
xpm2ps[0x412949]
=== Memory map: 
0040-005e3000 r-xp  fc:03 7799252
 /usr/local/gromacs/bin/xpm2ps
007e2000-007e3000 r-xp 001e2000 fc:03 7799252
 /usr/local/gromacs/bin/xpm2ps
007e3000-007e9000 rwxp 001e3000 fc:03 7799252
 /usr/local/gromacs/bin/xpm2ps
007e9000-007ea000 rwxp  00:00 0
00dce000-00def000 rwxp  00:00 0
 [heap]
7f20a5124000-7f20a513a000 r-xp  fc:03 17400029
/lib/libgcc_s.so.1
7f20a513a000-7f20a5339000 ---p 00016000 fc:03 17400029
/lib/libgcc_s.so.1
7f20a5339000-7f20a533a000 r-xp 00015000 fc:03 17400029
/lib/libgcc_s.so.1
7f20a533a000-7f20a533b000 rwxp 00016000 fc:03 17400029
/lib/libgcc_s.so.1
7f20a533b000-7f20a54a1000 r-xp  fc:03 17400032
/lib/libc-2.10.1.so
7f20a54a1000-7f20a56a ---p 00166000 fc:03 17400032
/lib/libc-2.10.1.so
7f20a56a-7f20a56a4000 r-xp 00165000 fc:03 17400032
/lib/libc-2.10.1.so
7f20a56a4000-7f20a56a5000 rwxp 00169000 fc:03 17400032
/lib/libc-2.10.1.so
7f20a56a5000-7f20a56aa000 rwxp  00:00 0
7f20a56aa000-7f20a56c1000 r-xp  fc:03 17400305
/lib/libpthread-2.10.1.so
7f20a56c1000-7f20a58c ---p 00017000 fc:03 17400305
/lib/libpthread-2.10.1.so
7f20a58c-7f20a58c1000 r-xp 00016000 fc:03 17400305
/lib/libpthread-2.10.1.so
7f20a58c1000-7f20a58c2000 rwxp 00017000 fc:03 17400305
/lib/libpthread-2.10.1.so
7f20a58c2000-7f20a58c6000 rwxp  00:00 0
7f20a58c6000-7f20a58c8000 r-xp  fc:03 17401201
/lib/libutil-2.10.1.so
7f20a58c8000-7f20a5ac7000 ---p 2000 fc:03 17401201
/lib/libutil-2.10.1.so
7f20a5ac7000-7f20a5ac8000 r-xp 1000 fc:03 17401201
/lib/libutil-2.10.1.so
7f20a5ac8000-7f20a5ac9000 rwxp 2000 fc:03 17401201
/lib/libutil-2.10.1.so
7f20a5ac9000-7f20a5acb000 r-xp  fc:03 17400035
/lib/libdl-2.10.1.so
7f20a5acb000-7f20a5ccb000 ---p 2000 fc:03 17400035
/lib/libdl-2.10.1.so
7f20a5ccb000-7f20a5ccc000 r-xp 2000 fc:03 17400035
/lib/libdl-2.10.1.so
7f20a5ccc000-7f20a5ccd000 rwxp 3000 fc:03 17400035
/lib/libdl-2.10.1.so
7f20a5ccd000-7f20a5d1b000 r-xp  fc:03 7921041
 /usr/local/lib/libopen-pal.so.0.0.0
7f20a5d1b000-7f20a5f1b000 ---p 0004e000 fc:03 7921041
 /usr/local/lib/libopen-pal.so.0.0.0
7f20a5f1b000-7f20a5f1c000 r-xp 0004e000 fc:03 7921041
 /usr/local/lib/libopen-pal.so.0.0.0
7f20a5f1c000-7f20a5f1e000 rwxp 0004f000 fc:03 7921041
 /usr/local/lib/libopen-pal.so.0.0.0
7f20a5f1e000-7f20a5f41000 rwxp  00:00 0
7f20a5f41000-7f20a5f89000 r-xp  fc:03 7921099
 /usr/local/lib/libopen-rte.so.0.0.0
Aborted


I note that someone already had the same problem. Could someone tell me if
this was fixed?

I'm using the gromacs version 4.5.1, in an i7 processor.

Thanks in advance,

--
Maurício M. Rigo
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[gmx-users] genbox solvent addition inhomogeneous?

[Pim Frederix]

Dear users,

When I'm trying to create my solve box of 12x12x12 nm I encounter some trouble. 
I'm using Gromacs 4.5 with the MARTINI force field to set up a system of 400 
dipeptide molecules in water. However when I use "genbox -cp  -cs  -vdwd 0.2 -o " I get an 
inhomogeneous distribution of the water beads: there is what looks like a cubic 
higher density water box in the middle ~9 nm of the output. When I then try to 
run a energy minimization with mdrun the simulation crashes quickly with

Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax < 100.
Potential Energy  =  7.8217890e+17
Maximum force =inf on atom 6750
Norm of force =inf

I've tried different vdwd's, using define = -DPOSRES, but I can't get round it. 
Using smaller 9x9x9 boxes with 150 dipeptides and further nothing different 
does work very satisfactory, but to study the assembled structure I would like 
to increase the size of the entire system.

Can anyone explain why this happens or suggest any solutions? Thanks very much,

Pim Frederix
PhD student University of Strathclyde
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Re: [gmx-users] g_hbond results inconsistent between v4.0.7 and v4.5.1

[Erik Marklund]

 chris.ne...@utoronto.ca skrev 2010-10-15 16.58:

If I redo this, selecting only a single acceptor atom and 64 donor
atoms, with a large cutoff distance of 3 nm, v4.0.7 gives me 44


should have read 4 nm above. the point is that there really are 44 
contacts, but v4.5.1 reports only 1.



contacts in one frame while v4.5.1 gives me only 1 contact. g_dist
confirms that there are 44 contacts within 4 nm (using both versions of
g_dist).



I recall streamlining some pbc-related things. Perhaps I need to revisit 
that part of the code.


--
---
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/

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[gmx-users] g_hbond results inconsistent between v4.0.7 and v4.5.1

[chris . neale]

If I redo this, selecting only a single acceptor atom and 64 donor
atoms, with a large cutoff distance of 3 nm, v4.0.7 gives me 44


should have read 4 nm above. the point is that there really are 44  
contacts, but v4.5.1 reports only 1.



contacts in one frame while v4.5.1 gives me only 1 contact. g_dist
confirms that there are 44 contacts within 4 nm (using both versions of
g_dist).



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[gmx-users] g_hbond results inconsistent between v4.0.7 and v4.5.1

[chris . neale]

Has anybody checked g_hbond results for consistency between v4.0.7 and v4.5.1?

My usage is:
g_hbond -f my.xtc -r 0.68 -contact -life -s my.tpr -ac

and I find that the output files hbnum.xvg, hbac.xvg, hblife.xvg, and  
the ac-reported lifetime of interactions are all different. To show  
the simplest metric, here are the differences for hbnum.xvg:


paste hbnum.4.0.7.xvg hbnum.4.5.1.xvg|grep -v '[#|@]'|head
 0 135   0   0  97   0
50 143   0  50 101   0
   100 135   0 100  95   0
   150 143   0 150 100   0
   200 142   0 200 100   0
   250 133   0 250  96   0
   300 143   0 300 100   0
   350 135   0 350  91   0
   400 144   0 400  97   0
   450 140   0 450  95   0

If I redo this, selecting only a single acceptor atom and 64 donor  
atoms, with a large cutoff distance of 3 nm, v4.0.7 gives me 44  
contacts in one frame while v4.5.1 gives me only 1 contact. g_dist  
confirms that there are 44 contacts within 4 nm (using both versions  
of g_dist).


Then I looked at the more standard actual h-bond usage for a single  
frame and gave SOL SOL as the selection. The numbers of h-bonds vary  
widely: 3915 vs. 7836. These numbers are nearly separated by 2x, but  
not exactly 2x. I can find no record of any intentional changes.


gpc-f109n001-$ echo -e "SOL\nSOL\n" |  
/project/pomes/cneale/GPC/exe/intel/gromacs-4.0.5/exec/bin/g_hbond -f  
../../8ns/RESULTS/3.2/0/0/0-205ns.xtc -n index.ndx -s  
make_nrexl10_tpr/nrexl10.gromacs4.0.5.tpr -e 0

 :-)  G  R  O  M  A  C  S  (-:

   Gromacs Runs One Microsecond At Cannonball Speeds

:-)  VERSION 4.0.5  (-:


  Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
   Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org for more information.

 This program is free software; you can redistribute it and/or
  modify it under the terms of the GNU General Public License
 as published by the Free Software Foundation; either version 2
 of the License, or (at your option) any later version.

  :-)  /project/pomes/cneale/GPC/exe/intel/gromacs-4.0.5/exec/bin/g_hbond  (-:

Option Filename  Type Description

  -f ../../8ns/RESULTS/3.2/0/0/0-205ns.xtc  InputTrajectory: xtc trr
   trj gro g96 pdb cpt
  -s make_nrexl10_tpr/nrexl10.gromacs4.0.5.tpr  InputRun input file:
   tpr tpb tpa
  -n  index.ndx  Input, Opt!  Index file
-num  hbnum.xvg  Output   xvgr/xmgr file
  -g  hbond.log  Output, Opt. Log file
 -ac   hbac.xvg  Output, Opt. xvgr/xmgr file
-disthbdist.xvg  Output, Opt. xvgr/xmgr file
-ang  hbang.xvg  Output, Opt. xvgr/xmgr file
 -hxhbhelix.xvg  Output, Opt. xvgr/xmgr file
-hbn  hbond.ndx  Output, Opt. Index file
-hbm  hbmap.xpm  Output, Opt. X PixMap compatible matrix file
-don  donor.xvg  Output, Opt. xvgr/xmgr file
-dan  danum.xvg  Output, Opt. xvgr/xmgr file
-lifehblife.xvg  Output, Opt. xvgr/xmgr file
-nhbdistnhbdist.xvg  Output, Opt. xvgr/xmgr file

Option   Type   Value   Description
--
-[no]h   bool   no  Print help info and quit
-niceint19  Set the nicelevel
-b   time   0   First frame (ps) to read from trajectory
-e   time   0   Last frame (ps) to read from trajectory
-dt  time   0   Only use frame when t MOD dt = first time (ps)
-[no]xvgrbool   yes Add specific codes (legends etc.) in the output
xvg files for the xmgrace program
-[no]ins bool   no  Analyze solvent insertion
-a   real   30  Cutoff angle (degrees, Acceptor - Donor -
Hydrogen)
-r   real   0.35Cutoff radius (nm, X - Acceptor, see next option)
-[no]da  bool   yes Use distance Donor-Acceptor (if TRUE) or
Hydrogen-Acceptor (FALSE)
-r2  real   0   Second cutoff radius. Mainly useful with -contact
and -ac
-abinreal   1   Binwidth angle distribution (degrees)
-rbinreal   0.005   Binwidth distance distribution (nm)
-[no]nitacc  bool   yes Regard nitrogen atoms as acceptors
-[no]

Re: [gmx-users] Re: Re: Re: g_velacc problem (Florian Dommert)

[Florian Dommert]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

On 10/15/2010 01:09 AM, Eudes Fileti wrote:
> Dear Florian, thanks again.
> I have worked with confined systems, where motion 
> in a given direction/plane is preferred. The accuracy of the MSD 
> approach for calculating the diffusion coefficient has been 
> questioned for this my system. So I need to calculate 
> D via VACF. Considering my limited abilities to programming 
> I wonder if it would be possible to you send me more 
> details about the changes that I should implement the program. 
> 
> Any help will be very useful!

As I mentioned, in my opinion you just have to insert an if statement,
when adding the z-direction of the velocity to the VACF. I will take a
look at it at ASAP and report back.

Cheers,

Flo


> Bests
> eef
> ___
> Eudes Eterno Fileti
> Física da Matéria Condensada
> Simulação Computacional de Nano-estruturas via Dinâmica Molecular
> 
> 
> 
> 
> Message: 1
> Date: Thu, 14 Oct 2010 17:22:38 +0200
> From: Florian Dommert  >
> Subject: Re: [gmx-users] Re: g_velacc problem (Florian Dommert)
> To: Discussion list for GROMACS users  >
> Message-ID: <4cb7203e.1020...@icp.uni-stuttgart.de
> >
> Content-Type: text/plain; charset=ISO-8859-1
> 
> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
> 
> On 10/14/2010 04:41 PM, Eudes Fileti wrote:
> > Dear Florian, thanks for the help. I wonder just one more thing.
> > Is it possible to obtain the lateral diffusion coefficient in a
> specific
> > plane (say xy)
> > using g_velacc? Or it is only possible with g_msd?
> 
> I am not sure, but the MSD is nothing else than the integrated VACF, so
> if you modify the code correspondingly it should work. The modification
> shouldn't be that hard, because you just have to prevent summing up a
> certain direction of the velocity.
> 
> /Flo
> 
> > Bests
> > eef
> > ___
> > Eudes Eterno Fileti
> > Física da Matéria Condensada
> > Simulação Computacional de Nano-estruturas via Dinâmica Molecular
> >
> >
> >
> >
> 
> 
> - --
> Florian Dommert
> Dipl.-Phys.
> 
> Institute for Computational Physics
> 
> University Stuttgart
> 
> Pfaffenwaldring 27
> 70569 Stuttgart
> 
> Phone: +49(0)711/685-6-3613
> Fax:   +49-(0)711/685-6-3658
> 
> EMail: domm...@icp.uni-stuttgart.de
> 
> Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert
> 
> 


- -- 
Florian Dommert
Dipl.-Phys.

Institute for Computational Physics

University Stuttgart

Pfaffenwaldring 27
70569 Stuttgart

Phone: +49(0)711/685-6-3613
Fax:   +49-(0)711/685-6-3658

EMail: domm...@icp.uni-stuttgart.de
Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert
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Version: GnuPG v1.4.10 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

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[gmx-users] Questions about REMD calculations

[chris . neale]

Stefane,

for more information on what Mark is talking about here, check out his  
publication:


M. J. Abraham and J. E. Gready (2008) "Ensuring Mixing Efficiency of
Replica-Exchange Molecular Dynamics Simulations" J. Chem. Theory Comput.
(4), 1119-1128.


Dear all,

I come back to you for several questions about the futures  
replica-exchange calculations that i would like to perform. The  
system of interest will contain 12 peptides (with 7 residues each)  
and 4 water molecules, it come from a previous MD performed in  
NPT ensemble. With these systems, i would like to study the  
aggregation process between the peptides.


After reading several paper about REMD method and playing with the  
Temperature generator for REMD-simulations web server  
(http://folding.bmc.uu.se/remd/), i suspect that this system is too  
big for REMD. Indeed if use the following parameters in the webserver


Pdes 0.2
Temperature range 290 - 600


IMO there are a lot of published REMD studies that use a temperature
range far in excess of what they really needed. Indeed, there are
several that were then so short that they didn't get much value for the
higher-temperature replicas. REMD is useful for enhancing sampling,
perhaps because barriers are easier to cross at higher temperatures. In
principle, you want as large a temperature range as will allow you to
traverse the highest barrier readily. That is rarely known in advance,
but your expectation of what these peptides will do in the simulation
should guide you. If they were going to wander around on their own and
not agglomerate, then a matter of tens of degrees is probably enough :-)
If they're going to tie knots around each other (a la prions), then
maybe no reasonable temperature will ever break them up.

Otherwise, I agree with the other posts.

Mark


Number of water molecules 41380
Number of protein atoms 1092
Including all H ~ 1656
Number of hydrogens in protein ~ 240
Number of constraints ~ 1092
Number of vsites ~ 0
Number of degrees of freedom ~ 250464
Energy loss due to constraints 520.59 (kJ/mol K)

I obtain 271 replicas (ouch !!) . If i assume that for each replica  
app. 16 CPU, The simulations will be too big and will cost a lot CPU  
time.


So my question is can i reduce safely the number of water in system  
to reduce the number of replicas ?


For example for 1 mol of water the number of replicas will be  
135. It is not bad. It is a good option to overcome this limitation.


I have also read the number of replicas can be significantly reduced  
by using variants of REMD for example replica exchange with solute  
tempering (REST) from Berne and co-workers. Is this method is  
implemented in GROMACS ?


Or Can i use the REMD in implicit solvant for example with the  
coarse grain OPEP force field as described in Chebaro, et al.  
(2008).J. Phys. Chem. B 113(1): 267-274. or by Wang and Voth in J.  
Phys. Chem. B 112(41): 13079-13090.


Any advices and comments are welcome

Stefane



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Re: [gmx-users] g_hbond on concatenated trajectory

[Erik Marklund]

 The tricky part is that if you look at the first line in the file 
hbm.xpm you are looking at the bottom row of the matrix when displayed 
with gimp or after converting to xpm2ps. The same line corresponds to 
the first hbond in hbn.ndx. That sentence in the manual is therefore a 
bit ambiguous.


Erik

Carla Jamous skrev 2010-10-15 13.29:
I'm sorry I don't understand, because your last answer doesn't 
correspond to what's written in the manual. I'm using gromacs 4.0.3 
and the manual says:


-hbm: existence matrix. Ordering is identical to that in -hbn index file.

And yes, my trajectory is concatenated the way I intended to, but I 
will check anyway.


Carla

On Fri, Oct 15, 2010 at 1:23 PM, Erik Marklund > wrote:


 Carla Jamous skrev 2010-10-15 12.05:

Hi everyone,


please I need some help on g_hbond.

I concatenated 3 trajectories. I ran g_hbond on the
concatenated trajectory. I got the result of h_bonds.
Then I wanted to run g_hbond on each of my 3 trajectories.
Here, I get a different result, it means: if I take the first
10ps of my concatenated trajectory and I run g_hbond on these
10ps. I get some H-bonds eg. Gly(N)...H(gly)...O
  but this same H-bond
doesn't appear in the first 10ps of my concatenated
trajectory's HBmap.

Please does anyone have an idea where I might have done a mistake?

Thank you,
Carla

Have you confirmed that the concaternation was done the way you
intended?


-- 
---

Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.se 
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--
---
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Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/

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Re: [gmx-users] g_hbond on concatenated trajectory

[Carla Jamous]

I'm sorry I don't understand, because your last answer doesn't correspond to
what's written in the manual. I'm using gromacs 4.0.3 and the manual says:

-hbm: existence matrix. Ordering is identical to that in -hbn index file.

And yes, my trajectory is concatenated the way I intended to, but I will
check anyway.

Carla

On Fri, Oct 15, 2010 at 1:23 PM, Erik Marklund  wrote:

>  Carla Jamous skrev 2010-10-15 12.05:
>
>> Hi everyone,
>>
>>
>> please I need some help on g_hbond.
>>
>> I concatenated 3 trajectories. I ran g_hbond on the concatenated
>> trajectory. I got the result of h_bonds.
>> Then I wanted to run g_hbond on each of my 3 trajectories. Here, I get a
>> different result, it means: if I take the first 10ps of my concatenated
>> trajectory and I run g_hbond on these 10ps. I get some H-bonds eg.
>> Gly(N)...H(gly)...O
>>   but this same H-bond doesn't appear
>> in the first 10ps of my concatenated trajectory's HBmap.
>>
>> Please does anyone have an idea where I might have done a mistake?
>>
>> Thank you,
>> Carla
>>
>>  Have you confirmed that the concaternation was done the way you intended?
>
>
> --
> ---
> Erik Marklund, PhD student
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,75124 Uppsala, Sweden
> phone:+46 18 471 4537fax: +46 18 511 755
> er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/
>
> --
> gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] g_hbond on concatenated trajectory

[Erik Marklund]

 Carla Jamous skrev 2010-10-15 12.05:

Hi everyone,

please I need some help on g_hbond.

I concatenated 3 trajectories. I ran g_hbond on the concatenated 
trajectory. I got the result of h_bonds.
Then I wanted to run g_hbond on each of my 3 trajectories. Here, I get 
a different result, it means: if I take the first 10ps of my 
concatenated trajectory and I run g_hbond on these 10ps. I get some 
H-bonds eg. Gly(N)...H(gly)...O
   but this same H-bond doesn't 
appear in the first 10ps of my concatenated trajectory's HBmap.


Please does anyone have an idea where I might have done a mistake?

Thank you,
Carla


Have you confirmed that the concaternation was done the way you intended?

--
---
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/

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[gmx-users] Fatal error in g_enemat using GMX4.5.1

[zhongjin]

Hi all,
   I am using gmx4.5.1 g_enemat ,came across a error,
g_enemat -f pull.edr -groups -emat,
Opened pull.edr as single precision energy file
Will read groupnames from inputfile
Read 1 groups
group 0WARNING! could not find group (null):K-K (0,0)in energy file

Will select half-matrix of energies with 2 elements
Last energy frame read 136 time  135.400  
Will build energy half-matrix of 1 groups, 2 elements, over 137 frames
Matrix of Coul-SR energy ranges from 100.00 to 0.00

Back Off! I just backed up Coul-SRemat.xpm to ./#Coul-SRemat.xpm.1#

---
Program g_enemat, VERSION 4.5.1
Source code file: matio.c, line: 943

Fatal error:
hi (0.00) <= lo (0.00)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

"I Ripped the Cord Right Out Of the Phone" (Capt. Beefheart)

I have set energygrps  = K  SOL CNT CL  in .mdp file.

I USE g_enemat -f pull.edr -groups -emat,and show:
40  Coul-SR:K-K   
 41  LJ-SR:K-K   42  Coul-14:K-K 43  LJ-14:K-K   44  Coul-SR:K-SOL 
 45  LJ-SR:K-SOL 46  Coul-14:K-SOL   47  LJ-14:K-SOL 48  Coul-SR:K-CNT 
 49  LJ-SR:K-CNT 50  Coul-14:K-CNT   51  LJ-14:K-CNT 52  Coul-SR:K-CL  
 53  LJ-SR:K-CL  54  Coul-14:K-CL55  LJ-14:K-CL  56  Coul-SR:K-rest
 57  LJ-SR:K-rest58  Coul-14:K-rest
 59  LJ-14:K-rest60  Coul-SR:SOL-SOL   
 61  LJ-SR:SOL-SOL   62  Coul-14:SOL-SOL   
 63  LJ-14:SOL-SOL   64  Coul-SR:SOL-CNT   
 65  LJ-SR:SOL-CNT   66  Coul-14:SOL-CNT   
 67  LJ-14:SOL-CNT   68  Coul-SR:SOL-CL  69  LJ-SR:SOL-CL70  Coul-14:SOL-CL
 71  LJ-14:SOL-CL72  Coul-SR:SOL-rest  
 73  LJ-SR:SOL-rest  74  Coul-14:SOL-rest  
 75  LJ-14:SOL-rest  76  Coul-SR:CNT-CNT   
 77  LJ-SR:CNT-CNT   78  Coul-14:CNT-CNT   
 79  LJ-14:CNT-CNT   80  Coul-SR:CNT-CL  81  LJ-SR:CNT-CL82  Coul-14:CNT-CL
 83  LJ-14:CNT-CL84  Coul-SR:CNT-rest  
 85  LJ-SR:CNT-rest  86  Coul-14:CNT-rest  
 87  LJ-14:CNT-rest  88  Coul-SR:CL-CL   89  LJ-SR:CL-CL 90  Coul-14:CL-CL 
 91  LJ-14:CL-CL 92  Coul-SR:CL-rest   
 93  LJ-SR:CL-rest   94  Coul-14:CL-rest   
 95  LJ-14:CL-rest   96  Coul-SR:rest-rest 
 97  LJ-SR:rest-rest 98  Coul-14:rest-rest 
 99  LJ-14:rest-rest100  T-Other   
101  T-Water_and_ions 
What is the problem,anybody could help me? Thanks!
Zhongjin He 



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Re: [gmx-users] g_hbond on concatenated trajectory

[Erik Marklund]

 Yes, and it's the y-direction that is tricky. If I'm not mistaken, the 
first row in the matrix is the *bottom* line in the graphical output. 
Thus, the bottom line in the picture would be the first hbond in the 
corresponding index file.


Erik

Carla Jamous skrev 2010-10-15 12.12:
No, I don't think so because I did an .eps file (with xpm2ps) that 
indicates the Time(ps) in x-axis and Hydrogen Bond Index in y-axis.

This is the way I'm reading my matrix.

Carla

On Fri, Oct 15, 2010 at 12:09 PM, Erik Marklund > wrote:


 Carla Jamous skrev 2010-10-15 12.05:

Hi everyone,

please I need some help on g_hbond.

I concatenated 3 trajectories. I ran g_hbond on the
concatenated trajectory. I got the result of h_bonds.
Then I wanted to run g_hbond on each of my 3 trajectories.
Here, I get a different result, it means: if I take the first
10ps of my concatenated trajectory and I run g_hbond on these
10ps. I get some H-bonds eg. Gly(N)...H(gly)...O
  but this same H-bond
doesn't appear in the first 10ps of my concatenated
trajectory's HBmap.

Please does anyone have an idea where I might have done a mistake?

Thank you,
Carla

The first thing to check is if you're reading the matrix upside
down. Sounds trivial, but it's an eaasy mistake to do.

Cheers,

-- 
---

Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.se 
http://folding.bmc.uu.se/

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--
---
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/

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Re: [gmx-users] g_hbond on concatenated trajectory

[Carla Jamous]

No, I don't think so because I did an .eps file (with xpm2ps) that indicates
the Time(ps) in x-axis and Hydrogen Bond Index in y-axis.
This is the way I'm reading my matrix.

Carla

On Fri, Oct 15, 2010 at 12:09 PM, Erik Marklund wrote:

>  Carla Jamous skrev 2010-10-15 12.05:
>
>  Hi everyone,
>>
>> please I need some help on g_hbond.
>>
>> I concatenated 3 trajectories. I ran g_hbond on the concatenated
>> trajectory. I got the result of h_bonds.
>> Then I wanted to run g_hbond on each of my 3 trajectories. Here, I get a
>> different result, it means: if I take the first 10ps of my concatenated
>> trajectory and I run g_hbond on these 10ps. I get some H-bonds eg.
>> Gly(N)...H(gly)...O
>>   but this same H-bond doesn't appear
>> in the first 10ps of my concatenated trajectory's HBmap.
>>
>> Please does anyone have an idea where I might have done a mistake?
>>
>> Thank you,
>> Carla
>>
>>  The first thing to check is if you're reading the matrix upside down.
> Sounds trivial, but it's an eaasy mistake to do.
>
> Cheers,
>
> --
> ---
> Erik Marklund, PhD student
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,75124 Uppsala, Sweden
> phone:+46 18 471 4537fax: +46 18 511 755
> er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/
>
> --
> 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!
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>
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Re: [gmx-users] g_hbond on concatenated trajectory

[Erik Marklund]

 Carla Jamous skrev 2010-10-15 12.05:

Hi everyone,

please I need some help on g_hbond.

I concatenated 3 trajectories. I ran g_hbond on the concatenated 
trajectory. I got the result of h_bonds.
Then I wanted to run g_hbond on each of my 3 trajectories. Here, I get 
a different result, it means: if I take the first 10ps of my 
concatenated trajectory and I run g_hbond on these 10ps. I get some 
H-bonds eg. Gly(N)...H(gly)...O
   but this same H-bond doesn't 
appear in the first 10ps of my concatenated trajectory's HBmap.


Please does anyone have an idea where I might have done a mistake?

Thank you,
Carla

The first thing to check is if you're reading the matrix upside down. 
Sounds trivial, but it's an eaasy mistake to do.


Cheers,

--
---
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/

--
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[gmx-users] g_hbond on concatenated trajectory

[Carla Jamous]

Hi everyone,

please I need some help on g_hbond.

I concatenated 3 trajectories. I ran g_hbond on the concatenated trajectory.
I got the result of h_bonds.
Then I wanted to run g_hbond on each of my 3 trajectories. Here, I get a
different result, it means: if I take the first 10ps of my concatenated
trajectory and I run g_hbond on these 10ps. I get some H-bonds eg.
Gly(N)...H(gly)...O
   but this same H-bond doesn't appear
in the first 10ps of my concatenated trajectory's HBmap.

Please does anyone have an idea where I might have done a mistake?

Thank you,
Carla
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