Re: [gmx-users] vdw modifier and coulomb modifier

[Mark Abraham]

Hi,

On Fri, Oct 2, 2015 at 5:36 AM Parvez Mh  wrote:

> Dear all,
>
> What does vdw and coulomb modifier do in simulation?. Does these option
> affect simulation accuracy.


These are documented in the .mdp options parts of the manuals. They have
various effects on your model physics. You should choose them to match your
simulation needs, particularly with respect to the force field you are
intending to use.


> I did not find these term in literature or any
> book, why did gromacs introduce these option?
>

Several MD packages and/or force fields do various different things with
short-ranged non-bonded forces. Sometimes they call different things by the
same name (and vice-versa). Some of the things are still thought to be
sensible to do. :-) Some of the things are even documented. In general, you
should understand the equations they claim to implement, and do your own
numerical experiments! :-)

When there are multiple basic kinds of thing and several ways one might
vary some them, it is convenient to describe both the theme and variant,
rather than combine both into one name. Thus "modifiers."

Mark


> Thanks
> Masrul
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Re: [gmx-users] automate gmx sasa

[Andrei Neamtu]

Hello!

Many thanks Teemu!

Andrei

On Sat, Oct 3, 2015 at 9:14 AM, Teemu Murtola 
wrote:

> Hi,
>
> On Sat, Oct 3, 2015 at 8:18 AM Andrei Neamtu 
> wrote:
>
> > In previous versions if one wants to provide in a script an automatic
> >
> > echo 'two indexes' | g_sas .
> >
> > it was fairly easy
> >
> > In version 5 gmx sasa expects EOF (Ctrl D) character to end up the
> > selection.
> >
> > How can one provide automatic selection of index groups in version 5?
> > probably it is a basic Bash question but I am stucked in here for several
> > hours! :)
>
>
> It is even easier in Gromacs 5; there is no need for the echo at all. ;) If
> you want to select groups 0 and 1, you can just use
>
>   gmx sasa -surface 0 -output 1 ...
>
> And the same works for arbitrary selections; you just need to be careful
> with quoting. See
>
>   gmx help selections cmdline
>
> for all the alternatives, including how to read more complex selections
> from a file.
>
> Best regards,
> Teemu
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Re: [gmx-users] Gromacs and Gcc5.2

[Mark Abraham]

Hi,

On Fri, Oct 2, 2015 at 9:58 AM Nicolas Cheron <
nicolas.cheron.bou...@gmail.com> wrote:

> Dear all,
>
> I am wondering if there is an official statement regarding compiling

Gromacs with gcc5.2.0 (or any gcc from the 5.x branch).


It satisfies the technical requirements (in the install guide), so go ahead.

Is it recommended
> or not?


It's probably best overall (which is why the install guide recommends you
get the latest version of your compiler), but the actual optimum depends on
your simulation, hardware and other infrastructure.


> Should we expect improvements?


Only minor ones. Minor regressions have been known, too.

I have tried quickly some small
> benchmarks (with Gromacs 4.6.3 and Gromacs 5.1) and found improvement on
> ns/day between 1 and 3% (with respect to gcc4.8.5).
>

Seems normal.


> Also, during compilation I get several warnings such as:
>
> In file included from /usr/local/openmpi-gnu/include/mpi.h:253:0,
>  from
> /home2/ncheron/Programs/gromacs-5.1/src/gromacs/utility/gmxmpi.h:59,
>  from
>
> /home2/ncheron/Programs/gromacs-5.1/src/gromacs/legacyheaders/types/commrec.h:45,
>  from
>
> /home2/ncheron/Programs/gromacs-5.1/src/gromacs/legacyheaders/gmx_ga2la.h:40,
>  from
>
> /home2/ncheron/Programs/gromacs-5.1/src/gromacs/domdec/domdec_constraints.cpp:55:
> /usr/local/openmpi-gnu/include/mpi_portable_platform.h:374:34: warning:
> invalid suffix on literal; C++11 requires a space between literal and
> string macro [-Wliteral-suffix]
>
>
> _STRINGIFY(__GNUC__)"."_STRINGIFY(__GNUC_MINOR__)"."_STRINGIFY(__GNUC_PATCHLEVEL__)
>
> I don't think it is relevant and I am not worried about it, but just wanted
> to check with you.
>

That's a known issue with older OpenMPI headers (and not a problem for
running GROMACS). It's probably fixed in the latest version of OpenMPI, as
James suggested.

Mark

Thank you.
>
> Nicolas
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[gmx-users] dssp on results of HREX simulation

[Shyno Mathew]

Dear all,

I am getting errors while using do_dssp. I am able to select the main chain
for analysis.

Following is the error I am getting:











*There are 120 residues in your selected groupdssp
cmd='/vega/cheme/users/sm3334/DSSP -i dd7XLZVM -o ddkpNsfY > /dev/null 2>
/dev/null'Reading frame   0 time 5000.000   Back Off! I just backed up
dd7XLZVM to
./#dd7XLZVM.1#---Program
do_dssp_mpi, VERSION 4.6.7Source code file:
/vega/cheme/users/sm3334/GROMACSwPLUMED/gromacs-4.6.7/src/tools/gmx_do_dssp.c,
line: 669Fatal error:Failed to execute command: Try specifying your dssp
version with the -ver option.*


Here is the location of DSSP:
/vega/cheme/users/sm3334/DSSP

As mentioned in the gromacs website/mailing list, I included the path in
the .bashrc file
I tried all the following options, but I am still getting error:

export DSSP=/vega/cheme/users/sm3334/DSSP
export DSSP=/vega/cheme/users/sm3334/GROMACSwPLUMED/gromacs
-4.6.7/src/tools/do_dssp.c
export DSSP=/vega/cheme/users/sm3334/GROMACSwPLUMED/bin/do_dssp_mpi
DSSP=/vega/cheme/users/sm3334/GROMACSwPLUMED/bin/do_dssp_mpi

Sincerely,
Shyno

-- 
Shyno Mathew
PhD Candidate
Department of Chemical Engineering
Graduate Assistant
Office of Graduate Student Affairs
The Fu Foundation School Of Engineering and Applied Science
Columbia University
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Re: [gmx-users] bond, angles and dihedrals in the topology file

[faride badalkhani]

Thank you for your great help on specbond.dat file. I defined it and I
could go ahead until Energy minimization step. I have used this minim.mdp
file


; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator= steep; Algorithm (steep = steepest descent
minimization)
emtol  = 1000.0  ; Stop minimization when the maximum force <
1000.0 kJ/mol/nm
emstep   = 0.01  ; Energy step size
nsteps= 5  ; Maximum number of (minimization) steps to
perform

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist  = 1; Frequency to update the neighbor list and
long range forces
ns_type   = grid; Method to determine neighbor list
(simple, grid)
rlist = 1.0; Cut-off for making neighbor list
(short range forces)
coulombtype= PME; Treatment of long range electrostatic
interactions
rcoulomb = 1.0; Short-range electrostatic cut-off
rvdw   = 1.0; Short-range Van der Waals cut-off
pbc = xyz ; Periodic Boundary Conditions (yes/no)


But when I run mdrun -v -deffnm em command, I get this error:

Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 1000 (which may not be possible for your system).
It stopped because the algorithm tried to make a new step whose size was too
small, or there was no change in the energy since last step. Either way, we
regard the minimization as converged to within the available machine
precision, given your starting configuration and EM parameters.

Double precision normally gives you higher accuracy, but this is often not
needed for preparing to run molecular dynamics.
You might need to increase your constraint accuracy, or turn
off constraints altogether (set constraints = none in mdp file)

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 90 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  = -2.3956744e+05
Maximum force =  1.5824519e+05 on atom 380
Norm of force =  1.7695243e+03

gcq#187: "Been There, Done It" (Beavis and Butthead)

farideh@farideh-P61A-D3:~/FARIDEH$

I changed the emtol, emstep, and nsteps for a few times. However, I
couldn't resolve this problem. Could you tell me if there is something
wrong with the minim.mdp file?

You can see all the files via:
https://www.dropbox.com/s/sq2c103yxi4mc28/Farideh.zip?dl=0

Truly yours,
Farideh

On Wed, Sep 30, 2015 at 9:13 PM, faride badalkhani <
farideh.kham...@gmail.com> wrote:

> Dear Chandan,
> Thanks a lot for your answer.
> Truly yours,
> Farideh
>
>
> On Wednesday, September 30, 2015, Chandan Choudhury 
> wrote:
> > Dear Farideh,
> >
> > You may have a look at
> >
> https://code.google.com/p/molecular-simulation-of-soft-matter/issues/detail?id=1
> > for one such example.
> >
> > Chandan
> >
> > On Wed, Sep 30, 2015 at 8:29 PM, faride badalkhani <
> > farideh.kham...@gmail.com> wrote:
> >
> >> Thank you for your time and answer. You are right, Dendrimers are
> composed
> >> of three main architectural components, a central core from which
> multiple
> >> arms emanate in an outward direction to form interior layers, and the
> >> reactive peripheral surface groups. Could you tell me if there is a
> sample
> >> specbond file for hyperbranched polymers?
> >>
> >> Regards,
> >> Farideh
> >>
> >> On Wed, Sep 30, 2015 at 6:07 PM, Justin Lemkul  wrote:
> >>
> >> >
> >> >
> >> > On 9/30/15 8:24 AM, faride badalkhani wrote:
> >> >
> >> >> I want to simulate a dendrimer (a hyperbranched polymer) in water. I
> >> have
> >> >> used the GROMOS 53A6 force field parameters, and I have done the
> >> following
> >> >> steps:
> >> >> 1- Defining new atom types that were not exist in .atp file.
> >> >> 2- Adding appropriate bonds, angles, dihedrals, and impropers into
> the
> >> >> ffbonded.itp file.
> >> >> 3- Defining nonbonded parameters in ffnonbonded.itp file according to
> >> >> GROMOS FF parameters.
> >> >> 4- Introducing residue building blocks along with [bonds], [angles],
> >> >> [impropers], and [dihedrals] in .rtp file.
> >> >>
> >> >> After using pdb2gmx I receive this command:
> >> >>
> >> >> You have successfully generated a topology from: g3n.pdb
> >> >> The CA force field and the spce water model are used.
> >> >>
> >> >> Then I define box and solvent without any problems, but there are
> many
> >> >> errors when I execute grompp command as follows:
> >> >> Error 892 [file topol.top, line 6147]
> >> >> No default G96Angle types
> >> >>
> >> >> and
> >> >> Error 904 [file topol.top, line 6159]
> >> >> No default Proper Dih. types
> >> >>
> >> >> However, when I checked these lines I understood that
> >> >> 1- many of these bonds, angles, and dihedrals are related to atoms
> that
> >> 

Re: [gmx-users] GMXLIB does not induce residuetype.dat

[João M . Damas]

The definition seems fine. In the pdb2gmx standard output, you should check
that directory is the one being opened.

If it is, please do a "ls ${GMXLIB}" and check the output, if the file is
there (and not inside the ff directory). Even though I am guessing this is
just a typo problem, and you are using "residuestype.dat" while the file is
"residuetypes.dat".

João

On Sat, Oct 3, 2015 at 4:55 AM, Barnett, James W 
wrote:

> On Thu, 2015-10-01 at 20:21 +, Ebert Maximilian wrote:
> > Dear list,
> >
> > I have my own force field working folder so I cloned the entire top
> folder to
> > no mess with the original files. I added residues to the residue type
> file to
> > add my residues to the protein group. My FF is included due to the GMXLIB
> > environmental variable but my modified residuestype.dat not. Any idea
> why?
>
> Can you give an example of how it is not included? Is there a specific
> GROMACS
> command that is not finding it, or is it something else?
>
> --
> James “Wes” Barnett, Ph.D. Candidate
> Louisiana Board of Regents Fellow
>
> Chemical and Biomolecular Engineering
> Tulane University
> 341-B Lindy Boggs Center for Energy and Biotechnology
> 6823 St. Charles Ave
> New Orleans, Louisiana 70118-5674
> jbarn...@tulane.edu
> --
> Gromacs Users mailing list
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>



-- 
João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
Tel:+351-214469613
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[gmx-users] Reminder: Farideh Khamseh wants to share "FF" with you

[Farideh via Dropbox]

Hi there,

Here's a reminder that Farideh (farideh.kham...@gmail.com) invited you to a 
shared folder called "FF."

View "FF"
https://www.dropbox.com/l/shmDslNps43wOZKf9pVB5g/invite?text=1

Enjoy!
- The Dropbox Team
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Re: [gmx-users] Install Gromacs on VirtualBox

[Simon Dürr]

After running make check I can install via sudo make install.
gmx --version returns:
http://pastebin.com/Gnx09wah

The CMakeCache file is the following:
http://pastebin.com/9wb0e1tw

Cheers,
Simon

2015-10-02 17:58 GMT-04:00 Szilárd Páll :
> Should have asked for the CMakeCache file too, could you post that to a
> file sharing service?
>
> If you happen to have GMX_SIMD other than SSE2, that would explain the
> issue - although I can't imagine why would the instruction set detection
> fail.
>
> Do you get an "illegal instruction" error if you e.g. try to run "gmx
> -version" from the build tree?
>
> Cheers,
>
> --
> Szilárd
>
> On Fri, Oct 2, 2015 at 11:12 PM, Simon Dürr 
> wrote:
>
>> Sure.
>>
>> >cat /proc/cpuinfo
>> >
>> > processor : 0
>> > vendor_id : GenuineIntel
>> > cpu family : 6
>> > model : 69
>> > model name : Intel(R) Core(TM) i7-4550U CPU @ 1.50GHz
>> > stepping : 1
>> > microcode : 0x19
>> > cpu MHz : 2095.205
>> > cache size : 6144 KB
>> > physical id : 0
>> > siblings : 1
>> > core id : 0
>> > cpu cores : 1
>> > apicid : 0
>> > initial apicid : 0
>> > fdiv_bug : no
>> > f00f_bug : no
>> > coma_bug : no
>> > fpu : yes
>> > fpu_exception : yes
>> > cpuid level : 5
>> > wp : yes
>> > flags : fpu vme de pse tsc msr pae mce cx8 apic mtrr pge mca cmov pat
>> pse36 clflush mmx fxsr sse sse2 rdtscp constant_tsc pni monitor ssse3
>> > bugs :
>> > bogomips : 4190.41
>> > clflush size : 64
>> > cache_alignment : 64
>> > address sizes : 39 bits physical, 48 bits virtual
>>
>> Cheers,
>> Simon
>>
>> 2015-10-02 5:36 GMT-04:00 Szilárd Páll :
>> > Hi,
>> >
>> > Can you share the CPUID flags shown in /proc/cpuinfo?
>> >
>> >
>> > --
>> > Szilárd
>> >
>> > On Thu, Oct 1, 2015 at 7:03 PM, Simon Dürr 
>> > wrote:
>> >
>> >> I used this:
>> >>
>> >> > cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=OFF
>> >> -DGMX_USE_RDTSCP=OFF
>> >>
>> >> But Still:
>> >> Test project /home/simon/gromacs-5.0.6/build
>> >>   Start  1: TestUtilsUnitTests
>> >>  1/15 Test  #1: TestUtilsUnitTests ...***Exception:
>> >> Illegal  0.29 sec
>> >>
>> >>   Start  2: PreprocessingTests
>> >>  2/15 Test  #2: PreprocessingTests ...***Exception:
>> >> Illegal  0.23 sec
>> >>
>> >>   Start  3: CommandLineUnitTests
>> >>  3/15 Test  #3: CommandLineUnitTests .***Exception:
>> >> Illegal  0.36 sec
>> >>
>> >>   Start  4: FFTUnitTests
>> >>  4/15 Test  #4: FFTUnitTests .***Exception:
>> >> Illegal  0.32 sec
>> >>
>> >>   Start  5: RandomUnitTests
>> >>  5/15 Test  #5: RandomUnitTests ..***Exception:
>> >> Illegal  0.25 sec
>> >>
>> >>   Start  6: OnlineHelpUnitTests
>> >>  6/15 Test  #6: OnlineHelpUnitTests ..***Exception:
>> >> Illegal  0.30 sec
>> >>
>> >>   Start  7: OptionsUnitTests
>> >>  7/15 Test  #7: OptionsUnitTests .***Exception:
>> >> Illegal  0.31 sec
>> >>
>> >>   Start  8: UtilityUnitTests
>> >>  8/15 Test  #8: UtilityUnitTests .***Exception:
>> >> Illegal  0.26 sec
>> >>
>> >>   Start  9: FileIOTests
>> >>  9/15 Test  #9: FileIOTests ..***Exception:
>> >> Illegal  0.31 sec
>> >>
>> >>   Start 10: SimdUnitTests
>> >> 10/15 Test #10: SimdUnitTests ***Exception:
>> >> Illegal  0.30 sec
>> >>
>> >>   Start 11: LegacyToolsTests
>> >> 11/15 Test #11: LegacyToolsTests .***Exception:
>> >> Illegal  0.30 sec
>> >>
>> >>   Start 12: AnalysisDataUnitTests
>> >> 12/15 Test #12: AnalysisDataUnitTests ***Exception:
>> >> Illegal  0.23 sec
>> >>
>> >>   Start 13: SelectionUnitTests
>> >> 13/15 Test #13: SelectionUnitTests ...***Exception:
>> >> Illegal  0.35 sec
>> >>
>> >>   Start 14: TrajectoryAnalysisUnitTests
>> >> 14/15 Test #14: TrajectoryAnalysisUnitTests ..***Exception:
>> >> Illegal  0.35 sec
>> >>
>> >>   Start 15: MdrunTests
>> >> 15/15 Test #15: MdrunTests ...***Exception:
>> >> Illegal  0.28 sec
>> >>
>> >>
>> >> 0% tests passed, 15 tests failed out of 15
>> >>
>> >> Label Time Summary:
>> >> GTest  =   3.63 sec
>> >> IntegrationTest=   0.81 sec
>> >> UnitTest   =   3.63 sec
>> >>
>> >> Total Test time (real) =   4.61 sec
>> >>
>> >>
>> >> The following tests FAILED:
>> >>  1 - TestUtilsUnitTests (ILLEGAL)
>> >>  2 - PreprocessingTests (ILLEGAL)
>> >>  3 - CommandLineUnitTests (ILLEGAL)
>> >>  4 - FFTUnitTests (ILLEGAL)
>> >>  5 - RandomUnitTests (ILLEGAL)
>> >>  6 - OnlineHelpUnitTests (ILLEGAL)
>> >>  7 - OptionsUnitTests (ILLEGAL)
>> >>  8 - UtilityUnitTests (ILLEGAL)
>> >>  9 - FileIOTests (ILLEGAL)
>> >> 10 - SimdUnitTests (ILLEGAL)
>> >> 11 - LegacyToolsTests (ILLEGAL)
>> >> 12 - AnalysisDataUnitTests (ILLEGAL)
>> >> 13 - SelectionUnitTests (ILLEGAL)
>> >> 14 - TrajectoryAnalysisUnitTests (ILLEGAL)
>> >> 15 - 

Re: [gmx-users] dssp on results of HREX simulation

[Shyno Mathew]

Dear all,


*I was able to fix the error mentioned in the previous message. Here is
what I did:*

wget ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-i386 -O
/vega/cheme/users/sm3334/DSSP/dssp


chmod a+x /vega/cheme/users/sm3334/DSSP/dssp

Modify the .bashrc file
export DSSP=/vega/cheme/users/sm3334/DSSP/dssp

*Now I have a question regarding the secondary structure plot. *
How can I make sure the plots shows the maximum x value, y value completely?

Please view the plot here:

https://drive.google.com/file/d/0B-CUIoblZxdlV3JFdTZFQlJUYnc/view?usp=sharing



Following are the contents of the .m2p file:
black  = no   ; Obsolete
titlefont= Times-Roman  ; A PostScript Font
titlefontsize= 300  ; Font size (pt)
legend   = yes  ; Show the legend
legendfont   = Times-Roman  ; A PostScript Font
legendfontsize   = 250  ; Font size (pt)
xbox = 1.0  ; x-size of a matrix element
ybox = 20.0 ; y-size of a matrix element
matrixspacing= 30.0 ; Space between 2 matrices
xoffset  = 0.0  ; Between matrix and bounding box
yoffset  = 0.0  ; Between matrix and bounding box
x-major  = 1000 ; Major ticks on x axis every ..
frames
x-minor  = 500  ; Id. Minor ticks
x-firstmajor = 5000 ; First frame for major tick
x-majorat0   = no   ; Major tick at first frame
x-majorticklen   = 40.0  ; x-majorticklength
x-minorticklen   = 20.0  ; x-minorticklength
x-label  =  ; Used when there is none in the
.xpm
x-fontsize   = 250  ; Font size (pt)
x-font   = Times-Roman  ; A PostScript Font
x-tickfontsize   = 200  ; Font size (pt)
x-tickfont   = Helvetica; A PostScript Font
y-major  = 20
y-minor  = 10
y-firstmajor = 0
y-majorat0   = no
y-majorticklen   = 40.0
y-minorticklen   = 20.0
y-label  =
y-fontsize   = 250
y-font   = Times-Roman
y-tickfontsize   = 200
y-tickfont   = Helvetica

thanks,

Shyno



On Sat, Oct 3, 2015 at 8:48 PM, Shyno Mathew  wrote:

> Dear all,
>
>
> wget ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-i386 -O
> /vega/cheme/users/sm3334/DSSP/dssp
>
> chmod a+x /vega/cheme/users/sm3334/DSSP/dssp
>
> Modify the .bashrc file
> export DSSP=/vega/cheme/users/sm3334/DSSP/dssp
>
> *Now I have a question regarding the secondary structure plot. *
> How can I make sure the plots shows the maximum x value, y value
> completely?
> Please view the plot here:
>
> https://drive.google.com/file/d/0B-CUIoblZxdlV3JFdTZFQlJUYnc/view?usp=sharing
>
>
> Following are the contents of the .m2p file:
> black  = no   ; Obsolete
> titlefont= Times-Roman  ; A PostScript Font
> titlefontsize= 300  ; Font size (pt)
> legend   = yes  ; Show the legend
> legendfont   = Times-Roman  ; A PostScript Font
> legendfontsize   = 250  ; Font size (pt)
> xbox = 1.0  ; x-size of a matrix element
> ybox = 20.0 ; y-size of a matrix element
> matrixspacing= 30.0 ; Space between 2 matrices
> xoffset  = 0.0  ; Between matrix and bounding box
> yoffset  = 0.0  ; Between matrix and bounding box
> x-major  = 1000 ; Major ticks on x axis every ..
> frames
> x-minor  = 500  ; Id. Minor ticks
> x-firstmajor = 5000 ; First frame for major tick
> x-majorat0   = no   ; Major tick at first frame
> x-majorticklen   = 40.0  ; x-majorticklength
> x-minorticklen   = 20.0  ; x-minorticklength
> x-label  =  ; Used when there is none in the
> .xpm
> x-fontsize   = 250  ; Font size (pt)
> x-font   = Times-Roman  ; A PostScript Font
> x-tickfontsize   = 200  ; Font size (pt)
> x-tickfont   = Helvetica; A PostScript Font
> y-major  = 20
> y-minor  = 10
> y-firstmajor = 0
> y-majorat0   = no
> y-majorticklen   = 40.0
> y-minorticklen   = 20.0
> y-label  =
> y-fontsize   = 250
> y-font   = Times-Roman
> y-tickfontsize   = 200
> y-tickfont   = Helvetica
>
> thanks,
> Shyno
>
> On Sat, Oct 3, 2015 at 1:56 PM, Shyno Mathew  wrote:
>
>> Dear all,
>>
>> I am getting errors while using do_dssp. 

Re: [gmx-users] dssp on results of HREX simulation

[Shyno Mathew]

Dear all,


wget ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-i386 -O
/vega/cheme/users/sm3334/DSSP/dssp

chmod a+x /vega/cheme/users/sm3334/DSSP/dssp

Modify the .bashrc file
export DSSP=/vega/cheme/users/sm3334/DSSP/dssp

*Now I have a question regarding the secondary structure plot. *
How can I make sure the plots shows the maximum x value, y value completely?
Please view the plot here:
https://drive.google.com/file/d/0B-CUIoblZxdlV3JFdTZFQlJUYnc/view?usp=sharing

Following are the contents of the .m2p file:
black  = no   ; Obsolete
titlefont= Times-Roman  ; A PostScript Font
titlefontsize= 300  ; Font size (pt)
legend   = yes  ; Show the legend
legendfont   = Times-Roman  ; A PostScript Font
legendfontsize   = 250  ; Font size (pt)
xbox = 1.0  ; x-size of a matrix element
ybox = 20.0 ; y-size of a matrix element
matrixspacing= 30.0 ; Space between 2 matrices
xoffset  = 0.0  ; Between matrix and bounding box
yoffset  = 0.0  ; Between matrix and bounding box
x-major  = 1000 ; Major ticks on x axis every ..
frames
x-minor  = 500  ; Id. Minor ticks
x-firstmajor = 5000 ; First frame for major tick
x-majorat0   = no   ; Major tick at first frame
x-majorticklen   = 40.0  ; x-majorticklength
x-minorticklen   = 20.0  ; x-minorticklength
x-label  =  ; Used when there is none in the
.xpm
x-fontsize   = 250  ; Font size (pt)
x-font   = Times-Roman  ; A PostScript Font
x-tickfontsize   = 200  ; Font size (pt)
x-tickfont   = Helvetica; A PostScript Font
y-major  = 20
y-minor  = 10
y-firstmajor = 0
y-majorat0   = no
y-majorticklen   = 40.0
y-minorticklen   = 20.0
y-label  =
y-fontsize   = 250
y-font   = Times-Roman
y-tickfontsize   = 200
y-tickfont   = Helvetica

thanks,
Shyno

On Sat, Oct 3, 2015 at 1:56 PM, Shyno Mathew  wrote:

> Dear all,
>
> I am getting errors while using do_dssp. I am able to select the main
> chain for analysis.
>
> Following is the error I am getting:
>
>
>
>
>
>
>
>
>
>
>
> *There are 120 residues in your selected groupdssp
> cmd='/vega/cheme/users/sm3334/DSSP -i dd7XLZVM -o ddkpNsfY > /dev/null 2>
> /dev/null'Reading frame   0 time 5000.000   Back Off! I just backed up
> dd7XLZVM to
> ./#dd7XLZVM.1#---Program
> do_dssp_mpi, VERSION 4.6.7Source code file:
> /vega/cheme/users/sm3334/GROMACSwPLUMED/gromacs-4.6.7/src/tools/gmx_do_dssp.c,
> line: 669Fatal error:Failed to execute command: Try specifying your dssp
> version with the -ver option.*
>
>
> Here is the location of DSSP:
> /vega/cheme/users/sm3334/DSSP
>
> As mentioned in the gromacs website/mailing list, I included the path in
> the .bashrc file
> I tried all the following options, but I am still getting error:
>
> export DSSP=/vega/cheme/users/sm3334/DSSP
> export DSSP=/vega/cheme/users/sm3334/GROMACSwPLUMED/gromacs
> -4.6.7/src/tools/do_dssp.c
> export DSSP=/vega/cheme/users/sm3334/GROMACSwPLUMED/bin/do_dssp_mpi
> DSSP=/vega/cheme/users/sm3334/GROMACSwPLUMED/bin/do_dssp_mpi
>
> Sincerely,
> Shyno
>
> --
> Shyno Mathew
> PhD Candidate
> Department of Chemical Engineering
> Graduate Assistant
> Office of Graduate Student Affairs
> The Fu Foundation School Of Engineering and Applied Science
> Columbia University
>



-- 
Shyno Mathew
PhD Candidate
Department of Chemical Engineering
Graduate Assistant
Office of Graduate Student Affairs
The Fu Foundation School Of Engineering and Applied Science
Columbia University

On Sat, Oct 3, 2015 at 1:56 PM, Shyno Mathew  wrote:

> Dear all,
>
> I am getting errors while using do_dssp. I am able to select the main
> chain for analysis.
>
> Following is the error I am getting:
>
>
>
>
>
>
>
>
>
>
>
> *There are 120 residues in your selected groupdssp
> cmd='/vega/cheme/users/sm3334/DSSP -i dd7XLZVM -o ddkpNsfY > /dev/null 2>
> /dev/null'Reading frame   0 time 5000.000   Back Off! I just backed up
> dd7XLZVM to
> ./#dd7XLZVM.1#---Program
> do_dssp_mpi, VERSION 4.6.7Source code file:
> /vega/cheme/users/sm3334/GROMACSwPLUMED/gromacs-4.6.7/src/tools/gmx_do_dssp.c,
> line: 669Fatal error:Failed to execute command: Try specifying your dssp
> version with the -ver option.*
>
>
> Here is the location of DSSP:
> /vega/cheme/users/sm3334/DSSP
>
> As mentioned in the gromacs website/mailing list, I included the path in
> the .bashrc file
> I tried all the following options, 

Re: [gmx-users] automate gmx sasa

[Teemu Murtola]

Hi,

On Sat, Oct 3, 2015 at 8:18 AM Andrei Neamtu  wrote:

> In previous versions if one wants to provide in a script an automatic
>
> echo 'two indexes' | g_sas .
>
> it was fairly easy
>
> In version 5 gmx sasa expects EOF (Ctrl D) character to end up the
> selection.
>
> How can one provide automatic selection of index groups in version 5?
> probably it is a basic Bash question but I am stucked in here for several
> hours! :)


It is even easier in Gromacs 5; there is no need for the echo at all. ;) If
you want to select groups 0 and 1, you can just use

  gmx sasa -surface 0 -output 1 ...

And the same works for arbitrary selections; you just need to be careful
with quoting. See

  gmx help selections cmdline

for all the alternatives, including how to read more complex selections
from a file.

Best regards,
Teemu
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