Re: [gmx-users] Trajectory has one atom less

[Teemu Murtola]

What atoms do you have in your groups A and B? Without the -fgroup option
(new in version 2016), Gromacs tools only support trajectories that contain
the first N atoms from the topology file. The trajectory file does not
contain atom indices.

So if your groups have other atoms than 1-18109, you cannot use a
trajectory that contains only them together with the original topology.
Prior to 2016, you can possibly create a topology for your subset with
convert-tpr, and also update your index file to match the new topology.

Best regards,
Teemu

On Fri, Aug 5, 2016, 10:16 Alexander Alexander 
wrote:

> Dear gromacs user,
>
> From my case.xtc I am just interested in two groups (A and B) of it to have
> in my "case_noPBC.xtc", so, I make a case.ndx file to choose them together
> in "gmx trjconv ... -f case.xtc ... -n case.ndx ...". In all of the above
> steps I see the total atoms number of two groups together is 18109 which is
> expectedly the sum of the two required groups atoms (A 109 + B 18000).
> But when I invoke "gmx pairdist -f case_noPBC.xtc ... -ref B -sel A ...
> -selgrouping ...", an unknown inconsistency happens just because of one
> atom difference as below:
>
> Inconsistency in user input:
> Trajectory has less atoms (18109) than what is required for evaluating the
> provided selections (atoms up to index 18110 are required).
>
> Do you know why, please?
> Thanks
> Alex
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Re: [gmx-users] problem compiling template

[Teemu Murtola]

Hi,

On Fri, Jun 10, 2016 at 8:51 PM Michael Brunsteiner <
michael.brunstei...@tugraz.at> wrote:

> I just installed a pristine gromacs 5.1.2, on my lubuntu 64bit vanilla
> desktop, as in:
>
> prompt> cmake .. -DGMX_GPU=ON
> -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-5.1.2-bin -DGMX_BUILD_OWN_FFTW=ON
> prompt> make -j 6
> prompt> make install
>
> this worked ... then if I go to the resulting
> /usr/local/gromacs-5.1.2-bin/share/gromacs/template
> and say (as recommended in the README file there)
>
> prompt> . /usr/local/gromacs-5.1.2-bin/bin/GMXRC.bash
> prompt> cmake .
>
> I get:
>
> prompt> make
> Linking CXX executable template
> /usr/bin/ld: cannot find -lgmxfftw
> collect2: error: ld returned 1 exit status
> make[2]: *** [template] Error 1
> make[1]: *** [CMakeFiles/template.dir/all] Error 2
> make: *** [all] Error 2
>

Yes, this is a documented limitation at <
http://manual.gromacs.org/documentation/5.1.2/doxygen/html-user/page_usinglibrary.xhtml>.
You can either use the Makefile.pkg installed with the template (if you
have pkg-config), or you can build Gromacs with GMX_BUILD_OWN_FFTW=OFF.

if I do the same not in the installation but in the distribution
> directory then I get:
>
> prompt> make
> [100%] Building CXX object CMakeFiles/template.dir/template.o
> /usr/local/software/gromacs-5.1.2/share/template/template.cpp:38:40:
> fatal error: gromacs/trajectoryanalysis.h: No such file or directory
>   #include 
>  ^
> compilation terminated.
>

Most likely, you should install a separate gromacs-dev package or similar
from your distribution, since the headers might be packaged in such.
Ideally, the template should also get installed from the development
package, since it is not really useful without.

Best regards,
Teemu
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Re: [gmx-users] distance between two groups

[Teemu Murtola]

To calculate the distances from your ligand to multiple residues, a much
better way than a loop over multiple gmx distance calls would be to use gmx
pairdist, which should be able to calculate the distances you want in one
go.

Teemu

On Wed, Jun 8, 2016, 03:35 Justin Lemkul  wrote:

>
>
> On 6/7/16 8:12 PM, Qasim Pars wrote:
> > Dear gmx users,
> >
> > How can I calculate the distance between the central of mass of two
> groups
> > ( for example: ligand and protein)? As far as I understand gmx mindist
> does
> > not do it.
> >
>
> This is what gmx distance does.  The exact syntax is given in an example on
> http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0#g_dist
>
> > And is that possible to calculate the distance per residue as a function
> of
> > time? I would like to calculate the distance between ligand and each
> > residue as a function of time.
> >
>
> Invoke a series of calls to gmx distance with appropriate index groups.
> Otherwise, to get the time-average, you can use gmx mdmat, but that will
> be an
> average minimum distance, not an average COM distance.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
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Re: [gmx-users] 'gmx rdf' and 'gmx select' questions

[Teemu Murtola]

Hi,

On Fri, May 27, 2016 at 9:19 PM Eric Smoll  wrote:

> (1) What is the difference between 'res' and 'mol' position specifiers? I
> assume 'res' refers the set of all atoms that have the same gro-file
> residue-number *and* residue name. Is this correct? What does 'mol'
> indicate?
>

You are correct about 'res': it refers to a residue, which is typically
inferred from residue numbers and names. 'mol' stands for molecule, and can
be used with .tpr input, where it refers to molecules specified in the
topology.


> (2) 'gmx rdf' in Gromacs 5.1.2 allows the user to specify the '-ref' and
> '-sel' groups with 'gmx select' style selection strings on the commandline.
> It appears that there is an option to provide selections from a file with
> the '-sf' flag. 'gmx help selections cmdline' suggests that  '-sf file.dat'
> should be provided as an argument to a selection. If the '-ref' and '-sel'
> groups are not identical, can this flag be used twice with two different
> files? For example:
>
> gmx rdf -ref -sf file1.dat -sel -sf file2.dat
>
> Is this correct?
>

Yes, this is correct. Also if the selections are identical, you can still
use the -sf flag twice, with the same file both times. It is also possible
to put both selections into the same file and just use -sf once, after both
options (like -ref -sel -sf file.dat).

Best regards,
Teemu
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Re: [gmx-users] Invalid selection near '&' syntax error -- easy way to avoid?

[Teemu Murtola]

Hi,

On Tue, May 24, 2016 at 8:22 PM Christopher Neale <
chris.ne...@alum.utoronto.ca> wrote:

> Thank you for the help. After a but of fiddling your suggestion did lead
> to the solution:
>
> echo -e "\"group_&_1\"\n\"group_&_2\" | gmx ...
>
> Is this really what you had in mind?


That will work, although you will have less escaping if you use single
quotes like

echo -e '"group_&_1"\n"group_&_2"' | gmx ...

or

gmx rdf -ref '"group_&_1"' -sel '"group_&_2"' ...


> If so, I think I'll still submit a feature request since I doubt we can
> expect all users to come up with that on their own.


This is documented in the help that you can access with 'help syntax' in
the interactive selection prompt, or, e.g., here: <
http://manual.gromacs.org/documentation/5.1.2/onlinehelp/selections.html#selection-syntax
>

"Strings that contain non-alphanumeric characters should be enclosed in
double quotes as in the examples."

It is impractical to write a parser that can guess what the user tries to
mean with all kinds of weird strings that can have other meanings; what
would you, for example, expect to happen if you create an index group named
"x-y<3" or "resname GLY", and then just type that as the selection, without
quotes? Treating some punctuation characters differently from others would
not provide a very intuitive syntax, either...

I think a reasonable resolution for such a feature request would be to add
an explicit example of selecting such a group in the selection examples.

And if you think make_ndx creates groups that are inconveniently named and
you cannot robustly rename them, you can use gmx select to create exactly
the same groups (with the exception of the splitting options in make_ndx),
and also provide names for them in one go.


> Also, interactive selection is not available with all tools (see e.g. gmx
> traj).
>

I'm not sure what you are referring to with this. Yes, the selection syntax
is not available for all tools, and that is a valid reason to use index
files. But for tools that support them, I think it is still clearer to pass
the selections as command-line arguments instead of piping them. And there
are cases where it is very difficult to pipe the proper selections.

Best regards,
Teemu
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Re: [gmx-users] Invalid selection near '&' syntax error -- easy way to avoid?

[Teemu Murtola]

Hi,

On Sat, May 21, 2016 at 1:09 AM Christopher Neale <
chris.ne...@alum.utoronto.ca> wrote:

> I find that gmx make_ndx will create groups with names that have
> ampersands in them and that this complicates piping the group name back
> into an analysis tool. I have included an example below. There is an
> obvious solution with sed to rename the group in the .ndx file after
> creation (this is what I am doing now). However, I'm thinking about posting
> a redmine feature request since ideally I think the tool will not require
> an external step for name-based selection and I wanted to ask here first
> just in case I am missing something.
>

Three points:

   - If you need to select a group with non-alphanumeric names in gmx rdf
   or other selection-enabled tools, you simply need to put the group name in
   double quotes.
   - There is no need to pipe the selections to gmx rdf. You can simply
   write "gmx rdf -ref '' -sel ''", which at least to me is
   much more obvious.
   - There can be cases where writing an intermediate index file is
   justified, but for one-off groups, it is easier to just specify them
   directly to gmx rdf or other tools as a static selection like "name A B and
   resname 1 to 64", passed directly to the command-line options. Or if you
   need to reuse the same selection multiple times, you can put it in a file
   and pass it using -sf (like -ref -sf myselection.txt, or even -ref -sel -sf
   myselection.txt, which reads both selections from the same file).

Best regards,
Teemu
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Re: [gmx-users] gmx distance

[Teemu Murtola]

Hi,

On Mon, May 2, 2016 at 10:04 AM  wrote:

> I want to calculate distances between two groups center of masses in z
> direction. I use the gmx distance command:
> " gmx distance -f all.xtc -s e-.25.tpr -n index.ndx -select ' com of group
> "PROT" plus com of group "NPROT"'  -oxyz distxyz.xvg"
>
> But in my output files, I don't have distxyz.xvg file.


Please provide you Gromacs version with such queries. There has been a bug
in gmx distance that was fixed for 5.0.6 which could cause exactly this
behavior (see 4843 ).

Best regards,
Teemu
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Re: [gmx-users] Cannot write trajectory frame

[Teemu Murtola]

This is true, but unfortunately recent versions of Gromacs may not properly
use the support present in 32-bit operating systems because of
http://redmine.gromacs.org/issues/1834.

You haven't specified your Gromacs version or anything else about your
environment, so there is not much more we can guess.

Best regards,
Teemu

On Sun, Jan 3, 2016, 15:25 Mark Abraham  wrote:

> Hi,
>
> Most modern file systems do not have such a limitation, and all modern
> operating systems support at least one of them, so all you need to do is
> have disks formatted accordingly.
>
> Mark
>
> On Sun, Jan 3, 2016 at 1:22 PM masoud keramati 
> wrote:
>
> > yes that's true .. and i'm searching for a way to remove this limitation
> > but ,what you mean by "get a real one" ?
> >
> > On Sun, Jan 3, 2016 at 2:02 PM, Mark Abraham 
> > wrote:
> >
> > > Hi,
> > >
> > > As you've read in the archive, this depends solely on your file system.
> > Get
> > > a real one! :-)
> > >
> > > Mark
> > >
> > > On Sun, 3 Jan 2016 11:17 masoud keramati 
> > > wrote:
> > >
> > > > Hello and happy new year!
> > > >
> > > > i have seen this issue in archive,
> > > > the problem is with .trr size that can not reach more than 2GB and i
> > > think
> > > > that is my problem too.
> > > > my question is ,can i write .trr file with another file name and then
> > > > finally append them?
> > > > is it a true way?
> > > >
> > > >
> > > > tnx for your responding ;-)
> > > > --
> > > > Gromacs Users mailing list
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> > > > posting!
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> > > >
> > > --
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Re: [gmx-users] GMX analysis (g_gyrate) cannot open just the md.trr file

[Teemu Murtola]

http://redmine.gromacs.org/issues/1834 is possibly related. But there is
not enough information in that issue to understand what exactly is wrong,
or for providing an actual fix.

Best regards,
Teemu

On Sun, Nov 29, 2015, 17:20 Sajjad Kavyani  wrote:

> Hi,
> Thanks so much for the response.
> The resulted files were copied from an external NTFS HD to the ext4 file
> system (UBUNTU installation partition). Reading from both terminates the
> analysis.
> I can read and analyse the NVT, NPT or em.trr files (other .trr or .xtc
> files), but as you mentioned the problem might be with >2GB condition.
> And it is noteworthy that the VMD can easily open and read them (the md.trr
> files)!!
>
> So where is the problem? Could you please help me to find and solve that?
>
> -Sajjad
>
> On Sun, Nov 29, 2015 at 6:07 PM, Justin Lemkul  wrote:
>
> >
> >
> > On 11/29/15 9:28 AM, Erik Marklund wrote:
> >
> >> Dear Sajjad,
> >>
> >> As you can see, you don’t have a file called md.trr. Provide another
> file
> >> with the -f option.
> >>
> >>
> > It's there, along with md.xtc, but both are > 2 GB, so the file system
> > probably cannot handle files of that size given that neither can be
> opened.
> >
> > -Justin
> >
> >
> > Kind regards,
> >> Erik
> >>
> >> On 29 Nov 2015, at 11:45, Sajjad Kavyani 
> >>> wrote:
> >>>
> >>> Dear all,
> >>> Recently, I simulated a system with gromacs 5.0.4. But now, when I am
> >>> trying to run a g_gyrate (or any other) a fatal error appear with:
> >>>
> >>> Can not open file:
> >>> md.trr
> >>> For more information and tips for troubleshooting, please check the
> >>> GROMACS
> >>> website...
> >>>
> >>> This is also happened with the .xtc file.
> >>>
> >>> The ls -l output :
> >>>
> >>> -rw-r--r-- 1 sajjad sajjad780 Aug  2 11:03 em.edr
> >>> -rw-r--r-- 1 sajjad sajjad 412160 Aug  2 11:03 em.gro
> >>> -rw-r--r-- 1 sajjad sajjad  15619 Aug  2 11:03 em.log
> >>> -rw-r--r-- 1 sajjad sajjad   3103 Aug  2 11:03 em.mdp
> >>> -rw-r--r-- 1 sajjad sajjad   3104 Aug  2 11:03 em.mdp~
> >>> -rw-r--r-- 1 sajjad sajjad 262120 Aug  2 11:03 em.tpr
> >>> -rw-r--r-- 1 sajjad sajjad 110016 Aug  2 11:03 em.trr
> >>> -rw-r--r-- 1 sajjad sajjad  17105 Aug  2 11:03 G5_box.gro
> >>> -rw-r--r-- 1 sajjad sajjad 104065 Aug  2 11:03 G5_copy.itp
> >>> -rw-r--r-- 1 sajjad sajjad  17105 Aug  2 11:03 G5.gro
> >>> -rw-r--r-- 1 sajjad sajjad 104065 Aug  2 11:07 G5.itp
> >>> -rw-r--r-- 1 sajjad sajjad 104065 Aug  2 11:03 G5.itp~
> >>> -rw-r--r-- 1 sajjad sajjad 636064 Aug  2 11:07 G5.ods
> >>> -rw-r--r-- 1 sajjad sajjad 412160 Aug  2 11:03 G5_water.gro
> >>> -rw-r--r-- 1 sajjad sajjad 886305 Aug  2 11:03 gyrate2.xvg
> >>> -rw-r--r-- 1 sajjad sajjad 653382 Aug  2 11:03 gyrate2.xvg~
> >>> -rw-r--r-- 1 sajjad sajjad 141214 Aug  2 11:03 index.ndx
> >>> -rw-r--r-- 1 sajjad sajjad153 Aug  2 11:03 ion.itp
> >>> -rw-r--r-- 1 sajjad sajjad940 Aug  2 11:03 ions.mdp
> >>> -rw-r--r-- 1 sajjad sajjad  50981 Aug  2 11:03 martini_v2.2.itp~
> >>> -rw-r--r-- 1 sajjad sajjad  50994 Aug  2 11:03
> >>> martini_v2.2_P1P5mod.itp
> >>> -rw-r--r-- 1 sajjad sajjad  50917 Aug  2 11:03
> >>> martini_v2.2_P1P5mod.itp~
> >>> -rw-r--r-- 1 sajjad sajjad 221556 Aug  2 11:03 md.cpt
> >>> -rw-r--r-- 1 sajjad sajjad   38727904 Aug  2 11:07 md.edr
> >>> -rw-r--r-- 1 sajjad sajjad 631991 Aug  2 11:03 md_extract.gro
> >>> -rw-r--r-- 1 sajjad sajjad 631952 Aug  2 11:03 md.gro
> >>> -rw-r--r-- 1 sajjad sajjad   33962116 Aug  2 11:03 md.log
> >>> -rw-r--r-- 1 sajjad sajjad   4021 Aug  2 11:03 md.mdp
> >>> -rw-r--r-- 1 sajjad sajjad   4021 Aug  2 11:07 md.mdp~
> >>> -rw-r--r-- 1 sajjad sajjad  11575 Aug  2 11:03 mdout.mdp
> >>> -rw-r--r-- 1 sajjad sajjad 221556 Aug  2 11:03 md_prev.cpt
> >>> -rw-r--r-- 1 sajjad sajjad 262036 Aug  2 11:03 md.tpr
> >>> -rw-r--r-- 1 sajjad sajjad 3301099032 Aug  2 11:07 md.trr
> >>> -rw-r--r-- 1 sajjad sajjad 3540368244 Aug  2 11:07 md.xtc
> >>> -rw-r--r-- 1 sajjad sajjad 221556 Aug  2 11:03 npt.cpt
> >>> -rw-r--r-- 1 sajjad sajjad 414904 Aug  2 11:03 npt.edr
> >>> -rw-r--r-- 1 sajjad sajjad 631952 Aug  2 11:03 npt.gro
> >>> -rw-r--r-- 1 sajjad sajjad 379243 Aug  2 11:07 npt.log
> >>> -rw-r--r-- 1 sajjad sajjad   4058 Aug  2 11:07 npt.mdp
> >>> -rw-r--r-- 1 sajjad sajjad   4057 Aug  2 11:03 npt.mdp~
> >>> -rw-r--r-- 1 sajjad sajjad 221556 Aug  2 11:03 npt_prev.cpt
> >>> -rw-r--r-- 1 sajjad sajjad 262120 Aug  2 11:03 npt.tpr
> >>> -rw-r--r-- 1 sajjad sajjad   35405832 Aug  2 11:03 npt.trr
> >>> -rw-r--r-- 1 sajjad sajjad   37885780 Aug  2 11:03 npt.xtc
> >>> -rw-r--r-- 1 sajjad sajjad 221300 Aug  2 11:03 nvt.cpt
> >>> -rw-r--r-- 1 sajjad sajjad  44960 Aug  2 11:07 nvt.edr
> >>> -rw-r--r-- 1 sajjad sajjad 631952 Aug  2 11:03 nvt.gro
> >>> -rw-r--r-- 1 sajjad sajjad  63990 Aug  2 11:03 nvt.log
> 

Re: [gmx-users] gmx sasa output confusion

[Teemu Murtola]

That was also part of the bug fix: with the fixed version, you should get
the same number of rows and the same areas on each row, but the first
column will have the correct residue numbers.

Teemu

On Thu, Nov 5, 2015, 19:12 Francesco Carbone <fra.carbo...@gmail.com> wrote:

> Thank you for your reply,
> Everything makes sens, the only thing that I still haven't understood is
> the reason for which I have multiple lines for the residues.
> Are those atoms? then why are there, if I want the single residue?
>
> Regards,
>
> Fra
>
> On 5 November 2015 at 16:33, Teemu Murtola <teemu.murt...@gmail.com>
> wrote:
>
> > Hi,
> >
> > The issue with incorrect legends and X axis has been fixed in 5.0.6.
> >
> > As for the four columns, you are asking gmx sasa to calculate the same
> > numbers twice, so you get them twice: according to gmx sasa -h, the area
> of
> > -surface selection is always calculated, and -output (which is optional)
> > just specifies extra groups on top of this to calculate the area for.
> >
> > As for the legends for the extra columns, no one has just had the time to
> > implement nice output for all possible cases.
> >
> > Best regards,
> > Teemu
> >
> > On Wed, Nov 4, 2015 at 7:20 PM Francesco Carbone <fra.carbo...@gmail.com
> >
> > wrote:
> >
> > > Good afternoon,
> > > I calculated the residue area (-or) over my trajectory, but I have
> > trouble
> > > understanding the output.
> > >
> > > With gromacs 4.6 I obtain a clean file:
> > >
> > >   residue   value   standard dev
> > > 27 4.654781.19505
> > > 280.990566   0.966795
> > > 29 1.77202   0.629798
> > > 300.389708   0.374724
> > > 31   0  0
> > > 32   0  0
> > > 33   0  0
> > > 34   0  0
> > >
> > > with gromacs 5 instead I see odd things:
> > >
> > > 1) the titles between -or and -oa results are swapped.
> > > -or gives "title "Area per atom over the trajectory"", while -oa "title
> > > "Area per residue over the trajectory"".
> > > xaxis is set correct (res with -or and atom with -oa)
> > >
> > > 2)  I have 18 times the same residues plus 4 columns with only s0 and
> s1
> > > with legend ("Average" and "Standard dev")
> > >
> > > I'm using this command:
> > >
> > > gmx sasa -s file.tpr -f file.xtc -n file.ndx -or ciao5.xvg -surface
> > Protein
> > > -output Protein -dt 5000
> > >
> > > Is there some changes I have missed ?
> > >
> > --
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Re: [gmx-users] gmx sasa output confusion

[Teemu Murtola]

Hi,

The issue with incorrect legends and X axis has been fixed in 5.0.6.

As for the four columns, you are asking gmx sasa to calculate the same
numbers twice, so you get them twice: according to gmx sasa -h, the area of
-surface selection is always calculated, and -output (which is optional)
just specifies extra groups on top of this to calculate the area for.

As for the legends for the extra columns, no one has just had the time to
implement nice output for all possible cases.

Best regards,
Teemu

On Wed, Nov 4, 2015 at 7:20 PM Francesco Carbone 
wrote:

> Good afternoon,
> I calculated the residue area (-or) over my trajectory, but I have trouble
> understanding the output.
>
> With gromacs 4.6 I obtain a clean file:
>
>   residue   value   standard dev
> 27 4.654781.19505
> 280.990566   0.966795
> 29 1.77202   0.629798
> 300.389708   0.374724
> 31   0  0
> 32   0  0
> 33   0  0
> 34   0  0
>
> with gromacs 5 instead I see odd things:
>
> 1) the titles between -or and -oa results are swapped.
> -or gives "title "Area per atom over the trajectory"", while -oa "title
> "Area per residue over the trajectory"".
> xaxis is set correct (res with -or and atom with -oa)
>
> 2)  I have 18 times the same residues plus 4 columns with only s0 and s1
> with legend ("Average" and "Standard dev")
>
> I'm using this command:
>
> gmx sasa -s file.tpr -f file.xtc -n file.ndx -or ciao5.xvg -surface Protein
> -output Protein -dt 5000
>
> Is there some changes I have missed ?
>
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Re: [gmx-users] gmx distance

[Teemu Murtola]

If you do not specify any other options, this will give you these minimum
distance from the com to the K atoms. If you specify the com as the -ref
selection and the K atoms as -sel, then adding -selgrouping none should
give you the 97 distances you want.

Best regards,
Teemu

On Mon, Oct 19, 2015, 12:37 Deva Priya <devapriyac...@gmail.com> wrote:

> Hello Teemu,
>
> Thanks for your response. I updated to GMX 5.1 and tried to use gmx
> pairdist.
>
> There are few examples of using pairdist correctly. So, please forgive my
> question.
>
> I tried to specify "name K" and on the second option, "com of group 13".
> This results in a distance file, which I am not sure is what I want.
>
> Do I need to specify each atom number of K with com of group 13 and then
> average the distances? or is there an easier way to do this? I have 97 K
> atoms in my simulation.
>
> Thanks again for your help.
>
> Deva
>
>
> On Mon, Oct 19, 2015 at 12:40 AM, Teemu Murtola <teemu.murt...@gmail.com>
> wrote:
>
> > No, this does not calculate what you want. If you had an even number of K
> > atoms, it would even refuse to calculate. What you get is the distance
> > between the first and second K, third and fourth K, and so on, and
> finally
> > between the last K and the com.
> >
> > You can get the individual distances with gmx pairdist (from Gromacs
> 5.1),
> > and average them yourself.
> >
> > Best regards,
> > Teemu
> >
> > On Mon, Oct 19, 2015, 00:53 Deva Priya <devapriyac...@gmail.com> wrote:
> >
> > > I think I figured it out.
> > >
> > > It should be selected as "name K plus com of group XX". Running the
> > command
> > > with -oall confirms that it calculates distance for each atom with
> name K
> > > and com of other group.
> > >
> > > I would still appreciate any comment, if this is a faulty solution.
> > >
> > > Thanks,
> > >
> > >
> > > On Sun, Oct 18, 2015 at 4:42 PM, Deva Priya <devapriyac...@gmail.com>
> > > wrote:
> > >
> > > > Hello,
> > > >
> > > > I am trying to set up a calculation to measure distance between the
> > > > following groups.
> > > >
> > > > group A = center of mass of a selection of atoms
> > > > group B = atoms of another group (all K atoms)
> > > >
> > > > Is it possible to specify the command such that the distance output
> is
> > > the
> > > > average distance between group A and each atom of group B. So, the
> > answer
> > > > could be reported as average distance between all K atoms and center
> of
> > > > mass of group B.
> > > >
> > > > Any advice is greatly appreciated.
> > > >
> > > > Thanks,
> > > > Deva
> > > >
> > > >
> > > --
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> > > posting!
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> > >
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Re: [gmx-users] gmx distance

[Teemu Murtola]

No, this does not calculate what you want. If you had an even number of K
atoms, it would even refuse to calculate. What you get is the distance
between the first and second K, third and fourth K, and so on, and finally
between the last K and the com.

You can get the individual distances with gmx pairdist (from Gromacs 5.1),
and average them yourself.

Best regards,
Teemu

On Mon, Oct 19, 2015, 00:53 Deva Priya  wrote:

> I think I figured it out.
>
> It should be selected as "name K plus com of group XX". Running the command
> with -oall confirms that it calculates distance for each atom with name K
> and com of other group.
>
> I would still appreciate any comment, if this is a faulty solution.
>
> Thanks,
>
>
> On Sun, Oct 18, 2015 at 4:42 PM, Deva Priya 
> wrote:
>
> > Hello,
> >
> > I am trying to set up a calculation to measure distance between the
> > following groups.
> >
> > group A = center of mass of a selection of atoms
> > group B = atoms of another group (all K atoms)
> >
> > Is it possible to specify the command such that the distance output is
> the
> > average distance between group A and each atom of group B. So, the answer
> > could be reported as average distance between all K atoms and center of
> > mass of group B.
> >
> > Any advice is greatly appreciated.
> >
> > Thanks,
> > Deva
> >
> >
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Re: [gmx-users] ligand contact map

[Teemu Murtola]

Hi,

At least for some definitions of contacts, you can get what you want with
suitable use of gmx select. With a suitable selection that selects residues
that you consider to be in contact, and depending on what you want, -on,
-om, or -of should give you something useful.

Best regards,
Teemu

On Fri, Oct 16, 2015, 09:05 Albert  wrote:

> Hello:
>
> I would like to calculate which residues does my ligand contact with
> during the MD simulation. I am just wondering is there any module for
> calculating ligand contact map?
>
> Thank you very much
>
> Albert
> --
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Re: [gmx-users] Analysis of old xtc file using gromacs-5 tools

[Teemu Murtola]

Thanks for the clarification. I updated the Redmine issue (
http://redmine.gromacs.org/issues/1834) with a summary and next steps. I
unfortunately do not have access to various systems to test the issue, but
I put some guesses on the possible reasons in the issue.

Best regards,
Teemu

On Tue, Oct 6, 2015, 07:37 Venkat Reddy <venkat...@gmail.com> wrote:

> Hi,
> Sorry for the confusion. Now I have generated a small xtc file and a very
> big pdb file. I can able to access small xtc file but unable to read the
> large pdb file (~10GB) (terminating with the same error as reported
> earlier). Does it mean my installation has some problem?
>
> On Mon, Oct 5, 2015 at 7:41 PM, Teemu Murtola <teemu.murt...@gmail.com>
> wrote:
>
> > Hi,
> >
> > That unfortunately doesn't tell us anything, since 1.5GB can still be
> read
> > with 32-bit file operations. You didn't answer any of the questions: can
> > you open very small xtc files, or very large (requiring 64-bit access)
> > gro/pdb files, or not? We are still thinking that you should be able to
> > open any files smaller than 2GB just fine, but you are making confusing
> > claims that seem to contradict this, so this needs to be sorted out
> before
> > we can really conclude anything.
> >
> > Best regards,
> > Teemu
> >
> > On Mon, Oct 5, 2015, 08:32 Venkat Reddy <venkat...@gmail.com> wrote:
> >
> > > Hi,
> > > Sorry for the delay in reply.
> > > I am able to access pdb/gro files of size 1.5 GB with Gromacs-5.1
> > version.
> > > My Desktop is 32-bit whereas my xtc files were generated on our super
> > > cluster, which runs on 64-bit O.S.
> > >
> > > On Fri, Oct 2, 2015 at 9:46 AM, Teemu Murtola <teemu.murt...@gmail.com
> >
> > > wrote:
> > >
> > > > Hi,
> > > >
> > > > On Thu, Oct 1, 2015 at 6:30 PM Szilárd Páll <pall.szil...@gmail.com>
> > > > wrote:
> > > >
> > > > > On Thu, Oct 1, 2015 at 8:01 AM, Venkat Reddy <venkat...@gmail.com>
> > > > wrote:
> > > > > > Gromacs-5.1 version can not read xtc files. However, it can
> access
> > > > single
> > > > > > frame gro/pdb files.
> > > > > >
> > > > >
> > > > > That's a bold claim that IMO requires equally strong proof.
> > > > >
> > > >
> > > > I agree with Szilard. Are you saying that you cannot even read a
> > > > single-frame xtc file with just a few kB in size? How about other
> > binary
> > > > files (e.g., trr)? How about large (>2GB) gro files?
> > > >
> > > > In your other mail to the list you were talking about a 32-bit Ubuntu
> > VM.
> > > > > Are you sure you're not running into in incompatibility issue
> between
> > > the
> > > > > 32-bit binaries vs 64-bit xtc file(s) you're trying to read?
> > > > >
> > > >
> > > > I would still suspect that the underlying reason is that for some
> > reason,
> > > > 5.1 gets compiled without large file support in your system, which
> > makes
> > > > even plain fopen() fail on large files. The build system should give
> an
> > > > error if it cannot find 64-bit file support, but the check may be
> > > > imperfect. Someone who can reproduce the issue (i.e., has access to a
> > > > similar OS and other environment) should try what is actually
> required
> > to
> > > > get 64-bit file support working there. Based on the information you
> > > posted
> > > > in Redmine, the build system already checks that off_t is 64-bit
> > without
> > > > any extra defines on your system. The checks in the build system have
> > not
> > > > changed between 5.0 and 5.1, though.
> > > >
> > > > Teemu
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
> > > >
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> > > >
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> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-requ...@gromacs.org.
> > > >
> > >
> > >
> > >
> > > --
> > > With Best Wishes

Re: [gmx-users] Analysis of old xtc file using gromacs-5 tools

[Teemu Murtola]

Hi,

That unfortunately doesn't tell us anything, since 1.5GB can still be read
with 32-bit file operations. You didn't answer any of the questions: can
you open very small xtc files, or very large (requiring 64-bit access)
gro/pdb files, or not? We are still thinking that you should be able to
open any files smaller than 2GB just fine, but you are making confusing
claims that seem to contradict this, so this needs to be sorted out before
we can really conclude anything.

Best regards,
Teemu

On Mon, Oct 5, 2015, 08:32 Venkat Reddy <venkat...@gmail.com> wrote:

> Hi,
> Sorry for the delay in reply.
> I am able to access pdb/gro files of size 1.5 GB with Gromacs-5.1 version.
> My Desktop is 32-bit whereas my xtc files were generated on our super
> cluster, which runs on 64-bit O.S.
>
> On Fri, Oct 2, 2015 at 9:46 AM, Teemu Murtola <teemu.murt...@gmail.com>
> wrote:
>
> > Hi,
> >
> > On Thu, Oct 1, 2015 at 6:30 PM Szilárd Páll <pall.szil...@gmail.com>
> > wrote:
> >
> > > On Thu, Oct 1, 2015 at 8:01 AM, Venkat Reddy <venkat...@gmail.com>
> > wrote:
> > > > Gromacs-5.1 version can not read xtc files. However, it can access
> > single
> > > > frame gro/pdb files.
> > > >
> > >
> > > That's a bold claim that IMO requires equally strong proof.
> > >
> >
> > I agree with Szilard. Are you saying that you cannot even read a
> > single-frame xtc file with just a few kB in size? How about other binary
> > files (e.g., trr)? How about large (>2GB) gro files?
> >
> > In your other mail to the list you were talking about a 32-bit Ubuntu VM.
> > > Are you sure you're not running into in incompatibility issue between
> the
> > > 32-bit binaries vs 64-bit xtc file(s) you're trying to read?
> > >
> >
> > I would still suspect that the underlying reason is that for some reason,
> > 5.1 gets compiled without large file support in your system, which makes
> > even plain fopen() fail on large files. The build system should give an
> > error if it cannot find 64-bit file support, but the check may be
> > imperfect. Someone who can reproduce the issue (i.e., has access to a
> > similar OS and other environment) should try what is actually required to
> > get 64-bit file support working there. Based on the information you
> posted
> > in Redmine, the build system already checks that off_t is 64-bit without
> > any extra defines on your system. The checks in the build system have not
> > changed between 5.0 and 5.1, though.
> >
> > Teemu
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
>
>
>
> --
> With Best Wishes
> Venkat Reddy Chirasani
> PhD student
> Laboratory of Computational Biophysics
> Department of Biotechnology
> IIT Madras
> Chennai
> INDIA-600036
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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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Re: [gmx-users] Insert molecules in system with minimum distance between them

[Teemu Murtola]

Hi,
On Thu, Oct 1, 2015 at 3:23 PM Justin Lemkul  wrote:

> On 9/30/15 12:15 PM, Ebert Maximilian wrote:
> > I am trying to add n-number of molecules in my prepare
> protein+water+ions box but keep a minimum distance of 1 nm in all
> directions between the newly inserted molecules. On top of that I want to
> replace solvent molecules with the newly added molecules. So basically I am
> looking for gmx genion with the -rmin flag for non ions.
> > Which tool could I use?
>
> No GROMACS tool will do this.  You can use gmx insert-molecules in concert
> with
> a positions.dat file (with pre-computed locations for the molecules),
> followed
> by gmx solvate.
>

I extended gmx insert-molecules to this direction in 5165
, which had been in my backlog for some
time now; feedback is welcome (I haven't yet tested the new functionality,
though). The option to control the minimum distance is not there yet, but
should not be technically difficult to add. The biggest question is how
many different minimum distances are required, how would they be specified
from the command line, and how they would interact with the different
distance measures in the tool? At least solute-inserted, solvent-inserted,
and inserted-inserted distances might need different treatment, and then
there are also the van der Waals radii for the atoms that are currently
used.

Best regards,
Teemu
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Re: [gmx-users] Analysis of old xtc file using gromacs-5 tools

[Teemu Murtola]

Hi,

On Thu, Oct 1, 2015 at 6:30 PM Szilárd Páll  wrote:

> On Thu, Oct 1, 2015 at 8:01 AM, Venkat Reddy  wrote:
> > Gromacs-5.1 version can not read xtc files. However, it can access single
> > frame gro/pdb files.
> >
>
> That's a bold claim that IMO requires equally strong proof.
>

I agree with Szilard. Are you saying that you cannot even read a
single-frame xtc file with just a few kB in size? How about other binary
files (e.g., trr)? How about large (>2GB) gro files?

In your other mail to the list you were talking about a 32-bit Ubuntu VM.
> Are you sure you're not running into in incompatibility issue between the
> 32-bit binaries vs 64-bit xtc file(s) you're trying to read?
>

I would still suspect that the underlying reason is that for some reason,
5.1 gets compiled without large file support in your system, which makes
even plain fopen() fail on large files. The build system should give an
error if it cannot find 64-bit file support, but the check may be
imperfect. Someone who can reproduce the issue (i.e., has access to a
similar OS and other environment) should try what is actually required to
get 64-bit file support working there. Based on the information you posted
in Redmine, the build system already checks that off_t is 64-bit without
any extra defines on your system. The checks in the build system have not
changed between 5.0 and 5.1, though.

Teemu
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Re: [gmx-users] Analysis of old xtc file using gromacs-5 tools

[Teemu Murtola]

Thanks for testing it, I see that there is still room for improvement in
getting more context information into the error messages. I'm a bit
confused by the difference between your original report of system.xtc vs
traj.xtc in the new message, but that may not matter that much. Is your xtc
file larger that 2GB in size?

On Wed, Sep 30, 2015, 07:53 Venkat Reddy <venkat...@gmail.com> wrote:

> Hi Teemu,
> Thank you for providing the patch. But the patched version is giving
> following error message:
>
> Program: gmx rdf, VERSION 5.2-dev
> Source file: src/gromacs/utility/path.cpp (line 406)
> Function:static void gmx::File::throwOnError(const
> gmx::File::NotFoundInfo&)
>
> System I/O error:
> Failed to access file 'traj.xtc'.
> The file could not be opened.
>   Reason: Value too large for defined data type
>   (call to fopen() returned error code 75)
>
> I would like to inform you that I have installed this patched version to a
> non-standard location.
>
>
> On Wed, Sep 30, 2015 at 8:39 AM, Teemu Murtola <teemu.murt...@gmail.com>
> wrote:
>
> > Hi,
> >
> > I now changed the check to provide more details (in 5140
> > <https://gerrit.gromacs.org/5140>). If you haven't figured out what the
> > issue was, you could try building the source code from the above link,
> and
> > running it to get more details.
> >
> > There is not much we can do to help diagnose the issue further, unless
> you
> > can provide additional information on the file system contents. Also note
> > that if you provide an input file name that looks like a valid file name
> > (with the correct extension), Gromacs 5.1 will use it as is, or give an
> > error if it does not exist. Previous versions silently tried to append
> all
> > kinds of extensions if the file did not exist (or could not be read) even
> > in such a case, and could then use some other file as input.
> >
> > Best regards,
> > Teemu
> >
> > On Sat, Sep 26, 2015 at 11:56 AM Teemu Murtola <teemu.murt...@gmail.com>
> > wrote:
> >
> > > This error has nothing to do with the contents of the file, but rather
> > the
> > > operating system appears to be telling Gromacs that the file cannot be
> > > opened or that it is not a regular file. With the information here,
> it's
> > > difficult to say anything more; if you want to debug this further, the
> > > relevant function is gmx::File::exists().
> > >
> > > It would be useful to know what's the problem so that the check (or the
> > > error message) can be improved.
> > >
> > > Best regards,
> > > Teemu
> > >
> > > On Fri, Sep 25, 2015, 21:20 Venkat Reddy <venkat...@gmail.com> wrote:
> > >
> > >> Hi Tsjerk,
> > >> Thank you for the quick reply. Yes I can access it with other
> versions,
> > >> like 4.5.5, 5.0.4.
> > >>
> > >> On Fri, Sep 25, 2015 at 11:33 PM, Tsjerk Wassenaar <tsje...@gmail.com
> >
> > >> wrote:
> > >>
> > >> > Hi Venkat,
> > >> >
> > >> > Does it exist? Is it accessible? The XTC format did not change since
> > the
> > >> > early years of Gromacs. Can you access it with a different version?
> > >> >
> > >> > Cheers,
> > >> >
> > >> > Tsjerk
> > >> > On Sep 25, 2015 19:52, "Venkat Reddy" <venkat...@gmail.com> wrote:
> > >> >
> > >> > > Dear all,
> > >> > > I have a trajectory file generated by gromacs-4.5.5. Recently I
> > tried
> > >> to
> > >> > > plot radial distribution function using 'gmx rdf' tool available
> in
> > >> > > gromacs-5.1. But I am getting the following error.
> > >> > > Error in user input:
> > >> > > Invalid command-line options
> > >> > >   In command-line option -f
> > >> > > File 'system.xtc' does not exist or is not accessible.
> > >> > >
> > >> > > I knew that gromacs old trajectories can be analysed using new
> > version
> > >> > > tools. But why I am facing this error?
> > >> > >
> > >> > >
> > >> > > With regards
> > >> > > Venkat Reddy Chirasani
> > >> > > PhD student
> > >> > > Laboratory of Computational Biophysics
> > >> > > Department of Biotechnology
> > >> > > IIT Madras

Re: [gmx-users] Analysis of old xtc file using gromacs-5 tools

[Teemu Murtola]

Are you saying that you cannot open any xtc files? If that is the case,
then this may not have anything to do with 64-bit for support. Can your
Gromacs compilation open any files? You will need to isolate the problem a
bit to help diagnosing it, since we don't have access to your system.

Teemu

On Thu, Oct 1, 2015, 07:48 Venkat Reddy <venkat...@gmail.com> wrote:

> Hi,
> 1) Yes, I can access the same xtc with older gromacs versions.
> 2) I can't access even smaller xtc files with 5.1
> I will file a bug report for the same.
> Thank you
>
>
>
> On Wed, Sep 30, 2015 at 9:28 PM, Teemu Murtola <teemu.murt...@gmail.com>
> wrote:
>
> > Hi,
> >
> > This sounds like the build system is not compiling Gromacs with 64-bit
> file
> > support like it should. Can you access the same file on the same system
> > with earlier Gromacs versions? Can you access smaller files with 5.1?
> >
> > Could you file a bug report at redmine.gromacs.org, and include at least
> > the following:
> > * information on your operating system
> > * contents of CMakeCache.txt, src/config.h, and src/gmxpre-config.h from
> > your build tree
> > * how you invoked cmake to configure the build.
> >
> > Teemu
> >
> > On Wed, Sep 30, 2015, 11:59 Venkat Reddy <venkat...@gmail.com> wrote:
> >
> > > Hi Teemu,
> > > Thanks for the prompt reply. Yes, the xtc file size is larger than 2GB
> > > (approx. 50GB) and both system.xtc and traj.xtc are same files. I am
> > > extremely sorry for the confusion :)
> > >
> > > On Wed, Sep 30, 2015 at 11:31 AM, Teemu Murtola <
> teemu.murt...@gmail.com
> > >
> > > wrote:
> > >
> > > > Thanks for testing it, I see that there is still room for improvement
> > in
> > > > getting more context information into the error messages. I'm a bit
> > > > confused by the difference between your original report of system.xtc
> > vs
> > > > traj.xtc in the new message, but that may not matter that much. Is
> your
> > > xtc
> > > > file larger that 2GB in size?
> > > >
> > > > On Wed, Sep 30, 2015, 07:53 Venkat Reddy <venkat...@gmail.com>
> wrote:
> > > >
> > > > > Hi Teemu,
> > > > > Thank you for providing the patch. But the patched version is
> giving
> > > > > following error message:
> > > > >
> > > > > Program: gmx rdf, VERSION 5.2-dev
> > > > > Source file: src/gromacs/utility/path.cpp (line 406)
> > > > > Function:static void gmx::File::throwOnError(const
> > > > > gmx::File::NotFoundInfo&)
> > > > >
> > > > > System I/O error:
> > > > > Failed to access file 'traj.xtc'.
> > > > > The file could not be opened.
> > > > >   Reason: Value too large for defined data type
> > > > >   (call to fopen() returned error code 75)
> > > > >
> > > > > I would like to inform you that I have installed this patched
> version
> > > to
> > > > a
> > > > > non-standard location.
> > > > >
> > > > >
> > > > > On Wed, Sep 30, 2015 at 8:39 AM, Teemu Murtola <
> > > teemu.murt...@gmail.com>
> > > > > wrote:
> > > > >
> > > > > > Hi,
> > > > > >
> > > > > > I now changed the check to provide more details (in 5140
> > > > > > <https://gerrit.gromacs.org/5140>). If you haven't figured out
> > what
> > > > the
> > > > > > issue was, you could try building the source code from the above
> > > link,
> > > > > and
> > > > > > running it to get more details.
> > > > > >
> > > > > > There is not much we can do to help diagnose the issue further,
> > > unless
> > > > > you
> > > > > > can provide additional information on the file system contents.
> > Also
> > > > note
> > > > > > that if you provide an input file name that looks like a valid
> file
> > > > name
> > > > > > (with the correct extension), Gromacs 5.1 will use it as is, or
> > give
> > > an
> > > > > > error if it does not exist. Previous versions silently tried to
> > > append
> > > > > all
> > > > > > kinds of extensions if the file did not exist (or could not be
> > rea

Re: [gmx-users] Analysis of old xtc file using gromacs-5 tools

[Teemu Murtola]

Hi,

This sounds like the build system is not compiling Gromacs with 64-bit file
support like it should. Can you access the same file on the same system
with earlier Gromacs versions? Can you access smaller files with 5.1?

Could you file a bug report at redmine.gromacs.org, and include at least
the following:
* information on your operating system
* contents of CMakeCache.txt, src/config.h, and src/gmxpre-config.h from
your build tree
* how you invoked cmake to configure the build.

Teemu

On Wed, Sep 30, 2015, 11:59 Venkat Reddy <venkat...@gmail.com> wrote:

> Hi Teemu,
> Thanks for the prompt reply. Yes, the xtc file size is larger than 2GB
> (approx. 50GB) and both system.xtc and traj.xtc are same files. I am
> extremely sorry for the confusion :)
>
> On Wed, Sep 30, 2015 at 11:31 AM, Teemu Murtola <teemu.murt...@gmail.com>
> wrote:
>
> > Thanks for testing it, I see that there is still room for improvement in
> > getting more context information into the error messages. I'm a bit
> > confused by the difference between your original report of system.xtc vs
> > traj.xtc in the new message, but that may not matter that much. Is your
> xtc
> > file larger that 2GB in size?
> >
> > On Wed, Sep 30, 2015, 07:53 Venkat Reddy <venkat...@gmail.com> wrote:
> >
> > > Hi Teemu,
> > > Thank you for providing the patch. But the patched version is giving
> > > following error message:
> > >
> > > Program: gmx rdf, VERSION 5.2-dev
> > > Source file: src/gromacs/utility/path.cpp (line 406)
> > > Function:static void gmx::File::throwOnError(const
> > > gmx::File::NotFoundInfo&)
> > >
> > > System I/O error:
> > > Failed to access file 'traj.xtc'.
> > > The file could not be opened.
> > >   Reason: Value too large for defined data type
> > >   (call to fopen() returned error code 75)
> > >
> > > I would like to inform you that I have installed this patched version
> to
> > a
> > > non-standard location.
> > >
> > >
> > > On Wed, Sep 30, 2015 at 8:39 AM, Teemu Murtola <
> teemu.murt...@gmail.com>
> > > wrote:
> > >
> > > > Hi,
> > > >
> > > > I now changed the check to provide more details (in 5140
> > > > <https://gerrit.gromacs.org/5140>). If you haven't figured out what
> > the
> > > > issue was, you could try building the source code from the above
> link,
> > > and
> > > > running it to get more details.
> > > >
> > > > There is not much we can do to help diagnose the issue further,
> unless
> > > you
> > > > can provide additional information on the file system contents. Also
> > note
> > > > that if you provide an input file name that looks like a valid file
> > name
> > > > (with the correct extension), Gromacs 5.1 will use it as is, or give
> an
> > > > error if it does not exist. Previous versions silently tried to
> append
> > > all
> > > > kinds of extensions if the file did not exist (or could not be read)
> > even
> > > > in such a case, and could then use some other file as input.
> > > >
> > > > Best regards,
> > > > Teemu
> > > >
> > > > On Sat, Sep 26, 2015 at 11:56 AM Teemu Murtola <
> > teemu.murt...@gmail.com>
> > > > wrote:
> > > >
> > > > > This error has nothing to do with the contents of the file, but
> > rather
> > > > the
> > > > > operating system appears to be telling Gromacs that the file cannot
> > be
> > > > > opened or that it is not a regular file. With the information here,
> > > it's
> > > > > difficult to say anything more; if you want to debug this further,
> > the
> > > > > relevant function is gmx::File::exists().
> > > > >
> > > > > It would be useful to know what's the problem so that the check (or
> > the
> > > > > error message) can be improved.
> > > > >
> > > > > Best regards,
> > > > > Teemu
> > > > >
> > > > > On Fri, Sep 25, 2015, 21:20 Venkat Reddy <venkat...@gmail.com>
> > wrote:
> > > > >
> > > > >> Hi Tsjerk,
> > > > >> Thank you for the quick reply. Yes I can access it with other
> > > versions,
> > > > >> like 4.5.5, 5.0.4.
> > > > >>
> > > > >> On Fri, Sep 25, 2015 

Re: [gmx-users] Analysis of old xtc file using gromacs-5 tools

[Teemu Murtola]

Hi,

I now changed the check to provide more details (in 5140
<https://gerrit.gromacs.org/5140>). If you haven't figured out what the
issue was, you could try building the source code from the above link, and
running it to get more details.

There is not much we can do to help diagnose the issue further, unless you
can provide additional information on the file system contents. Also note
that if you provide an input file name that looks like a valid file name
(with the correct extension), Gromacs 5.1 will use it as is, or give an
error if it does not exist. Previous versions silently tried to append all
kinds of extensions if the file did not exist (or could not be read) even
in such a case, and could then use some other file as input.

Best regards,
Teemu

On Sat, Sep 26, 2015 at 11:56 AM Teemu Murtola <teemu.murt...@gmail.com>
wrote:

> This error has nothing to do with the contents of the file, but rather the
> operating system appears to be telling Gromacs that the file cannot be
> opened or that it is not a regular file. With the information here, it's
> difficult to say anything more; if you want to debug this further, the
> relevant function is gmx::File::exists().
>
> It would be useful to know what's the problem so that the check (or the
> error message) can be improved.
>
> Best regards,
> Teemu
>
> On Fri, Sep 25, 2015, 21:20 Venkat Reddy <venkat...@gmail.com> wrote:
>
>> Hi Tsjerk,
>> Thank you for the quick reply. Yes I can access it with other versions,
>> like 4.5.5, 5.0.4.
>>
>> On Fri, Sep 25, 2015 at 11:33 PM, Tsjerk Wassenaar <tsje...@gmail.com>
>> wrote:
>>
>> > Hi Venkat,
>> >
>> > Does it exist? Is it accessible? The XTC format did not change since the
>> > early years of Gromacs. Can you access it with a different version?
>> >
>> > Cheers,
>> >
>> > Tsjerk
>> > On Sep 25, 2015 19:52, "Venkat Reddy" <venkat...@gmail.com> wrote:
>> >
>> > > Dear all,
>> > > I have a trajectory file generated by gromacs-4.5.5. Recently I tried
>> to
>> > > plot radial distribution function using 'gmx rdf' tool available in
>> > > gromacs-5.1. But I am getting the following error.
>> > > Error in user input:
>> > > Invalid command-line options
>> > >   In command-line option -f
>> > > File 'system.xtc' does not exist or is not accessible.
>> > >
>> > > I knew that gromacs old trajectories can be analysed using new version
>> > > tools. But why I am facing this error?
>> > >
>> > >
>> > > With regards
>> > > Venkat Reddy Chirasani
>> > > PhD student
>> > > Laboratory of Computational Biophysics
>> > > Department of Biotechnology
>> > > IIT Madras
>> > > Chennai
>> > > INDIA-600036
>> > > --
>> > > Gromacs Users mailing list
>> > >
>> > > * Please search the archive at
>> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> > > posting!
>> > >
>> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> > >
>> > > * For (un)subscribe requests visit
>> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> > > send a mail to gmx-users-requ...@gromacs.org.
>> > >
>> > --
>> > Gromacs Users mailing list
>> >
>> > * Please search the archive at
>> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> > posting!
>> >
>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >
>> > * For (un)subscribe requests visit
>> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> > send a mail to gmx-users-requ...@gromacs.org.
>> >
>>
>>
>>
>> --
>> With Best Wishes
>> Venkat Reddy Chirasani
>> PhD student
>> Laboratory of Computational Biophysics
>> Department of Biotechnology
>> IIT Madras
>> Chennai
>> INDIA-600036
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>>
>
-- 
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* Please search the archive at 
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Re: [gmx-users] Analysis of old xtc file using gromacs-5 tools

[Teemu Murtola]

This error has nothing to do with the contents of the file, but rather the
operating system appears to be telling Gromacs that the file cannot be
opened or that it is not a regular file. With the information here, it's
difficult to say anything more; if you want to debug this further, the
relevant function is gmx::File::exists().

It would be useful to know what's the problem so that the check (or the
error message) can be improved.

Best regards,
Teemu

On Fri, Sep 25, 2015, 21:20 Venkat Reddy  wrote:

> Hi Tsjerk,
> Thank you for the quick reply. Yes I can access it with other versions,
> like 4.5.5, 5.0.4.
>
> On Fri, Sep 25, 2015 at 11:33 PM, Tsjerk Wassenaar 
> wrote:
>
> > Hi Venkat,
> >
> > Does it exist? Is it accessible? The XTC format did not change since the
> > early years of Gromacs. Can you access it with a different version?
> >
> > Cheers,
> >
> > Tsjerk
> > On Sep 25, 2015 19:52, "Venkat Reddy"  wrote:
> >
> > > Dear all,
> > > I have a trajectory file generated by gromacs-4.5.5. Recently I tried
> to
> > > plot radial distribution function using 'gmx rdf' tool available in
> > > gromacs-5.1. But I am getting the following error.
> > > Error in user input:
> > > Invalid command-line options
> > >   In command-line option -f
> > > File 'system.xtc' does not exist or is not accessible.
> > >
> > > I knew that gromacs old trajectories can be analysed using new version
> > > tools. But why I am facing this error?
> > >
> > >
> > > With regards
> > > Venkat Reddy Chirasani
> > > PhD student
> > > Laboratory of Computational Biophysics
> > > Department of Biotechnology
> > > IIT Madras
> > > Chennai
> > > INDIA-600036
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
>
>
>
> --
> With Best Wishes
> Venkat Reddy Chirasani
> PhD student
> Laboratory of Computational Biophysics
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Re: [gmx-users] gmx rdf gromacs 5.1 question!

[Teemu Murtola]

Hi,

indeed, this appears to be a bug, likely originating already from 5.0
times. I'll try to fix that soon. But it is just a convenience option,
anyways: you can always write each of your selections as "mol_com of ...",
and it should work the same.

Best regards,
Teemu

On Fri, Sep 25, 2015 at 11:50 AM Stelios Karozis <
skaro...@ipta.demokritos.gr> wrote:

> Hi Teemu
> Thanks for your response, but -seltype is not available as a flag for
> gmx rdf in gromacs 5.1 documentation, nor recognizable from cmd (I gave
> it a try...)
>
> --
> Karozis Stelios
> Chemical Engineer, MSc
> Research Associate at EREL
> NCSR D- INRASTES
> tel:0030 210 650 3403
> e-mail: skaro...@ipta.demokritos.gr
>
>
> On Fri, 25 Sep 2015 11:23:39 +0300, "Teemu Murtola"
> <teemu.murt...@gmail.com> wrote :
>
> > Hi,
> >
> > You should use -seltype instead of -selrpos in this case.
> >
> > Best regards,
> > Teemu
> >
> > On Fri, Sep 25, 2015, 11:12 Stelios Karozis
> > <skaro...@ipta.demokritos.gr> wrote:
> >
> > > Greeting everyone,
> > > I strated using gromacs 5.1 and I have difficulties with gmx rdf
> > > command. With older version of gromacs I used -xy -rdf mol_com
> > >  flags. As far as I can understand, the equivalent flags for
> > > gromacs 5.1 are -xy -selrpos mol_com but the result is not correct.
> > > For instance the first peak is at 0nm and not close to 0.5nm...
> > > I believe I am not using the right flags.
> > >
> > > Thanks in advance for your help
> > >
> > > --
> > > Karozis Stelios
> > > Chemical Engineer, MSc
> > > Research Associate at EREL
> > > NCSR D- INRASTES
> > > tel:0030 210 650 3403
> > > e-mail: skaro...@ipta.demokritos.gr
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Re: [gmx-users] gmx rdf gromacs 5.1 question!

[Teemu Murtola]

Hi,

You should use -seltype instead of -selrpos in this case.

Best regards,
Teemu

On Fri, Sep 25, 2015, 11:12 Stelios Karozis 
wrote:

> Greeting everyone,
> I strated using gromacs 5.1 and I have difficulties with gmx rdf
> command. With older version of gromacs I used -xy -rdf mol_com
>  flags. As far as I can understand, the equivalent flags for gromacs 5.1
>  are -xy -selrpos mol_com but the result is not correct. For instance
>  the first peak is at 0nm and not close to 0.5nm...
> I believe I am not using the right flags.
>
> Thanks in advance for your help
>
> --
> Karozis Stelios
> Chemical Engineer, MSc
> Research Associate at EREL
> NCSR D- INRASTES
> tel:0030 210 650 3403
> e-mail: skaro...@ipta.demokritos.gr
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Re: [gmx-users] Problem with gmx-distance

[Teemu Murtola]

No, the atoms can be in a single group for this simple case of an atom-atom
distance.

The next line (after the prompt that you quote) should say something like
"(one per line, ..., Ctrl-D to end)". Following those instructions should
help (i.e., entering Ctrl-D).

Best regards,
Teemu

On Wed, Sep 16, 2015, 17:01 Justin Lemkul  wrote:

>
>
> On 9/16/15 9:06 AM, Timofey Tyugashev wrote:
> > I want to get the distance between atoms 3770 and 5182 in my trajectory
> > After consulting with the Manual I write command:
> > gmx distance -n ind2.ndx -f trj1_WT_md_40.xtc -s wt_md.gro -oav
> distav.xvg -oall
> > dist.xvg
> > and index file ind2.ndx:
> > [ LYS_241_ODG_C1' ]
> > 3770 5182
> >
> > The program responds like this:
> >
> > Available static index groups:
> >   Group  0 "LYS_241_ODG_C1'" (2 atoms)
> > Specify any number of selections for option 'select'
> > (Position pairs to calculate distances for):
> >
> > If I pick 0, it responds 'Selection '0' parsed' and then nothing happens.
> > What to do next? The manual is incredibly murky and there are no
> examples in the
> > net.
>
> Your atoms can't be in the same group.  That was the same as with g_dist.
>
> [ atom1 ]
> 3770
> [ atom2 ]
> 5182
>
> gmx distance -n -f -s -oav -oall -select 'com of group "atom1" plus com of
> group
> "atom2"'
>
> See "gmx help selections" and specifically "gmx help selections examples"
> for
> syntax of selections and a few simple examples.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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Re: [gmx-users] gmx sasa output group not recognised

[Teemu Murtola]

Hello,

On Fri, Sep 4, 2015 at 1:51 PM Francesco Carbone 
wrote:

> I've recently started using gromacs 5.0.4 and I can't make"gmx sasa" to
> recognise non-standard groups for the -output flag.
> I have three groups (G6P, Co-enzyme and strNADP+; all subset of the dimer )
> and every time I specify one of the three with "-output" flag I get:
> "Inconsistency in user input: Output selection is not a subset of the input
> selection ".
> I created the groups with make_ndx and "gmx sasa" see them correctly
> (option 10,11 and 12) and these are the commands that I tried:
>
> 1) gmx sasa -s Ameno_500.tpr -f Ameno_500.xtc -n Ameno.ndx -surface
> "Protein" -output "G6P" -o ciao.xvg -dt 250
>

Most likely, your G6P group is not a subset of the Protein group (which is
very likely if you have some non-standard residues or such). As mentioned
in 'gmx sasa -h', the group specified for -output should be a subset of
what is specified for -surface. There was no such check in g_sas in 4.6; it
just ignored any atoms in the output group that were not in the surface
group, which in my mind is worse (since that almost always means that the
user is not computing what they think they are).

I improved the error message to include more information here:
https://gerrit.gromacs.org/#/c/5050/

Best regards,
Teemu
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Re: [gmx-users] gmx sasa output group not recognised

[Teemu Murtola]

The other possibility is that your index groups do not have the atom
indices in an increasing order. If this is the case, just sort the atoms,
or don't use make_ndx as an intermediate step.

Teemu

On Fri, Sep 4, 2015, 14:20 Francesco Carbone <fra.carbo...@gmail.com> wrote:

> thank you for the reply, but the residues are in the same protein.
> I simply select a list of residues that interact with the substrate.
>
> (echo "r 171 263 201 202 205 395 365 239 360 258"; echo "name 10 G6P"; echo
> "q") | make_ndx -f $nameprod.gro -o $name1.ndx
>
> residues 171 263 201 202 205 395 365 239 360 258 are part of "Protein".
>
> Cheers,
>
> Francesco
>
> On 4 September 2015 at 12:12, Teemu Murtola <teemu.murt...@gmail.com>
> wrote:
>
> > Hello,
> >
> > On Fri, Sep 4, 2015 at 1:51 PM Francesco Carbone <fra.carbo...@gmail.com
> >
> > wrote:
> >
> > > I've recently started using gromacs 5.0.4 and I can't make"gmx sasa" to
> > > recognise non-standard groups for the -output flag.
> > > I have three groups (G6P, Co-enzyme and strNADP+; all subset of the
> > dimer )
> > > and every time I specify one of the three with "-output" flag I get:
> > > "Inconsistency in user input: Output selection is not a subset of the
> > input
> > > selection ".
> > > I created the groups with make_ndx and "gmx sasa" see them correctly
> > > (option 10,11 and 12) and these are the commands that I tried:
> > >
> > > 1) gmx sasa -s Ameno_500.tpr -f Ameno_500.xtc -n Ameno.ndx -surface
> > > "Protein" -output "G6P" -o ciao.xvg -dt 250
> > >
> >
> > Most likely, your G6P group is not a subset of the Protein group (which
> is
> > very likely if you have some non-standard residues or such). As mentioned
> > in 'gmx sasa -h', the group specified for -output should be a subset of
> > what is specified for -surface. There was no such check in g_sas in 4.6;
> it
> > just ignored any atoms in the output group that were not in the surface
> > group, which in my mind is worse (since that almost always means that the
> > user is not computing what they think they are).
> >
> > I improved the error message to include more information here:
> > https://gerrit.gromacs.org/#/c/5050/
> >
> > Best regards,
> > Teemu
> > --
> > Gromacs Users mailing list
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Re: [gmx-users] Analyze neighbors of a residue within a cutoff distance during simulation

[Teemu Murtola]

You do not need such a complicated loop for using gmx distance, since you
can just provide your selections directly to gmx distance and it will
evaluate them automatically for each frame.

But for these problem you describe, gmx pairdist (new in Gromacs 5.1)
probably can give you all the distances you want with a single invocation
(you still need to compute the average from the output file).

Best regards,
Teemu

On Tue, Sep 1, 2015, 14:32 Justin Lemkul  wrote:


On 9/1/15 5:15 AM, Tushar Ranjan Moharana wrote:
> Hi Everyone,
> I have simulated a protein in 40 % methanol. Now I want to analyze the
> average distance between any amino acid and all the methanol molecule
which
> comes to close to (less than 0.4 nm) that amino acid during the
simulation.
> I tried many GROMACS analysis tool for this but I couldn't succeed. Can
> anybody kindly suggest me which analysis tool will be useful for me.
>

Use gmx select to generate index groups for each frame in the trajectory
that
identify methanol molecules that meet your criteria, then run gmx distance
using
those index groups (you need to do a per-frame analysis, e.g. loop the
calls).

-Justin
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Re: [gmx-users] Measuring Bilayer thickness with gmx distance in CGMD simulations

[Teemu Murtola]

Please upgrade to 5.0.6. There was a bug with gmx distance -oxyz that
caused the output file to not appear (or to overwrite some unintended
files), which was fixed for the latest version.

On Tue, Jul 28, 2015, 17:34 Carlos Navarro Retamal cnava...@utalca.cl
wrote:

 Hi Justin,
 thanks for your reply.
 Is there a way, to analyse each component (x,y,z) of the distance without
 the flag -oxyz?
 For some reason, I’m unable to get this data with gmx distance.
 In fact, when i ran
 gmx distance -f trajout329K.xtc -s POPC-329K-2us.tpr -n index.ndx -oxyz
 the command line doesn’t generate anything (any *xvg file).
 I don’t know what I’m doing wrong
 Best,
 Carlos
 --
 Carlos Navarro Retamal
 Bioinformatics Engineering
 Ph. D (c) Applied Sciences.
 Center of Bioinformatics and Molecular Simulations. CBSM
 University of Talca
 Av. Lircay S/N, Talca, Chile
 T: (+56) 712201 798
 E: carlos.navarr...@gmail.com or cnava...@utalca.cl



 On July 28, 2015 at 9:34:32 AM, Justin Lemkul (jalem...@vt.edumailto:
 jalem...@vt.edu) wrote:

 July 28, 2015 at 6:09:51 AM GMT-3 ro Retamal wrote:
  Dear gmx users,
  I’m studying the implication of higher temperatures in the membrane
 thickness (d) of several bilayer during CGMD simulations.
  In order to measure d in a pure POPC membrane i create an index group
 containing only PO4 beads.
  Before everything, i remove PBC conditions in the simulations as
 following:
  trjconv -f POPC-300K-2us.xtc -s POPC-300K-2us.tpr -pbc nojump -o
 trajout300K.xtc
  trjconv -f POPC-329K-2us.xtc -s POPC-329K-2us.tpr -pbc nojump -o
 trajout329K.xtc
 
  Then, I used gmx distance:
  gmx distance -f trajout300K.xtc -s POPC-329K-2us.tpr -n index.ndx -oav
 avg-300K
  gmx distance -f trajout329K.xtc -s POPC-329K-2us.tpr -n index.ndx -oav
 avg-329K
 
  Finally, using g_analyse i analyse both *xvg files and i got:
 
  300K:
  Average distance: 4.090 nm
  Standard deviation: 1.451 nm
 
  329K:
  Average distance: 4.134 nm
  Standard deviation: 1.515 nm
 

 Those are pretty massive standard deviations; I wouldn't expect a membrane
 to
 fluctuate quite that much. Are you averaging only the z-component of the
 distance?

  Is it normal, that I’m getting a higher thickness at higher temperature?
 Or are my results are ‘ok', considering the values of both standard
 deviation?

 Your results are indistinguishable, given the huge standard deviations.

 -Justin

  In any case; I think this is strange, because using a different
 approximation/methods (GridMAT-MD) i got at 300K, d= 3.996 and at 329K d=
 3.869 ( more ‘normal’ results for this type of lipid at this temperatures).
  Am i missing something with my approximation that is 'disrupting' my
 results?
  I’ll prefer to use gmx distance to analyse d in my simulations,
 considering the extensive amount of time that will take me if i use
 GridMAT-MD to analyse my 1us of production data.
  Any thoughts/suggestions are more than welcome.
  Best,
  Carlos
 
 
  --
  Carlos Navarro Retamal
  Bioinformatics Engineering
  Ph. D (c) Applied Sciences.
  Center of Bioinformatics and Molecular Simulations. CBSM
  University of Talca
  Av. Lircay S/N, Talca, Chile
  T: (+56) 712201 798
  E: carlos.navarr...@gmail.com or cnava...@utalca.cl
 

 --
 ==

 Justin A. Lemkul, Ph.D.
 Ruth L. Kirschstein NRSA Postdoctoral Fellow

 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 629
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201

 jalem...@outerbanks.umaryland.edu | (410) 706-7441
 http://mackerell.umaryland.edu/~jalemkul

 ==
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Re: [gmx-users] angle between two vectors

[Teemu Murtola]

It's not clear from your question what you exactly want to calculate, but
g_sgangle (Gromacs 4.6 and earlier) and gmx gangle (Gromacs 5.0+) can
calculate angles between vectors. g_sgangle has somewhat limited
capabilities, but if you just want two vectors with endpoints at certain
atoms, it should do the trick.

Best regards,
Teemu

On Mon, Jul 20, 2015, 18:01 Natalia Alveal F. nalv...@bio.puc.cl wrote:

Dear Gromacs users,
with which tool of gromacs can compute the angle between two vectors of
different atoms number?
Thanks!
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Re: [gmx-users] Calculating hydrogen bonding density - issues with g_sas?

[Teemu Murtola]

Hi,

and sorry for a bit late reply. g_sas (or gmx sasa) does not compute the
volume correctly if your solute crosses a periodic boundary. In 5.1, there
is a note to this effect in the documentation, but it is tricky to actually
detect this condition in the code. But what this means is that you cannot
compute the volume of, e.g., a periodic slab using g_sas. With proper use
of trjconv, you can still compute the volume of a multi-molecule droplet.

Best regards,
Teemu

On Wed, Jul 8, 2015 at 6:59 PM Dan Gil dan.gil9...@gmail.com wrote:

 Is g_sas applicable to more than one molecule at a time?

 I have 4500 water molecules in the liquid state. I am using the command:
 g_sas -f traj.trr -s topol.tpr -tv volume.xvg


 On Tue, Jul 7, 2015 at 10:31 AM, Dan Gil dan.gil9...@gmail.com wrote:

  I am using the default radius of 0.14 nm. In this case, I believe that it
  is consistent. Nevertheless, I have tried using a probe much larger with
 no
  significant difference in the results.
  The way I am using g_sas is: I have 4500 water molecules. I specified
 that
  I want the volume of all of them.
 
  On Tue, Jul 7, 2015 at 10:11 AM, Mark Abraham mark.j.abra...@gmail.com
  wrote:
 
  Hi,
 
  Is the radius being used consistent with your assumption?
 
  Mark
 
  On Tue, Jul 7, 2015 at 3:58 PM Dan Gil dan.gil9...@gmail.com wrote:
 
   Hi,
  
   I am using g_hbond to count the number of h-bonds and then g_sas to
   calculate the volume. I want to get the number of hydrogen bonds per
   volume. But I am having issues with g_sas - the volume calculated is
  about
   one half of the expected value. For instance, in a pure water system
  (NVT,
   SPCE, T=300K) periodic in the x and y directions, volume was found to
 be
   about 60nm^3, whereas I expected 130nm^3.
  
   I would appreciate any advice!

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Re: [gmx-users] on the command gmx distance

[Teemu Murtola]

Hi,

On Mon, May 25, 2015 at 7:33 PM, Justin Lemkul jalem...@vt.edu wrote:

 On 5/25/15 3:48 AM, Brett wrote:

 Suppose I have completed a production MD, and I want to get the distance
 of
 OD1 of ASP204 in chain G and NH1 of ARG42 in chain A for the last 5 ns in
 the
 MD, will you please tell me the detailed command of gmx distance (how to
 write the input file and output file in the command) on how to get the
 distance?


 I'm not well versed in the new selection syntax (though it is really quite
 flexible), but this is trivial to do in conjunction with the old way of
 making index files with make_ndx and then calling gmx distance:

 chain G  r 204  a OD1
 chain A  r 42  a NH1

 Then just invoke gmx distance -select com of group x plus com of group y
 (subbing in x and y as appropriate).


The syntax to do this directly with selections is something like this:

resnr 204 and name OD1 and chain G plus resnr 42 and name NH1 and chain A

Just pass this to the -select option of gmx distance, and then provide the
appropriate input and output files.

Best regards,
Teemu
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Re: [gmx-users] command line with gangle

[Teemu Murtola]

By far the simplest method is to just pass your selections as command line
arguments, without any files:

  gmx gangle ... -group1 0 -group2 3

One goal for the selection implementation was that it's not necessary to
play around with complicated redirections to automate things.
On Mar 20, 2015 3:52 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 3/20/15 11:49 AM, ABEL Stephane 175950 wrote:

 Hello all,

 I have a stupid question :

 I would like to use gangle (v5.0.4) with the following command line

 gmx_mpi gangle -f conv3.xtc -s 60_SDS_CHARMM_5_NAP_504_run_1.tpr -n
 paipai_dist_theta.ndx -g1 plane -group1 -g2 plane -group2 -oav
 test_angle.xvg -b 39000 -e 4  test_angle.txt

 Without the test_angle.txt file I need to press the following buttons
 for selecting the group 0 and 3

 0 Enter Ctrl-D 3 Enter Ctrl D.

 How to include these commands in a text file (e.g.  test_angle.txt)  for
 that the calculation starts automatically (i.e. for instance with a bash
 script)


 http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts

 -Justin

 --
 ==

 Justin A. Lemkul, Ph.D.
 Ruth L. Kirschstein NRSA Postdoctoral Fellow

 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 629
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201

 jalem...@outerbanks.umaryland.edu | (410) 706-7441
 http://mackerell.umaryland.edu/~jalemkul

 ==
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Re: [gmx-users] g_select syntax unavailable in GROMACS 5.0 and 5.0.1

[Teemu Murtola]

Hi,

On Fri, Jan 2, 2015 at 4:12 AM, Kester Wong kester2...@ibs.re.kr wrote:

 The command gmx_mpi help selections did show the available subtopics,
 however I find this paragraph confusing:


 To get started with selections, run, e.g., gmx_mpi select without
 specifying

 selections on the command-line and use the interactive prompt to try out

 different selections. This tool provides output options that allow one to
 see

 what is actually selected by the given selections, and the interactive
 prompt

 reports syntax errors immediately, allowing one to try again. The subtopics

 listed below give more details on different aspects of selections.


I've rewritten it in 
https://gerrit.gromacs.org/#/c/4340/1/src/gromacs/selection/selhelp.cpp,
hopefully it is now clearer.

Although the paragraph above mentioened gmx_mpi select without specifying
 selections, I had to use gmx_mpi help selections positions to be able to
 see the thread SPECIFYING POSITIONS IN SELECTIONS.


You would likely benefit from reading the short section on selections from
the Gromacs manual. By running
  gmx select -s some structure file
you get an interactive prompt, where you can also type 'help' or 'help
positions' to get access to the help, as well as try out the selections.
The paragraph you reference was written with the assumption that if you are
reading it, you already know how to access the help, so it focuses on
providing some guidance on how to try things out in practice.

 For your second question, is there something wrong with just extending your
 existing selection with an additional clause, for example like this:
 resname SOL and res_com z = 10 and res_com z  15?

 Yep, this worked for my systems. I suppose this binning method has
 already taken into account the center of mass of the water droplet?


It depends on what you mean by taken into account the center of mass of
the water droplet. The selections are not magic; they select exactly what
you tell them, and this one selects water molecules that are have their
absolute z coordinates in range 10-15 (nm). If your droplet moves around
during your simulation in the z direction, then this is not a fixed slice
from the droplet. You can either center your trajectory on the droplet
center-of-mass before other processing, or use the upcoming 5.1 for the
analysis (where you can write selections like res_com z - 10  z of com of
resname SOL).


 How do I go from here, to producing the water density profile as a
 function of z-direction?


That's for you to solve. ;) I would likely write a separate (C++) tool for
this analysis instead of trying to piece it together from multiple small
tools and shell scripting, but different people have different preferences.

Best regards,
Teemu
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Re: [gmx-users] g_select syntax unavailable in GROMACS 5.0 and 5.0.1

[Teemu Murtola]

Hi,

Please check the manual for the version you're using, or preferably for the
latest patch release, in case some things have been improved. The short
section on selections in the manual (can't check the section number right
now) mentions two different ways to access the help, and -select 'help ...'
is not one of them. You can try, e.g., 'gmx help selections'.

The support for help through non-interactive selections like in -select
'help' was removed for 5.0 for a few different reasons. The main one is
that 'gmx help' provides a much more natural way to access the information,
in particular now that there are several different command line options
that accept selections (for example, 'gmx gangle' has two different options
that accept selections, and it's not exactly intuitive that these
would/should also accept requests for generic selection help). It's an
unfortunate coincidence that help all is now parsed as a valid selection
(that has the name help and selects all atoms).

For your second question, is there something wrong with just extending your
existing selection with an additional clause, for example like this:
resname SOL and res_com z = 10 and res_com z  15?

Best regards,
Teemu
On Jan 1, 2015 5:49 AM, Kester Wong kester2...@ibs.re.kr wrote:

 Dear all,


 I have recently posted a question on how generate data that allows me to
 plot a droplet profile as a function of z-direction.


 https://www.mail-archive.com/gromacs.org_gmx-users@maillist.sys.kth.se/msg08966.html

 Knowing that this procedure requires the use of g_select, I am able to
 look up some old posts on gmx-users mail list, however, typing g_select
 -select 'help position' and g_select -select 'help all' simply won't work
 (single quotation used instead of double quatation). I have tried these
 commands on GROMACS (5.0 single and 5.0.1 double precision).



 Also, I have another specific question on binning my water droplet along
 the z-direction:

 Firstly, I am only able to use g_select to define the bottom bin for water 
 droplet; could you please advise on indexing the bins from the bottom water 
 layer?

 g_select_mpi -f traj_comp.xtc -s topol.tpr -n system.ndx -b 9000 -e 1 
 -select 'resname SOL and res_com z  10' -on output-system.ndx


 How does one select SOL between z  10 and z  15, so on and so forth?


 Happy New Year,

 Kester


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Re: [gmx-users] g-select failed

[Teemu Murtola]

Hi,

On Mon, Sep 8, 2014 at 5:15 PM, Albert mailmd2...@gmail.com wrote:

 It works now. If I would like to select protein and z80, I use following
 select.dat file:

 up protein and z80;
 down protein and z80;

 but it failed with messages:

   In command-line option -sf
 Error in parsing selections from file 'select.dat'
   syntax error
   invalid selection 'up protein and z80'

 do you have any idea how to add additional options?


You can add complicated expressions using the keywords described in the
help (e.g., type 'help' or 'help keywords' in the interactive selection
prompt), as long as you follow the syntax. There is no keyword 'protein'
available; for this particular purpose, you can use 'group Protein' to
use the pre-defined, fixed index group that is automatically generated by
Gromacs.

Best regards,
Teemu
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Re: [gmx-users] g-select failed

[Teemu Murtola]

Hi,

On Mon, Sep 8, 2014 at 4:47 PM, Albert mailmd2...@gmail.com wrote:

 I am trying to make two groups for my lipids sytem by g_select with
 command line:

 g_select_mpi -sf select.dat -f em.gro

 here is the content of select.dat:

 up=z80;
 down=z80;

 but it failed with messages: ...


Your selection file only declares two selection variables (up and
down), but no actual selections. Since g_select expects to get some
selections, it gives the error message. You can specify your selections
like this if you want to give them names:

up z80;
down z80;

Best regards,
Teemu
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Re: [gmx-users] g_select syntax

[Teemu Murtola]

Hi,

On Sep 3, 2014 11:32 PM, Bin Liu fdusuperstr...@gmail.com wrote:
 Thank you for your explanation. Now I understand why the first selection
 gives more residues as it's simply a superset of the second selection. I
 just realized to accomplish what I initially want, i.e., to obtain the
 residue index list of LIPID whose center of mass is within 1.0 nm of the
 surface of protein, I just need

 group LIPID and res_com within 1.0 of group PROTEIN
 and
  g_select -sf selection.dat -f traj.trr -s traj.tpr -n system.ndx  -oi
 index.dat -seltype res_com -selrpos atom

Good to hear the explanation was useful.

 Again, I am a bit confused by that it seems the sole function of -seltype
 res_com is outputting residue index instead of atom index.

For g_select, it has no other effect, but for other tools using selections
(which exist in 5.0), it has a more intuitive meaning to influence the type
of positions that will be used for analysis.

 If I use
 -seltype atom instead, g_select will return all the corresponding atoms in
 the residues selected by the selection just above. What frustrates me most
 is I can't find a flag to be used in selection.dat to let g_select output
 residue index, not atom index.

-seltype res_com is exactly equivalent to prefixing every selection with
res_com of. The -seltype flag just provides a shorthand for doing this in
case there are many selections. Similarly, -selrpos res_com is just a
convenient alternative to specifying using res_com everywhere it is
applicable (like res_com x and res_com within ...).

Hope this helps,
Teemu
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Re: [gmx-users] g_select syntax

[Teemu Murtola]

Hi,

On Fri, Aug 29, 2014 at 4:19 AM, Bin Liu fdusuperstr...@gmail.com wrote:

 I am recently puzzled by the syntax and behaviour of g_select. I want to
 obtain the residue index list of LIPID whose center of mass is within 1.0
 nm of the surface of protein. In my case, each LIPID molecule consists of
 only one residue. I wrote the selection.dat as follows, and set -selrpos to
 atom and -seltype to res_com. Here I think Protein is the reference
 group, so -selrpos should be atom because I care about the distance to its
 surface. LIPID is the analysis group and I care about their individual
 center of mass. So -seltype should be res_com.

 selection.dat:
 resname LIPID and within 1.0 of group Protein;

 g_select -sf selection.dat -f traj.trr -s traj.tpr -n system.ndx  -oi
 index.dat -seltype res_com -selrpos atom


Yes, this should give you what you expect. It selects all LIPID atoms that
are within 1.0 nm from the protein, and then groups them by residue for the
-oi output.

However I tried another selection. This time instead of retrieving the
 residue index, I tried to retrieve the index of a key atom of the LIPID
 molecule.
 selection.dat:
 rdist = res_com within 1.0 of group Protein;
 group_C15 = (resname LIPID) and (rdist) and (name C15);
 group_C15;

 g_select -sf selection.dat -f traj.trr -s traj.tpr -n system.ndx  -oi
 index.dat -seltype atom -selrpos atom


res_com within has a different meaning from using -seltype res_com: your
second selection selects all C15 atoms that are in LIPID residues, and
where the center-of-mass of the whole residue is within 1 nm from the
protein (the last part is the res_com within expression).

-seltype res_com in the first example is equivalent to writing this, where
the res_com is in a very different location:
res_com of (resname LIPID and within 1.0 of group Protein)

Hopefully this helps understanding where the difference between the
selections comes from.

I thought these two selections should give the same number of indices per
 frame, as the second selection merely retrieve the atom indices of the
 corresponding key atoms in the LIPID molecules selected by the first
 selection. However the first selection gives significantly more indices
 than the second selection does. I guess my understanding of g_select syntax
 might be flawed. Please point out my misunderstanding. Thank you very much.


If you want to select the key atoms that match those from your first
selection, you need to write something more complex:

name C15 and same residue as (resname LIPID and within 1.0 of group
Protein)

The last selection should be self-explanatory.

Hope this helps,
Teemu
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Re: [gmx-users] g_select position variables

[Teemu Murtola]

Hi,

On Tue, Jul 29, 2014 at 6:18 AM, Cara Kreck cara_...@hotmail.com wrote:

 Is it possible to use a position variable in conjunction with x,y,z
 keywords in g_select?


Unfortunately, this is currently not possible.

I'm trying to select all molecules within a channel embedded in a membrane.
 In case the protein and/or membrane moves around I want to use position
 variables instead of numerical values to define the z range. I've tried
 this in my selection.dat file:

 solution = resname SOL or resname CL;
 top = res_com of resnr 1181;
 bottom = res_com of resnr 55;
 cavity = solution and z bottom to top;
 cavity;

 and
 cavity = solution and ztop and zbottom;
 cavity;

 But I get an invalid selection error. However, if I substitute top and
 bottom with numbers, it does work. Is there something wrong with my syntax
 or am I just trying to do the impossible?


Yes, this is as expected. There is currently no way to generate single
numbers from position-valued expressions like top and bottom above. It
may be difficult to implement either of the above syntaxes, but what could
be relatively easy is that one could write z of top to extract a number
which could then be used in comparisons. But it may take time before I get
around to implementing anything like this.

Best regards,
Teemu
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Re: [gmx-users] how to compile and make a C analyzing code under GROMACS 5.0

[Teemu Murtola]

Hi,

On Mon, Jul 28, 2014 at 7:45 PM, Mark Abraham mark.j.abra...@gmail.com
wrote:

 On Mon, Jul 28, 2014 at 6:05 PM, qiaobf qia...@gmail.com wrote:
   2) If the line with sqrt function is commented out, the g_density2 can
  be successfully generated. however, the ./g_density2 -h is not working
 to
  display the help contents. Could you please give me some suggestions?

 Things change. ;-) If you're deliberately bypassing the new wrapper binary,
 then you won't get the functionality it supports, like the new help module
 output.


There is also some information here:

http://jenkins.gromacs.org/job/Doxygen_Nightly_master/javadoc/html-user/page_usinglibrary.xhtml

It is not very explicit, but if you follow the links for gmx_run_cmain()
and parse_common_args() from there, you will probably find a solution at
least to the -h problem.

Best regards,
Teemu
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Re: [gmx-users] problem with calculating angles and dynamic selections

[Teemu Murtola]

No, this is not a bug, but a result of a conscious design. Internally, the
selections are always evaluated as sets of atoms, which are (currently)
handled as a sorted list of indices. So any basic selection operation
always results in sorted atoms. If you want something else, you can use
permute, merge or plus (which is only necessary for those few tools
that put significance to the order of atoms).

In addition to simplifying the implementation, this is much clearer. Or
what order would you expect the atoms to be if you provide a selection
name C A B, and your system has 10 A atoms, 5 B atoms and 3 C atoms? How
about if the system has molecules with multiple residues (so that splitting
by molecule or by residue results in different ordering)? Or if you combine
two arbitrary unsorted expressions with and or or?
On Jul 3, 2014 8:04 PM, Venkat Reddy venkat...@gmail.com wrote:

 Hi,
 I have tried gmx gangle -g1 angle option. Its sorting the atoms specified
 in the input. I think it might be a bug. gmx gangle  -g1 vector -g2 vector
 is doing fine.


 On Thu, Jul 3, 2014 at 7:42 PM, gigo g...@ibb.waw.pl wrote:

  Hi!
  I find it impossible to calculate (some) angles between atoms using
  dynamic selection in 'gmx gangle' command. The problem is, that the
 dynamic
  selection mechanism persistently sorts numbers of atoms specified in the
  input. So, if I have atoms A, B and C with ascending indexes, I am not
 able
  to calculate angle B-A-C - I only get value for A-B-C, no matter how I
  order them in the command line. Is there any way to do it without writing
  an index file (which I have to parse anyway, because the same mechanism
  sorts atoms in 'gmx select'...)? If not, I will submit a feature request
 on
  redmine - something like -nosort option...
  Regards,
 
  Grzegorz Wieczorek
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 --
 With Best Wishes
 Venkat Reddy Chirasani
 PhD student
 Laboratory of Computational Biophysics
 Department of Biotechnology
 IIT Madras
 Chennai
 INDIA-600036
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Re: [gmx-users] dynamic selection memory allocation problem

[Teemu Murtola]

Please try 'gmx gangle'. It does not have all the functionality of 'gmx
angle', which is why the old tool has not been replaced completely.


On Mon, Jun 30, 2014 at 11:03 PM, gigo g...@ibb.waw.pl wrote:

 Dear Teemu,
 Thank you very much for the reply and such a fast patching of the sources.
 I have another question. Are there any plans for importing the dynamic
 selection scheme into the angle command?
 Best,

 g


 On 2014-06-29 06:58, Teemu Murtola wrote:

 There were some hardcoded string buffers left from C days that were
 necessary for error handling that placed a somewhat arbitrary limitation
 of
 1024 characters per a single selection.

 For the matter of what you are trying to achieve, you can probably do that
 with gmx distance (with or without the fix for the limitation from
 Gerrit),
 but that tool may not be that well suited for the task. On purpose, I did
 not add functionality to do 1-to-many or many-to-many distances there,
 since that would better fit into another tool (which I or anyone else has
 not had time to write yet), but it seems that this is the functionality
 you
 desire.

 I would probably write a custom tool (based on the installed
 share/gromacs/template) that would actually calculate the properties you
 want, based on a selection that provides the ligand atoms of interest and
 the water molecules you want, but I understand that not everyone is fluent
 in C/C++.

 If your system is big, you can probably also make your selection
 substantially more effective by using multiple selections (it does not
 appear that you actually need the plus keyword if you are only interested
 in the -oall output) and a variable for the part after or that is always
 evaluated for ~all atoms:

   ligand_p = resname LIG and name P;
   resid 14497 and resname SOL and name LP1 or ligand_p;
   resid 14497 and resname SOL and name LP1 or ligand_p;
   resid 14497 and resname SOL and name LP1 or ligand_p;
   ...

 It also sounds that your script probably already has knowledge of the atom
 indices, so it could generate the selection to use those directly.

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Re: [gmx-users] dynamic selection memory allocation problem

[Teemu Murtola]

There were some hardcoded string buffers left from C days that were
necessary for error handling that placed a somewhat arbitrary limitation of
1024 characters per a single selection.

For the matter of what you are trying to achieve, you can probably do that
with gmx distance (with or without the fix for the limitation from Gerrit),
but that tool may not be that well suited for the task. On purpose, I did
not add functionality to do 1-to-many or many-to-many distances there,
since that would better fit into another tool (which I or anyone else has
not had time to write yet), but it seems that this is the functionality you
desire.

I would probably write a custom tool (based on the installed
share/gromacs/template) that would actually calculate the properties you
want, based on a selection that provides the ligand atoms of interest and
the water molecules you want, but I understand that not everyone is fluent
in C/C++.

If your system is big, you can probably also make your selection
substantially more effective by using multiple selections (it does not
appear that you actually need the plus keyword if you are only interested
in the -oall output) and a variable for the part after or that is always
evaluated for ~all atoms:

  ligand_p = resname LIG and name P;
  resid 14497 and resname SOL and name LP1 or ligand_p;
  resid 14497 and resname SOL and name LP1 or ligand_p;
  resid 14497 and resname SOL and name LP1 or ligand_p;
  ...

It also sounds that your script probably already has knowledge of the atom
indices, so it could generate the selection to use those directly.


On Fri, Jun 27, 2014 at 6:08 PM, gigo g...@ibb.waw.pl wrote:

 Dear Teemu,
 Thank you! My intention is to calculate many different distances, angles
 an dihedral angles, without prior knowlege of moluecules involved. First, I
 select water molecules that appear around my ligand docked in the protein,
 then analyze positions of these water molecules. I am interested in the
 solvation process, detailed interactions between the solvent and solute.
 Complicating the example that I gave does not change the error, though...
 Best Regards,

 g


 On 2014-06-27 15:48, Teemu Murtola wrote:

 My point about being non-illustrative was that it is impossible for people
 to suggest alternative solutions if they don't know what you are trying to
 achieve. If you really want to calculate the same distance multiple times,
 I'd suggest to calculate it just once, and have a postprocessing script to
 duplicate it in the output.
 On Jun 27, 2014 4:28 PM, gigo g...@ibb.waw.pl wrote:


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Re: [gmx-users] dynamic selection memory allocation problem

[Teemu Murtola]

My point about being non-illustrative was that it is impossible for people
to suggest alternative solutions if they don't know what you are trying to
achieve. If you really want to calculate the same distance multiple times,
I'd suggest to calculate it just once, and have a postprocessing script to
duplicate it in the output.
On Jun 27, 2014 4:28 PM, gigo g...@ibb.waw.pl wrote:

 Dear Teemu,
 Thank you for your reply.

  Please file a report a http://redmine.gromacs.org with files and the
 exact selection necessary to reproduce the problem (a single .gro
 structure
 is likely sufficient).


 I will do so.

  While your approach is likely a very inefficient way
 to use the selections (plus/merge is not designed for massive copying, and
 your selection probably evaluates some parts multiple times over all the
 atoms in the system), it would be useful to find out what is the actual
 problem.


 OK. What approach would you suggest for calculating many distances without
 writing an index file then?

  Your example is not particularly illustrative, as there is no point in
 computing the same distance 15 times...


 The purpose of the example was to show that the dynamic selection
 mechanism has a limited capacity in terms of the length of the input
 string, and not to show that my research is of any value for anybody. Id
 did the job, so it was illustrative.

 Thank you once more,

 g

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Re: [gmx-users] gmx gangle in the development version of gromacs

[Teemu Murtola]

On Thu, Mar 6, 2014 at 1:48 AM, Eric Smoll ericsm...@gmail.com wrote:

  As you have noted, whole_res_cog computes the center-of-geometry of the
  whole residue that contains an individual atom. So if each of your rings
 is
  within a single residue, this makes then selected as a unit, based on the
  center of the whole residue. If you only want to select based on the
 center
  of the ring, you can use part_res_cog. The difference is explained in
 'gmx
  help selections positions' (accessible also when writing help in the
  interactive selection prompt).

 I will try part_res_cog but I suspect it is not what I want. 'gmx help
 selections positions'
 states:
 part_ prefix calculates the centers for the selected atoms, but uses
 always the same atoms
 for the same residue/molecule. The used atoms are determined from the the
 largest group allowed by the selection.
 This first sentence sounds like it may preform the selection I desire but
 the second
 sentence is worrisome.  I have a molecule with a ring. My index file
 selects three atoms from this molecule to monitor - three atoms are needed
 for an normal
 vector calculation. If a cog is in the selection region but only one of the
 three atoms that
 define a given cog are in the selection region, will 'part_res_cog' result
 in the selection of all three atoms?


Yes, it will. If you have a selection like
  name A B C and z  0
and your residue has atoms A B C D E, then

   - -selrtype whole_res_cog will select either all or none of A-C, based
   on the CoG of A-E.
   - -selrtype part_res_cog will select either all or none of A-C, based on
   the CoG of A-C.
   - -selrtype dyn_res_cog will in this case do the same as part_res_cog.
   It requires quite a complex selection to make a difference between the two
   (for example, name A B C and atom z  0 and dyn_res_cog x  0, in which
   case the second x  0 condition only compares based on the CoG of the
   atoms that satisfy z  0). This is probably confusing and not usually
   necessary; it mostly makes sense as an output option from the selections
   only: dyn_res_cog of name A B C and z  0 computes the output position
   from those atoms that actually satisfy the z  0 condition.

If the residue index controls which atoms are grouped in a given 'residue',
 what
 controls the molecule specification?  What is it in the .gro file that
 defines an
 atom as belonging to a specific molecule?


There is nothing in a .gro file that specifies a molecule. This option only
works with a full .tpr file, in which case the molecule definitions from
the simulation topology are used.

This sounds like a very straightforward solution! I read up on the format
 of the
 .gro file.  It makes sense that I should be free to manipulate the residue
 numbers
 but are they any restrictions? For example. do the residue numbers need to
 be grouped and
 consecutive? I ask because a separate software (VMD) will not support
 residue number reassignment
 of various nonconsecutive atoms without disrupting the residue selection
 algorithm.


In Gromacs, a group of consecutive atoms with the same residue number is
treated as a single residue. If the same residue number repeats elsewhere,
then it is a different residue. There is no requirement on the numbers of
different residues being consecutive. So the atoms in a residue need to be
grouped together, but there are no other restrictions. Depending on what
you want to do with the numbers, it can be confusing, though, if the same
number repeats.

Teemu
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Re: [gmx-users] g_sas: unable to reproduce data from original article of the DCLM (Eisenhaber1995)

[Teemu Murtola]

Hi,

Thanks for the report. In relation to
https://gerrit.gromacs.org/#/c/2726/I had been planning to add some
tests for the actual algorithm used, and
this report made me prioritize this. Here's an intermediate result. I have
not yet tested the PBC-enabled computation at all, and haven't looked at
the development history in detail, so I cannot give a full picture.

But so far I've found that the algorithm implemented in g_sas does not work
correctly in the no-PBC case, except possibly with equally sized spheres.
It fails to reproduce even basic analytical results with two spheres of
unequal size (as long as the sphere that appears first in the coordinate
file is smaller). This appears to be fixed by removing (there should be
only one matching line)

  ra2max = radius[iat];

from src/tools/nsc.c (in 4.6 and earlier). This may not be the only problem
in the algorithm, but can you check whether such a modified version helps
with the -nopbc case? I'll post additional information once I have had time
to test more cases.

Best regards,
Teemu


On Sun, Feb 23, 2014 at 5:29 AM, João M. Damas jmda...@itqb.unl.pt wrote:

 Thank you for your fast reply and your suggestions! The results are in
 Attached Table 2 (see below).

- I followed your PBC suggestion, but used the -pbc flag instead (I
still ended up doing yours, read further ahead). While turning off PBC
 for
GMX4.0.4 leaves the results unchanged, doing the same for GMX4.6.3
 changes
the results closer to the 4.0.4 results. Different results from changing
PBC in different versions could possibly mean different boxes coming
 from
possible different processing. Since I'm providing to g_sas a .pdb file
only with ATOM records, one could assume g_sas is taking the box from
 the
.tpr file provided in -s. The .tpr file was created using
 pdb2gmx+grompp. I
checked the .gro files boxes and they are all the same (for the same
protein, of course). Maybe g_sas is guessing a box on its own (and
differently for different versions)? Thinking the -pbc flag may be
 behaving
weirdly, I have also made a batch equal to Attached Table 2 but running
 a
editconf -d 5 in between pdb2gmx and grompp (your suggestion), and the
results are all the same as with the smaller box, confirming the
-nopbc/-pbc differences as really weird... Any ideas?
- changing from single to double precison only causes changes that are,
at maximum, of a few square angstroms, but most commonly under 1 square
angstrom. This does not seem to be the answer either...

 Further input on this issue is deeply appreciated!

 Best,
 João

 P.S: g_sas issues a warning that comes from atomprop.c that starts with
 Masses and atomic (Van der Waals) radii will be guessed based on residue
 and atom names From what I read from the code, this means they will be
 fetched from vdwradii.dat and atommasses.dat instead of the topology. Maybe
 those files should mentioned in that warning? Just a minor remark.

 --
 Attached Table 2
 met  - method used, anl=analytical method, num=numerical method (DCLM)
 dots - number of points used for the numerical method
 src  - source of the data, paper=Eisenhaber1995, ASC=ASC software,
g{404,463}{sp,dp}=g_sas of GMX4.{0.4,6.3} {single,double} precision
 pbc  - PBC flag for g_sas, yes=-pbc, no=-nopbc
 Areas are in square angstrom
 ==
   met  dots src  pbc  4PTI  3FXN  1TIM
 ==
   anl paper3973.80   6943.80  20002.80
   anl   ASC3973.81   6943.80  20002.80

   num   122   paper3961.40   6968.30  19970.90
   num   122 ASC3961.44   6968.33  19970.90
   num   122  g404sp  yes   4165.31   7727.73  24110.10
   num   122  g404sp   no   4165.31   7727.73  24110.10
   num   122  g404dp  yes   4165.57   7722.80  24110.30
   num   122  g404dp   no   4165.57   7722.80  24110.30
   num   122  g463sp  yes   3825.86   6257.83  19867.90
   num   122  g463sp   no   4169.21   7731.63  24080.20
   num   122  g463dp  yes   3826.12   6258.51  19866.90
   num   122  g463dp   no   4169.47   7726.70  24080.30

   num   362   paper3971.80   6933.40  19997.10
   num   362 ASC3971.79   6933.37  19997.10
   num   362  g404sp  yes   4192.12   7704.33  24161.50
   num   362  g404sp   no   4192.12   7704.33  24161.50
   num   362  g404dp  yes   4191.91   7703.31  24160.20
   num   362  g404dp   no   4191.91   7703.31  24160.20
   num   362  g463sp  yes   3838.35   6248.43  19886.80
   num   362  g463sp   no   4195.02   7704.70  24132.10
   num   362  g463dp  yes   3838.24   6249.87  19884.70
   num   362  g463dp   no   4194.81   7703.68  24130.80

   num   642   paper3967.90   6944.40  19998.70
   num   642 ASC3967.78   6944.37  19998.70
   num   642  g404sp  yes   4187.54   7703.00  24148.90
   num   642  g404sp   no   4187.54   

Re: [gmx-users] g_sas: unable to reproduce data from original article of the DCLM (Eisenhaber1995)

[Teemu Murtola]

Hi,

On Thu, Feb 27, 2014 at 4:09 PM, Teemu Murtola teemu.murt...@gmail.comwrote:

 I'll post additional information once I have had time to test more cases.


I have now created http://redmine.gromacs.org/issues/1445 to track the
issue, and uploaded a fix to Gerrit: https://gerrit.gromacs.org/#/c/3199/.
My current set of tests is here: https://gerrit.gromacs.org/#/c/3200/

Looking at the history, as described in the Redmine issue, this should
explain incorrect results with -nopbc. The Redmine issue also provides an
explanation for why 4.0.4 gives the same results with -pbc and -nopbc. This
doesn't explain why it gives a slight underestimation with -pbc in 4.6.3,
but you could try repeating the tests with the fixed version to see whether
the PBC treatment or something else is giving rise to the underestimation.

Best regards,
Teemu
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Re: [gmx-users] Problems with mdrun (version 4.6.5) and CPU-type: Xeon E5472

[Teemu Murtola]

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Re: [gmx-users] future of shell completions in GROMACS

[Teemu Murtola]

Hi,

On Tue, Jan 21, 2014 at 11:23 AM, Djurre de Jong-Bruinink 
djurredej...@yahoo.com wrote:

 On a slightly related issue: the enviroment variable GMX_NO_CREDITS
 doesn't work anymore in gmx5b. That made my work in the terminal a lot
 easier too (Not that I think you guys don't deserve the credits!). Is that
 planned to be reimplemented? I also find the template/layout of the
 credits-section less structured and appealing than in the old version.


The -quiet and -nocopyright command-line options have largely replaced the
need for the environment variable. GMX_NO_CREDITS was added in 4.6 as a
workaround for the lack of such options (whose implementation required some
extra refactoring). Is there some need that isn't satisfied by these
options (and possibly shell aliases)?

Teemu
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Re: [gmx-users] future of shell completions in GROMACS

[Teemu Murtola]

Hi,

On Wed, Jan 22, 2014 at 7:40 PM, jkrie...@mrc-lmb.cam.ac.uk wrote:

 ok. I suppose I can try.


If you want to help, I suggest starting from the completion files generated
by https://gerrit.gromacs.org/#/c/2590/ (they get generated to
src/programs/completion when you run 'make completion'). Those work for
bash; nothing is generated for others. For zsh, it might be easiest to try
to use the same completions with bashcompinit. As Szilard said, you don't
necessarily need to know C/C++ (although the code that generates the
completions is written with those). What we would need is help in
investigating how to implement the support in the first place, and for
that, it is sufficient to have an outline of how the generated completions
should look like for tcsh or zsh. And then it would be nice to have some
people actually try out the completions.

Best regards,
Teemu
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Re: [gmx-users] question

[Teemu Murtola]

Instead of such a complicated script, I would use 'g_select -os', which
gives you the same output without any post-processing. Whether this matches
what the original poster wanted, or whether g_rdf is more suitable, depends
on what they want to count.

Best regards,
Teemu

On Tue, Jan 21, 2014 at 2:04 PM, jkrie...@mrc-lmb.cam.ac.uk wrote:

 Here is my python script as promised:

 # select filenames for reading and writing
 fr = open('chainA_T78-waters_index.ndx','r')
 fw = open('chainA_T78-waters_counts.xvg','w')

 line = fr.readline()
 t = line.split('_')[-1].split()[0]
 c = 0

 for line in fr:
 if line.find('[') == -1:
 c += len(line.split())
 else:
 fw.write(t + ' ' + str(c) + '\n')
 t = line.split('_')[-1].split()[0]
 c = 0

 fw.write(t + ' ' + str(c) + '\n')

 fr.close()
 fw.close()

 It reads in a file from g_select that looks as follows
 [ chain_A_T78_waters_0.000 ]
 45170 45172 55565 55566 55567 217685 217686 217688 217689 217690 217709
 217710 217711 355868 355870
 380249 380250 380251
 [ chain_A_T78_waters_2.000 ]
 55565 55566 55567 217686 217688 217689 217690 217709 217710 217711 289964
 355868 355870 380249 380250
 380251
 [ chain_A_T78_waters_4.000 ]
 45170 45171 45172 55565 55566 55567 217688 217689 217690 217709 217710
 217711 355869 367615 380249
 380250 380251

 and write out a file with counts that looks like this that xmgrace can read
 0.000 18
 2.000 16
 4.000 17

 Best wishes
 James

  I have no experience with g_rdf but that looks like it might work if you
  only want the average number. Anyhow I'm writing the script to count my
  g_select output now and I'll send it to you soon. This script should
 allow
  the number to be plotted over time.
 
  Best wishes
  James
 
  Dear Jkrieger
 
  Thanks for your attention.
 
  I have index file containing 2 group which are my interest.
 
  Unfortunately, I am beginner in scripting and I have no long time.
  I should do this analysis as soon as possible. Please if you write such
  a
  script, send me it.
 
  Is g_rdf -cn appropriate for my case?

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