Re: [gmx-users] g_mindist

[Justin Lemkul]

On 6/15/13 1:07 PM, Mahin Saberi wrote:

Hi gmx users
I really confused that How I determine the distances between center of mass
of a molecules and center of mass of number of other molecules?


Use g_dist with suitable index groups.

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] g_mindist

[Mahin Saberi]

Hi gmx users
I really confused that How I determine the distances between center of mass
of a molecules and center of mass of number of other molecules?
Please guide me
thanks a lot
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Re: [gmx-users] g_mindist - reg

[Justin Lemkul]

On 9/3/12 2:04 AM, Raj wrote:

hi all,

I would like to measure the hydrophobic interaction of the ligand against
the protein during the simulation . From the forum I learnt g_mindist will
be the better tool. But when i  used the command  g_mindist -f traj.xtc -s
topol.tpr -n index.ndx -on numcont.xvg -group and selected protein as group1
and ligand as group 2 i get the result like this

g_mindist -f traj.xtc -s pull.tpr -n index.ndx -on numcont.xvg -group
#
# g_mindist is part of G R O M A C S:
#
# Good ROcking Metal Altar for Chronical Sinners
#
@title "Number of Contacts < 0.6 nm"
@xaxis  label "Time (ps)"
@yaxis  label "Number"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "Protein-UNK"
0.00e+0021
1.00e+0021
2.00e+0021
3.00e+0021
4.00e+0021
5.00e+0021
6.00e+0021
7.00e+0021
8.00e+0021
9.00e+0021
1.00e+0121
1.10e+0121
1.20e+0121
1.30e+0121
1.40e+0121
1.50e+0121
1.60e+0121
1.70e+0121
1.80e+0121
1.90e+0121
2.00e+0121
2.10e+0121
2.20e+0121
2.30e+0121
2.40e+0121
2.50e+0121
2.60e+0121
2.70e+0121
2.80e+0121
2.90e+0121
3.00e+0121
3.10e+0121
3.20e+0121
3.30e+0121
3.40e+0121
3.50e+0121
3.60e+0121
3.70e+0121
3.80e+0121
3.90e+0121
4.00e+0121
4.10e+0121
4.20e+0121
4.30e+0121
4.40e+0121
4.50e+0121
4.60e+0121
4.70e+0121
4.80e+0121
4.90e+0121
5.00e+0121
5.10e+0121
5.20e+0121
5.30e+0121


I would like to know what ever the data I've obtained is the number of
hydrophobic interaction between the ligand and protein or I am wrong
somewhere. Please help me. Thanks in advance




If the index groups contain hydrophobic atoms, then yes.  If they contain other 
atoms, then no.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] g_mindist - reg

[Raj]

hi all,

I would like to measure the hydrophobic interaction of the ligand against
the protein during the simulation . From the forum I learnt g_mindist will
be the better tool. But when i  used the command  g_mindist -f traj.xtc -s
topol.tpr -n index.ndx -on numcont.xvg -group and selected protein as group1
and ligand as group 2 i get the result like this

g_mindist -f traj.xtc -s pull.tpr -n index.ndx -on numcont.xvg -group
#
# g_mindist is part of G R O M A C S:
#
# Good ROcking Metal Altar for Chronical Sinners
#
@title "Number of Contacts < 0.6 nm"
@xaxis  label "Time (ps)"
@yaxis  label "Number"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "Protein-UNK"
0.00e+0021
1.00e+0021
2.00e+0021
3.00e+0021
4.00e+0021
5.00e+0021
6.00e+0021
7.00e+0021
8.00e+0021
9.00e+0021
1.00e+0121
1.10e+0121
1.20e+0121
1.30e+0121
1.40e+0121
1.50e+0121
1.60e+0121
1.70e+0121
1.80e+0121
1.90e+0121
2.00e+0121
2.10e+0121
2.20e+0121
2.30e+0121
2.40e+0121
2.50e+0121
2.60e+0121
2.70e+0121
2.80e+0121
2.90e+0121
3.00e+0121
3.10e+0121
3.20e+0121
3.30e+0121
3.40e+0121
3.50e+0121
3.60e+0121
3.70e+0121
3.80e+0121
3.90e+0121
4.00e+0121
4.10e+0121
4.20e+0121
4.30e+0121
4.40e+0121
4.50e+0121
4.60e+0121
4.70e+0121
4.80e+0121
4.90e+0121
5.00e+0121
5.10e+0121
5.20e+0121
5.30e+0121


I would like to know what ever the data I've obtained is the number of
hydrophobic interaction between the ligand and protein or I am wrong
somewhere. Please help me. Thanks in advance
  



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Re: [gmx-users] g_mindist on 51-frame trajectory gives 51 minimum distances but <51 atom pairs

[Matthew Zwier]

Hi Peter,

Thanks for the reply.  I'm not using the contact information at all
(-on is unspecified), and yes, it still generates a result for >6A in
the distance output (-od) , but the result for which atoms are at the
reported distance is sometimes missing from the atom pair output (-o)
file.

MZ

On Thu, Jan 26, 2012 at 6:42 PM, Peter C. Lai  wrote:
> I have not read the source, but the default search radius for mindist is
> 6A. If you have no contacts within 6A of the atoms in the primary group
> to the target group for a given frame, will it still generate a result,
> since for all intents and purposes the array search should be null in
> that case?
>
> On 2012-01-26 12:32:15PM -0500, Matthew Zwier wrote:
>> Hi all,
>>
>> I'm running g_mindist (from 4.5.5) on a slew of very short
>> trajectories (51 frames) in order to obtain both minimum distances and
>> the corresponding atom pairs, using
>>
>> echo 10 11 | g_mindist -nice 10 -f seg.xtc -n $NDX -s $TPR -nopbc -o
>> mindist_pairs.out -xvg none
>>
>> where NDX and TPR are (valid) index and topology files, respectively,
>> and nopbc is specified because there is no periodic box (these are
>> GB/SA simulations).  This is on a 64-bit Linux box, with GROMACS and
>> all dependencies compiled with GCC.  For all trajectories, the
>> resulting mindist.xvg always contains 51 entries with reasonable
>> values (in the 1.1-1.5 nm range), but for a subset of the
>> trajectories, the corresponding mindist_pairs.out contains less than
>> 51 entries (as low as ~30 in some cases).
>>
>> Reading the source for gmx_mindist.c, it appears that this should
>> never occur, at least not without giving a nonsense value of the
>> minimum distance for that frame in the process (1 mm, it would appear
>> from the source!).  I'm either missing something in my reading of
>> gmx_mindist.c, I've found a bug (unlikely), or I've managed to
>> convince GCC to mis-compile g_mindist somehow (more likely, though
>> still somewhat baffling).  Can anyone help me figure out what's going
>> on?
>>
>> Cheers,
>> Matt Z.
>> --
>> gmx-users mailing list    gmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at 
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> --
> ==
> Peter C. Lai                    | University of Alabama-Birmingham
> Programmer/Analyst              | KAUL 752A
> Genetics, Div. of Research      | 705 South 20th Street
> p...@uab.edu                     | Birmingham AL 35294-4461
> (205) 690-0808                        |
> ==
>
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Re: [gmx-users] g_mindist on 51-frame trajectory gives 51 minimum distances but <51 atom pairs

[Peter C. Lai]

I have not read the source, but the default search radius for mindist is
6A. If you have no contacts within 6A of the atoms in the primary group
to the target group for a given frame, will it still generate a result,
since for all intents and purposes the array search should be null in
that case?

On 2012-01-26 12:32:15PM -0500, Matthew Zwier wrote:
> Hi all,
> 
> I'm running g_mindist (from 4.5.5) on a slew of very short
> trajectories (51 frames) in order to obtain both minimum distances and
> the corresponding atom pairs, using
> 
> echo 10 11 | g_mindist -nice 10 -f seg.xtc -n $NDX -s $TPR -nopbc -o
> mindist_pairs.out -xvg none
> 
> where NDX and TPR are (valid) index and topology files, respectively,
> and nopbc is specified because there is no periodic box (these are
> GB/SA simulations).  This is on a 64-bit Linux box, with GROMACS and
> all dependencies compiled with GCC.  For all trajectories, the
> resulting mindist.xvg always contains 51 entries with reasonable
> values (in the 1.1-1.5 nm range), but for a subset of the
> trajectories, the corresponding mindist_pairs.out contains less than
> 51 entries (as low as ~30 in some cases).
> 
> Reading the source for gmx_mindist.c, it appears that this should
> never occur, at least not without giving a nonsense value of the
> minimum distance for that frame in the process (1 mm, it would appear
> from the source!).  I'm either missing something in my reading of
> gmx_mindist.c, I've found a bug (unlikely), or I've managed to
> convince GCC to mis-compile g_mindist somehow (more likely, though
> still somewhat baffling).  Can anyone help me figure out what's going
> on?
> 
> Cheers,
> Matt Z.
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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-- 
==
Peter C. Lai| University of Alabama-Birmingham
Programmer/Analyst  | KAUL 752A
Genetics, Div. of Research  | 705 South 20th Street
p...@uab.edu| Birmingham AL 35294-4461
(205) 690-0808  |
==

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[gmx-users] g_mindist on 51-frame trajectory gives 51 minimum distances but <51 atom pairs

[Matthew Zwier]

Hi all,

I'm running g_mindist (from 4.5.5) on a slew of very short
trajectories (51 frames) in order to obtain both minimum distances and
the corresponding atom pairs, using

echo 10 11 | g_mindist -nice 10 -f seg.xtc -n $NDX -s $TPR -nopbc -o
mindist_pairs.out -xvg none

where NDX and TPR are (valid) index and topology files, respectively,
and nopbc is specified because there is no periodic box (these are
GB/SA simulations).  This is on a 64-bit Linux box, with GROMACS and
all dependencies compiled with GCC.  For all trajectories, the
resulting mindist.xvg always contains 51 entries with reasonable
values (in the 1.1-1.5 nm range), but for a subset of the
trajectories, the corresponding mindist_pairs.out contains less than
51 entries (as low as ~30 in some cases).

Reading the source for gmx_mindist.c, it appears that this should
never occur, at least not without giving a nonsense value of the
minimum distance for that frame in the process (1 mm, it would appear
from the source!).  I'm either missing something in my reading of
gmx_mindist.c, I've found a bug (unlikely), or I've managed to
convince GCC to mis-compile g_mindist somehow (more likely, though
still somewhat baffling).  Can anyone help me figure out what's going
on?

Cheers,
Matt Z.
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Re: [gmx-users] g_mindist -on

[Mark Abraham]

On 9/11/2011 9:09 PM, Steven Neumann wrote:

Dear gmx Users,
I am wondering what is the value of Number of Contacts (<0.6 nm) 
between two groups. When I specify one group - Ligand and second 
- protein residue - does it count every dostance within 0.6 nm between 
every atom from one group and every atom from the second specified group?




Does g_mindist -h answer your question? If not, how can the text be 
improved?


Mark
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[gmx-users] g_mindist -on

[Steven Neumann]

Dear gmx Users,

I am wondering what is the value of Number of Contacts (<0.6 nm) between
two groups. When I specify one group - Ligand and second - protein residue
- does it count every dostance within 0.6 nm between every atom from one
group and every atom from the second specified group?

Cheers,

Steven
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Re: [gmx-users] g_mindist doubt

[aiswarya pawar]

Hi Tsjerk,

i used the command in format-

g_mindist -f md.xtc -s md.tpr -n 13.ndx -od 13.xvg -on 13.xvg -o 13.out -b
500 -e 1500 -d 0.5

so here i obtain the output-

atmpair.out-

0.00e+0013 21161
1.00e+0013 21161
2.00e+0013 21161
3.00e+0013 21161
4.00e+0013 21161
5.00e+0013 21161
6.00e+0013 21161
7.00e+0013 21161
8.00e+0013 21161
9.00e+0013 21161
1.00e+0113 21161
1.10e+0113 21161
1.20e+0113 21161
1.30e+0113 21161
1.40e+0113 21161
1.50e+0113 18698
1.60e+0113 21161
1.70e+0113 18698
1.80e+0113 18698
1.90e+0113 18698
2.00e+0113 18698
2.10e+0113 21455
2.20e+0113  7142
2.30e+0113  7142


and distance output-

0.00e+00  1.360443e+00
1.00e+00  1.246777e+00
2.00e+00  1.386871e+00
3.00e+00  1.250959e+00
4.00e+00  1.314306e+00
5.00e+00  1.273990e+00
6.00e+00  1.175991e+00
7.00e+00  1.154678e+00
8.00e+00  1.249905e+00
9.00e+00  1.110049e+00
1.00e+01  1.023204e+00
1.10e+01  1.004968e+00
1.20e+01  1.214452e+00
1.30e+01  1.297469e+00
1.40e+01  1.307791e+00
1.50e+01  1.276168e+00
1.60e+01  1.552775e+00
1.70e+01  1.668275e+00
1.80e+01  1.786125e+00
1.90e+01  1.733398e+00
2.00e+01  1.656987e+00
2.10e+01  1.715875e+00
2.20e+01  1.848419e+00
2.30e+01  1.932844e+00


Now my doubt is the whether these distances shown are the exact distance ie
actual or the minimum distance measured between the two atoms.

Thanks

On Thu, Sep 22, 2011 at 12:13 PM, Tsjerk Wassenaar wrote:

> Hi Aiswarya,
>
> What did you do, what did you get, what did you expect and what is
> your hunch regarding the difference between your result and your
> expectation?
>
> Tsjerk
>
> On Thu, Sep 22, 2011 at 8:21 AM, aiswarya pawar
>  wrote:
> > Hi users,
> >
> > The g_mindist gives the minimum distance between the atoms other than the
> > actual distance.
> >
> > Thanks
> >
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
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> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
> --
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Re: [gmx-users] g_mindist doubt

[Mark Abraham]

On 22/09/2011 4:43 PM, Tsjerk Wassenaar wrote:

Hi Aiswarya,

What did you do, what did you get, what did you expect and what is
your hunch regarding the difference between your result and your
expectation?


And have you checked out g_mindist -h?

Mark



Tsjerk

On Thu, Sep 22, 2011 at 8:21 AM, aiswarya pawar
  wrote:

Hi users,

The g_mindist gives the minimum distance between the atoms other than the
actual distance.

Thanks

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Re: [gmx-users] g_mindist doubt

[Tsjerk Wassenaar]

Hi Aiswarya,

What did you do, what did you get, what did you expect and what is
your hunch regarding the difference between your result and your
expectation?

Tsjerk

On Thu, Sep 22, 2011 at 8:21 AM, aiswarya pawar
 wrote:
> Hi users,
>
> The g_mindist gives the minimum distance between the atoms other than the
> actual distance.
>
> Thanks
>
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>



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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[gmx-users] g_mindist doubt

[aiswarya pawar]

Hi users,

The g_mindist gives the minimum distance between the atoms other than the
actual distance.

Thanks
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[gmx-users] g_mindist on rhombic dodecahedron system

[Anna Marabotti]

Dear users,
following Tsjerk' suggestions, I simulate the protein which had some
problems in periodic distance violations in a triclinic box, using instead a
rhombic dodecahedron box created with the options:
 
editconf -f prot.gro -o prot_boxdod.gro -bt dodecahedron -d 1.5 -c
 
Minimization, PR-NVT and PR-NPT went OK (no error messages, potential energy
after minimization of about -1e+6). I run 30 ns full MD (no PR).
At the end of the production MD, I would like to repeat the g_mindist
analysis, so I can be sure my system does not suffer again of a periodic
distance violation.
I performed g_mindist on 4 different systems, and these are my results:
1) on the resulting trajectory: on average, the distance between two
periodic distances calculated on the entire protein (option = 1) is > 3 nm.
However, until 10 ns I can see several "spikes" going down to < 0.1 nm
2) on the resulting trajectory, applying trjconv -pbc nojump before
g_mindist: on average, the distance is < 0.1 nm
3) on the resulting trajectory, applying trjconv -pbc whole -ur compact
before g_mindist: the same as 1) (perfectly superimposable)
4) on the resulting trajectory, applying trjconv -pbc whole -ur compact,
then trjconv -pbc nojump, before g_mindist calculation: the same as 2)
(perfectly superimposable)
My questions are:
1) do I have to transform in some (other) way the trajectory before
calculating g_mindist? Do I have to calculate g_mindist in another way (eg.
using a different group for calculations)?
2) given these results, can I consider this trajectory suitable for
analysis? (maybe excluding the first 10 ns)
3) If not, what can I do more to have a suitable trajectory?
 
Many thanks for any suggestions, I'm quite frustrating for not understanding
where the problem comes from...
Anna
 
__
Anna Marabotti, Ph.D.
Laboratory of Bioinformatics and Computational Biology
Institute of Food Science - CNR
Via Roma, 64
83100 Avellino
Phone: +39 0825 299651
Fax: +39 0825 781585
E-mail: amarabo...@isa.cnr.it
Skype account: annam1972
Web site: http://bioinformatica.isa.cnr.it/anna/anna.htm
 
"When a man with a gun meets a man with a pen, the man with the gun is a
dead man"
(Roberto Benigni, about Roberto Saviano)
 
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Re: [gmx-users] g_mindist

[Justin A. Lemkul]

ahmet yıldırım wrote:

Dear Justin,

can you suggest me published paper related to about hydrophobic and 
hydrophilic contacts?




A few minutes on Google or the literature searching database of your choice 
should turn up something useful.  If you need to understand the definition or 
nature of such interactions, a basic biochemistry textbook should cover it.


-Justin

03 Temmuz 2011 00:24 tarihinde Justin A. Lemkul > yazdı:




ahmet yıldırım wrote:

Dear Justin,

You said before "you can obtain some idea by using g_mindist to
calculate hydrophobic and hydrophilic contacts between the
protein and ligand".

That is, I can explore whether there is hydrophobic or
hydrophilic feature of ligand using g_mindist tool. is this correct?
I did the calculations related to protein_ligand interactions
(protein contains two ligand). I plotted the graphs of distance
and numcount versus simulation time for each ligand. The number
of contacts in  ligand x is more than the other ligand y. Which
of this ligands are hydrophobic? Which is hydrophilic? I know
you are not private tutor. Please don't be angry :(


I certainly hope I haven't given the impression that I'm some angry
tyrant.  I'm happy to answer reasonable questions across the list,
time permitting.

To obtain information about hydrophobic and hydrophilic contacts,
you need to use special index groups that tell g_mindist (or any
other tool) which atoms to consider.  In this way, you can count how
many of each type of contact evolve over time.

-Justin

-- 
==__==


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-9080
http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin


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--
Ahmet YILDIRIM


--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] g_mindist

[ahmet yıldırım]

Dear Justin,

can you suggest me published paper related to about hydrophobic and
hydrophilic contacts?

03 Temmuz 2011 00:24 tarihinde Justin A. Lemkul  yazdı:

>
>
> ahmet yıldırım wrote:
>
>> Dear Justin,
>>
>> You said before "you can obtain some idea by using g_mindist to calculate
>> hydrophobic and hydrophilic contacts between the protein and ligand".
>>
>> That is, I can explore whether there is hydrophobic or hydrophilic feature
>> of ligand using g_mindist tool. is this correct?
>> I did the calculations related to protein_ligand interactions (protein
>> contains two ligand). I plotted the graphs of distance and numcount versus
>> simulation time for each ligand. The number of contacts in  ligand x is more
>> than the other ligand y. Which of this ligands are hydrophobic? Which is
>> hydrophilic? I know you are not private tutor. Please don't be angry :(
>>
>>
> I certainly hope I haven't given the impression that I'm some angry tyrant.
>  I'm happy to answer reasonable questions across the list, time permitting.
>
> To obtain information about hydrophobic and hydrophilic contacts, you need
> to use special index groups that tell g_mindist (or any other tool) which
> atoms to consider.  In this way, you can count how many of each type of
> contact evolve over time.
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-requ...@gromacs.org.
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>



-- 
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Re: [gmx-users] g_mindist

[Justin A. Lemkul]

ahmet yıldırım wrote:

Dear Justin,

You said before "you can obtain some idea by using g_mindist to 
calculate hydrophobic and hydrophilic contacts between the protein and 
ligand".


That is, I can explore whether there is hydrophobic or hydrophilic 
feature of ligand using g_mindist tool. is this correct?
I did the calculations related to protein_ligand interactions (protein 
contains two ligand). I plotted the graphs of distance and numcount 
versus simulation time for each ligand. The number of contacts in  
ligand x is more than the other ligand y. Which of this ligands are 
hydrophobic? Which is hydrophilic? I know you are not private tutor. 
Please don't be angry :(




I certainly hope I haven't given the impression that I'm some angry tyrant.  I'm 
happy to answer reasonable questions across the list, time permitting.


To obtain information about hydrophobic and hydrophilic contacts, you need to 
use special index groups that tell g_mindist (or any other tool) which atoms to 
consider.  In this way, you can count how many of each type of contact evolve 
over time.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] g_mindist

[ahmet yıldırım]

Dear Justin,

You said before "you can obtain some idea by using g_mindist to calculate
hydrophobic and hydrophilic contacts between the protein and ligand".

That is, I can explore whether there is hydrophobic or hydrophilic feature
of ligand using g_mindist tool. is this correct?
I did the calculations related to protein_ligand interactions (protein
contains two ligand). I plotted the graphs of distance and numcount versus
simulation time for each ligand. The number of contacts in  ligand x is more
than the other ligand y. Which of this ligands are hydrophobic? Which is
hydrophilic? I know you are not private tutor. Please don't be angry :(

Thanks in advance
-- 
Ahmet YILDIRIM
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Re: [gmx-users] g_mindist clarification

[Justin A. Lemkul]

Chandan Choudhury wrote:

Hi all !!

Can some one clarify me what the g_mindist does. As far as I understood, 
it takes two inputs from the index file. If I have more than one entry 
in both of the indexes than how would g_mindist function?


g_mindist finds the minimum distance between any two atom pairs in the supplied 
group(s).


-Justin

eg; echo "7 8" |  g_mindist  -s ../md30-60.tpr -n index.ndx -f 
../30-60.part0004.trr  -od mindist.xvg -nice 0 -b 35000 -e 4 -xvgr

My 7th and 8th indexes are :
[ N ]
1   11   20   29   38   47   56   65   74   83   92  101  110  119  
128  137  146  155
  164  173  183  193  202  211  220  229  238  247  256  265  274  283  
292  301  310  319
  328  337  346  355  365  375  384  393  402  411  420  429  438  447  
456  465  474  483
  492  501  510  519  528  537  547  557  566  575  584  593  602  611  
620  629  638  647
  656  665  674  683  692  701  710  719  729  739  748  757  766  775  
784  793  802  811
  820  829  838  847  856  865  874  883  892  901  911  921  930  939  
948  957  966  975
  984  993 1002 1011 1020 1029 1038 1047 1056 1065 1074 1083 1093 1103 
1112 1121 1130 1139
 1148 1157 1166 1175 1184 1193 1202 1211 1220 1229 1238 1247 1256 1265 
1275 1285 1294 1303
 1312 1321 1330 1339 1348 1357 1366 1375 1384 1393 1402 1411 1420 1429 
1438 1447 1457 1467
 1476 1485 1494 1503 1512 1521 1530 1539 1548 1557 1566 1575 1584 1593 
1602 1611 1620 1629
 1639 1649 1658 1667 1676 1685 1694 1703 1712 1721 1730 1739 1748 1757 
1766 1775 1784 1793

 1802 1811

[ O ]
 1858 1960 2062 2164 2266 2368 2470 2572 2674 2776 2878 2980 3082 3184 
3286 3388 3490 3592
 3694 3796 3898 4000 4102 4204 4306 4408 4510 4612 4714 4816 4918 5020 
5122 5224 5326 5428
 5530 5632 5734 5836 5938 6040 6142 6244 6346 6448 6550 6652 6754 1865 
1967 2069 2171 2273
 2375 2477 2579 2681 2783 2885 2987 3089 3191 3293 3395 3497 3599 3701 
3803 3905 4007 4109
 4211 4313 4415 4517 4619 4721 4823 4925 5027 5129 5231 5333 5435 5537 
5639 5741 5843 5945
 6047 6149 6251 6353 6455 6557 6659 6761 1872 1974 2076 2178 2280 2382 
2484 2586 2688 2790
 2892 2994 3096 3198 3300 3402 3504 3606 3708 3810 3912 4014 4116 4218 
4320 4422 4524 4626
 4728 4830 4932 5034 5136 5238 5340 5442 5544 5646 5748 5850 5952 6054 
6156 6258 6360 6462
 6564  6768 1879 1981 2083 2185 2287 2389 2491 2593 2695 2797 2899 
3001 3103 3205 3307
 3409 3511 3613 3715 3817 3919 4021 4123 4225 4327 4429 4531 4633 4735 
4837 4939 5041 5143
 5245 5347 5449 5551 5653 5755 5857 5959 6061 6163 6265 6367 6469 6571 
6673 6775 1886 1988
 2090 2192 2294 2396 2498 2600 2702 2804 2906 3008 3110 3212 3314 3416 
3518 3620 3722 3824
 3926 4028 4130 4232 4334 4436 4538 4640 4742 4844 4946 5048 5150 5252 
5354 5456 5558 5660
 5762 5864 5966 6068 6170 6272 6374 6476 6578 6680 6782 1893 1995 2097 
2199 2301 2403 2505
 2607 2709 2811 2913 3015 3117 3219 3321 3423 3525 3627 3729 3831 3933 
4035 4137 4239 4341
 4443 4545 4647 4749 4851 4953 5055 5157 5259 5361 5463 5565 5667 5769 
5871 5973 6075 6177
 6279 6381 6483 6585 6687 6789 1900 2002 2104 2206 2308 2410 2512 2614 
2716 2818 2920 3022
 3124 3226 3328 3430 3532 3634 3736 3838 3940 4042 4144 4246 4348 4450 
4552 4654 4756 4858
 4960 5062 5164 5266 5368 5470 5572 5674 5776 5878 5980 6082 6184 6286 
6388 6490 6592 6694
 6796 1907 2009 2111 2213 2315 2417 2519 2621 2723 2825 2927 3029 3131 
3233 3335 3437 3539
 3641 3743 3845 3947 4049 4151 4253 4355 4457 4559 4661 4763 4865 4967 
5069 5171 5273 5375
 5477 5579 5681 5783 5885 5987 6089 6191 6293 6395 6497 6599 6701 6803 
1914 2016 2118 2220
 2322 2424 2526 2628 2730 2832 2934 3036 3138 3240 3342 3444 3546 3648 
3750 3852 3954 4056
 4158 4260 4362 4464 4566 4668 4770 4872 4974 5076 5178 5280 5382 5484 
5586 5688 5790 5892
 5994 6096 6198 6300 6402 6504 6606 6708 6810 1921 2023 2125 2227 2329 
2431 2533 2635 2737
 2839 2941 3043 3145 3247 3349 3451 3553 3655 3757 3859 3961 4063 4165 
4267 4369 4471 4573
 4675 4777 4879 4981 5083 5185 5287 5389 5491 5593 5695 5797 5899 6001 
6103 6205 6307 6409

 6511 6613 6715 6817

With one entry in the g_mindist (-od) and g_dist produces the same graph.


--
Chandan kumar Choudhury
NCL, Pune
INDIA



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] g_mindist clarification

[Chandan Choudhury]

Hi all !!

Can some one clarify me what the g_mindist does. As far as I understood, it
takes two inputs from the index file. If I have more than one entry in both
of the indexes than how would g_mindist function?
eg; echo "7 8" |  g_mindist  -s ../md30-60.tpr -n index.ndx -f
../30-60.part0004.trr  -od mindist.xvg -nice 0 -b 35000 -e 4 -xvgr
My 7th and 8th indexes are :
[ N ]
1   11   20   29   38   47   56   65   74   83   92  101  110  119  128
137  146  155
  164  173  183  193  202  211  220  229  238  247  256  265  274  283  292
301  310  319
  328  337  346  355  365  375  384  393  402  411  420  429  438  447  456
465  474  483
  492  501  510  519  528  537  547  557  566  575  584  593  602  611  620
629  638  647
  656  665  674  683  692  701  710  719  729  739  748  757  766  775  784
793  802  811
  820  829  838  847  856  865  874  883  892  901  911  921  930  939  948
957  966  975
  984  993 1002 1011 1020 1029 1038 1047 1056 1065 1074 1083 1093 1103 1112
1121 1130 1139
 1148 1157 1166 1175 1184 1193 1202 1211 1220 1229 1238 1247 1256 1265 1275
1285 1294 1303
 1312 1321 1330 1339 1348 1357 1366 1375 1384 1393 1402 1411 1420 1429 1438
1447 1457 1467
 1476 1485 1494 1503 1512 1521 1530 1539 1548 1557 1566 1575 1584 1593 1602
1611 1620 1629
 1639 1649 1658 1667 1676 1685 1694 1703 1712 1721 1730 1739 1748 1757 1766
1775 1784 1793
 1802 1811

[ O ]
 1858 1960 2062 2164 2266 2368 2470 2572 2674 2776 2878 2980 3082 3184 3286
3388 3490 3592
 3694 3796 3898 4000 4102 4204 4306 4408 4510 4612 4714 4816 4918 5020 5122
5224 5326 5428
 5530 5632 5734 5836 5938 6040 6142 6244 6346 6448 6550 6652 6754 1865 1967
2069 2171 2273
 2375 2477 2579 2681 2783 2885 2987 3089 3191 3293 3395 3497 3599 3701 3803
3905 4007 4109
 4211 4313 4415 4517 4619 4721 4823 4925 5027 5129 5231 5333 5435 5537 5639
5741 5843 5945
 6047 6149 6251 6353 6455 6557 6659 6761 1872 1974 2076 2178 2280 2382 2484
2586 2688 2790
 2892 2994 3096 3198 3300 3402 3504 3606 3708 3810 3912 4014 4116 4218 4320
4422 4524 4626
 4728 4830 4932 5034 5136 5238 5340 5442 5544 5646 5748 5850 5952 6054 6156
6258 6360 6462
 6564  6768 1879 1981 2083 2185 2287 2389 2491 2593 2695 2797 2899 3001
3103 3205 3307
 3409 3511 3613 3715 3817 3919 4021 4123 4225 4327 4429 4531 4633 4735 4837
4939 5041 5143
 5245 5347 5449 5551 5653 5755 5857 5959 6061 6163 6265 6367 6469 6571 6673
6775 1886 1988
 2090 2192 2294 2396 2498 2600 2702 2804 2906 3008 3110 3212 3314 3416 3518
3620 3722 3824
 3926 4028 4130 4232 4334 4436 4538 4640 4742 4844 4946 5048 5150 5252 5354
5456 5558 5660
 5762 5864 5966 6068 6170 6272 6374 6476 6578 6680 6782 1893 1995 2097 2199
2301 2403 2505
 2607 2709 2811 2913 3015 3117 3219 3321 3423 3525 3627 3729 3831 3933 4035
4137 4239 4341
 4443 4545 4647 4749 4851 4953 5055 5157 5259 5361 5463 5565 5667 5769 5871
5973 6075 6177
 6279 6381 6483 6585 6687 6789 1900 2002 2104 2206 2308 2410 2512 2614 2716
2818 2920 3022
 3124 3226 3328 3430 3532 3634 3736 3838 3940 4042 4144 4246 4348 4450 4552
4654 4756 4858
 4960 5062 5164 5266 5368 5470 5572 5674 5776 5878 5980 6082 6184 6286 6388
6490 6592 6694
 6796 1907 2009 2111 2213 2315 2417 2519 2621 2723 2825 2927 3029 3131 3233
3335 3437 3539
 3641 3743 3845 3947 4049 4151 4253 4355 4457 4559 4661 4763 4865 4967 5069
5171 5273 5375
 5477 5579 5681 5783 5885 5987 6089 6191 6293 6395 6497 6599 6701 6803 1914
2016 2118 2220
 2322 2424 2526 2628 2730 2832 2934 3036 3138 3240 3342 3444 3546 3648 3750
3852 3954 4056
 4158 4260 4362 4464 4566 4668 4770 4872 4974 5076 5178 5280 5382 5484 5586
5688 5790 5892
 5994 6096 6198 6300 6402 6504 6606 6708 6810 1921 2023 2125 2227 2329 2431
2533 2635 2737
 2839 2941 3043 3145 3247 3349 3451 3553 3655 3757 3859 3961 4063 4165 4267
4369 4471 4573
 4675 4777 4879 4981 5083 5185 5287 5389 5491 5593 5695 5797 5899 6001 6103
6205 6307 6409
 6511 6613 6715 6817

With one entry in the g_mindist (-od) and g_dist produces the same graph.


--
Chandan kumar Choudhury
NCL, Pune
INDIA
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Re: [gmx-users] g_mindist

[Justin A. Lemkul]

Ramachandran G wrote:

Hi Gromacs users,
I used g_mindist to calculate the minimum distance between a residue 
and a group of water molecules.
Since distance is a length between two points in space, for the program 
considers the bunch of water molecules(15 number)

what specific point does the group consider ? Thank you.



The distance measured is that between the two closest atoms, whichever those may 
be.  Read the first few sentences of g_mindist -h.


-Justin


Yours sincerely,
Rama





--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] g_mindist

[Ramachandran G]

Hi Gromacs users,
I used g_mindist to calculate the minimum distance between a residue and
a group of water molecules.
Since distance is a length between two points in space, for the program
considers the bunch of water molecules(15 number)
what specific point does the group consider ? Thank you.

Yours sincerely,
Rama
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Re: [gmx-users] g_mindist output

[Mark Abraham]

On 9/03/2010 12:22 PM, Justin A. Lemkul wrote:



Dian Jiao wrote:

Hi gmx users,

I was running g_mindist as a batch job for a big number of files on a
pbs cluster. The huge amount of output was redirected to the error
file which has a size limit. Is there way to discard the output of
g_mindist. I tried /dev/null as below, it didn't work.

g_mindist -f tra.pdb -n tra.ndx-od log < grp.txt > /dev/null

where grp.txt is a input file which specifies the groups.



Use &>/dev/null. You can also use the -quiet flag (hidden option) to
suppress some of the information printed out by any of the Gromacs tools.


Or, depending on your shell, redirect both stdout and stderr to files so 
that you get to keep the output for when you need it. (Presumably only 
the PBS stderr is subject to the limitation you're running into. A child 
process stderr won't be.)


Mark
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Re: [gmx-users] g_mindist output

[Dian Jiao]

Thank you, Justin.

On Mon, Mar 8, 2010 at 6:22 PM, Justin A. Lemkul  wrote:

>
>
> Dian Jiao wrote:
>
>> Hi gmx users,
>>
>> I was running g_mindist as a batch job for a big number of files on a pbs
>> cluster. The huge amount of output was redirected to the error file which
>> has a size limit. Is there way to discard the output of g_mindist. I tried
>> /dev/null as below, it didn't work.
>>
>> g_mindist -f tra.pdb -n tra.ndx-od log < grp.txt > /dev/null
>>
>> where grp.txt is a input file which specifies the groups.
>>
>>
> Use &>/dev/null.  You can also use the -quiet flag (hidden option) to
> suppress some of the information printed out by any of the Gromacs tools.
>
> -Justin
>
>  Thanks in advance.
>>
>> D
>>
>>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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Re: [gmx-users] g_mindist output

[Justin A. Lemkul]

Dian Jiao wrote:

Hi gmx users,

I was running g_mindist as a batch job for a big number of files on a 
pbs cluster. The huge amount of output was redirected to the error file 
which has a size limit. Is there way to discard the output of g_mindist. 
I tried /dev/null as below, it didn't work.


g_mindist -f tra.pdb -n tra.ndx-od log < grp.txt > /dev/null

where grp.txt is a input file which specifies the groups.



Use &>/dev/null.  You can also use the -quiet flag (hidden option) to suppress 
some of the information printed out by any of the Gromacs tools.


-Justin


Thanks in advance.

D



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] g_mindist output

[Dian Jiao]

Hi gmx users,

I was running g_mindist as a batch job for a big number of files on a pbs
cluster. The huge amount of output was redirected to the error file which
has a size limit. Is there way to discard the output of g_mindist. I tried
/dev/null as below, it didn't work.

g_mindist -f tra.pdb -n tra.ndx-od log < grp.txt > /dev/null

where grp.txt is a input file which specifies the groups.

Thanks in advance.

D
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Re: [gmx-users] g_mindist periodic boundary condition

[Dian Jiao]

Sorry for the confusion, Tsjerk. Thanks.

On Thu, Mar 4, 2010 at 11:47 AM, Tsjerk Wassenaar  wrote:

> Hi Dian,
>
> Now why didn't I guess that you were trying on data obtained from
> Amber?! Maybe because you didn't explicitly mentioned it. It always
> helps to give a full account of what you were trying.
>
> Anyway, I don't know the format of the top of my head, so you'll have
> to look in another pdb file and copy/edit the line (I think it's
> angles and then lengths, all %8.3f, but I'm not sure), or you have to
> check the pdb format at www.rcsb.org/pdb
>
> Hope it helps,
>
> Tsjerk
>
> On Thu, Mar 4, 2010 at 6:04 PM, Dian Jiao  wrote:
> > Hi Tsjerk,
> >
> > My gromacs is 4.0.4.
> >
> > As it turns out, I do not have a CRYST1 keyword in my pdb file, so I
> guess
> > the box is not defined yet. The pdb was taken from the trajectory of
> AMBER
> > simulation, so it starts with the keyword "REMARK". How do I include box
> > dimensions in pdb file then? Just add "CRYST1 24 24 24" in the first
> line?
> > By the way is it CRYST1 or CRYSTL?
> >
> > And the command I was running was "g_mindist -f 1001.pdb -n 1001.ndx -od
> > 1001_C".
> >
> > Dian
> >
> > On Thu, Mar 4, 2010 at 12:38 AM, Tsjerk Wassenaar 
> wrote:
> >>
> >> Hi Dian,
> >>
> >> Which version of gromacs are you using? Can you assert that the pdb
> >> file has the correct box? It should have a line starting with CRYST1
> >> (grep "^CRYST1" file.pdb). Some versions of gromacs (3.3.2  I think)
> >> didn't write the CRYST1 record, and thus disallow PBC related
> >> operations.
> >>
> >> Cheers,
> >>
> >> Tsjerk
> >>
> >> On Thu, Mar 4, 2010 at 8:08 AM, Dian Jiao  wrote:
> >> > The box is 24X24X24 (Angstrom). The dummy atom I added at the end is
> >> > about
> >> > 31 A away from the closest water in the box. But if it is periodic,
> >> > shouldn't there be waters near the dummy too?
> >> >
> >> > On Wed, Mar 3, 2010 at 10:29 PM, Mark Abraham <
> mark.abra...@anu.edu.au>
> >> > wrote:
> >> >>
> >> >> On 4/03/2010 11:30 AM, Dian Jiao wrote:
> >> >>>
> >> >>> Hi Gromacs users,
> >> >>>
> >> >>> I was trying to compute minimum distance between groups in a cubic
> >> >>> water
> >> >>> box with g_mindist using periodic boundary condition. In order to
> test
> >> >>> this, I added one more "atom" which is far away from any of the
> other
> >> >>> atoms in the pdb file. The mindist between that atom and all the
> >> >>> waters
> >> >>> were computed. The output of g_mindist is 3.089281e+00. (the unit is
> >> >>> nm,
> >> >>> right?)
> >> >>
> >> >> You haven't said how big your box is, or how far "far away" is, so we
> >> >> can't tell whether you think 3nm is too big, too small, etc.
> >> >>
> >> >>> The manual shows that pbc is one of the option of g_mindist, but
> isn't
> >> >>> the default "yes"? I even tried with "-pbc" in the command, still
> did
> >> >>> not work. Can anyone tell me how to turn on PBC in g_mindist?
> >> >>
> >> >> See g_mindist -h. The -pbc flag turns PBC on, -nopbc turns it off.
> >> >>
> >> >> Mark
> >> >> --
> >> >> gmx-users mailing listgmx-users@gromacs.org
> >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> >> Please search the archive at http://www.gromacs.org/search before
> >> >> posting!
> >> >> Please don't post (un)subscribe requests to the list. Use the www
> >> >> interface or send it to gmx-users-requ...@gromacs.org.
> >> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >> >
> >> >
> >> > --
> >> > gmx-users mailing listgmx-users@gromacs.org
> >> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> > Please search the archive at http://www.gromacs.org/search before
> >> > posting!
> >> > Please don't post (un)subscribe requests to the list. Use the
> >> > www interface or send it to gmx-users-requ...@gromacs.org.
> >> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >> >
> >>
> >>
> >>
> >> --
> >> Tsjerk A. Wassenaar, Ph.D.
> >>
> >> Computational Chemist
> >> Medicinal Chemist
> >> Neuropharmacologist
> >> --
> >> gmx-users mailing listgmx-users@gromacs.org
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> Please search the archive at http://www.gromacs.org/search before
> posting!
> >> Please don't post (un)subscribe requests to the list. Use the
> >> www interface or send it to gmx-users-requ...@gromacs.org.
> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
> >
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before
> posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-requ...@gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> Computational Chemist
> Medicinal Chemist
> Neuropharmacologist
> --
> gmx-users mailing listgmx-users@gromacs.org
>

Re: [gmx-users] g_mindist periodic boundary condition

[Tsjerk Wassenaar]

Hi Dian,

Now why didn't I guess that you were trying on data obtained from
Amber?! Maybe because you didn't explicitly mentioned it. It always
helps to give a full account of what you were trying.

Anyway, I don't know the format of the top of my head, so you'll have
to look in another pdb file and copy/edit the line (I think it's
angles and then lengths, all %8.3f, but I'm not sure), or you have to
check the pdb format at www.rcsb.org/pdb

Hope it helps,

Tsjerk

On Thu, Mar 4, 2010 at 6:04 PM, Dian Jiao  wrote:
> Hi Tsjerk,
>
> My gromacs is 4.0.4.
>
> As it turns out, I do not have a CRYST1 keyword in my pdb file, so I guess
> the box is not defined yet. The pdb was taken from the trajectory of AMBER
> simulation, so it starts with the keyword "REMARK". How do I include box
> dimensions in pdb file then? Just add "CRYST1 24 24 24" in the first line?
> By the way is it CRYST1 or CRYSTL?
>
> And the command I was running was "g_mindist -f 1001.pdb -n 1001.ndx -od
> 1001_C".
>
> Dian
>
> On Thu, Mar 4, 2010 at 12:38 AM, Tsjerk Wassenaar  wrote:
>>
>> Hi Dian,
>>
>> Which version of gromacs are you using? Can you assert that the pdb
>> file has the correct box? It should have a line starting with CRYST1
>> (grep "^CRYST1" file.pdb). Some versions of gromacs (3.3.2  I think)
>> didn't write the CRYST1 record, and thus disallow PBC related
>> operations.
>>
>> Cheers,
>>
>> Tsjerk
>>
>> On Thu, Mar 4, 2010 at 8:08 AM, Dian Jiao  wrote:
>> > The box is 24X24X24 (Angstrom). The dummy atom I added at the end is
>> > about
>> > 31 A away from the closest water in the box. But if it is periodic,
>> > shouldn't there be waters near the dummy too?
>> >
>> > On Wed, Mar 3, 2010 at 10:29 PM, Mark Abraham 
>> > wrote:
>> >>
>> >> On 4/03/2010 11:30 AM, Dian Jiao wrote:
>> >>>
>> >>> Hi Gromacs users,
>> >>>
>> >>> I was trying to compute minimum distance between groups in a cubic
>> >>> water
>> >>> box with g_mindist using periodic boundary condition. In order to test
>> >>> this, I added one more "atom" which is far away from any of the other
>> >>> atoms in the pdb file. The mindist between that atom and all the
>> >>> waters
>> >>> were computed. The output of g_mindist is 3.089281e+00. (the unit is
>> >>> nm,
>> >>> right?)
>> >>
>> >> You haven't said how big your box is, or how far "far away" is, so we
>> >> can't tell whether you think 3nm is too big, too small, etc.
>> >>
>> >>> The manual shows that pbc is one of the option of g_mindist, but isn't
>> >>> the default "yes"? I even tried with "-pbc" in the command, still did
>> >>> not work. Can anyone tell me how to turn on PBC in g_mindist?
>> >>
>> >> See g_mindist -h. The -pbc flag turns PBC on, -nopbc turns it off.
>> >>
>> >> Mark
>> >> --
>> >> gmx-users mailing list    gmx-us...@gromacs.org
>> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> >> Please search the archive at http://www.gromacs.org/search before
>> >> posting!
>> >> Please don't post (un)subscribe requests to the list. Use the www
>> >> interface or send it to gmx-users-requ...@gromacs.org.
>> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>> >
>> >
>> > --
>> > gmx-users mailing list    gmx-us...@gromacs.org
>> > http://lists.gromacs.org/mailman/listinfo/gmx-users
>> > Please search the archive at http://www.gromacs.org/search before
>> > posting!
>> > Please don't post (un)subscribe requests to the list. Use the
>> > www interface or send it to gmx-users-requ...@gromacs.org.
>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>> >
>>
>>
>>
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>>
>> Computational Chemist
>> Medicinal Chemist
>> Neuropharmacologist
>> --
>> gmx-users mailing list    gmx-us...@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before posting!
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>> www interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
> --
> gmx-users mailing list    gmx-us...@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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>



-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist
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Re: [gmx-users] g_mindist periodic boundary condition

[Dian Jiao]

Hi Tsjerk,

My gromacs is 4.0.4.

As it turns out, I do not have a CRYST1 keyword in my pdb file, so I guess
the box is not defined yet. The pdb was taken from the trajectory of AMBER
simulation, so it starts with the keyword "REMARK". How do I include box
dimensions in pdb file then? Just add "CRYST1 24 24 24" in the first line?
By the way is it CRYST1 or CRYSTL?

And the command I was running was "g_mindist -f 1001.pdb -n 1001.ndx -od
1001_C".

Dian

On Thu, Mar 4, 2010 at 12:38 AM, Tsjerk Wassenaar  wrote:

> Hi Dian,
>
> Which version of gromacs are you using? Can you assert that the pdb
> file has the correct box? It should have a line starting with CRYST1
> (grep "^CRYST1" file.pdb). Some versions of gromacs (3.3.2  I think)
> didn't write the CRYST1 record, and thus disallow PBC related
> operations.
>
> Cheers,
>
> Tsjerk
>
> On Thu, Mar 4, 2010 at 8:08 AM, Dian Jiao  wrote:
> > The box is 24X24X24 (Angstrom). The dummy atom I added at the end is
> about
> > 31 A away from the closest water in the box. But if it is periodic,
> > shouldn't there be waters near the dummy too?
> >
> > On Wed, Mar 3, 2010 at 10:29 PM, Mark Abraham 
> > wrote:
> >>
> >> On 4/03/2010 11:30 AM, Dian Jiao wrote:
> >>>
> >>> Hi Gromacs users,
> >>>
> >>> I was trying to compute minimum distance between groups in a cubic
> water
> >>> box with g_mindist using periodic boundary condition. In order to test
> >>> this, I added one more "atom" which is far away from any of the other
> >>> atoms in the pdb file. The mindist between that atom and all the waters
> >>> were computed. The output of g_mindist is 3.089281e+00. (the unit is
> nm,
> >>> right?)
> >>
> >> You haven't said how big your box is, or how far "far away" is, so we
> >> can't tell whether you think 3nm is too big, too small, etc.
> >>
> >>> The manual shows that pbc is one of the option of g_mindist, but isn't
> >>> the default "yes"? I even tried with "-pbc" in the command, still did
> >>> not work. Can anyone tell me how to turn on PBC in g_mindist?
> >>
> >> See g_mindist -h. The -pbc flag turns PBC on, -nopbc turns it off.
> >>
> >> Mark
> >> --
> >> gmx-users mailing listgmx-users@gromacs.org
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> Please search the archive at http://www.gromacs.org/search before
> posting!
> >> Please don't post (un)subscribe requests to the list. Use the www
> >> interface or send it to gmx-users-requ...@gromacs.org.
> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
> >
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before
> posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-requ...@gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> Computational Chemist
> Medicinal Chemist
> Neuropharmacologist
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
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>
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Re: [gmx-users] g_mindist periodic boundary condition

[Mark Abraham]

On 4/03/2010 6:38 PM, Tsjerk Wassenaar wrote:

Hi Dian,

Which version of gromacs are you using? Can you assert that the pdb
file has the correct box? It should have a line starting with CRYST1
(grep "^CRYST1" file.pdb). Some versions of gromacs (3.3.2  I think)
didn't write the CRYST1 record, and thus disallow PBC related
operations.


Also, always copy and paste your actual command lines, so that we know 
what you've actually done, rather than filtering a description through 
your head and then adding our assumptions. Does -pbc vs -nopbc make a 
difference?


Mark


On Thu, Mar 4, 2010 at 8:08 AM, Dian Jiao  wrote:

The box is 24X24X24 (Angstrom). The dummy atom I added at the end is about
31 A away from the closest water in the box. But if it is periodic,
shouldn't there be waters near the dummy too?

On Wed, Mar 3, 2010 at 10:29 PM, Mark Abraham
wrote:


On 4/03/2010 11:30 AM, Dian Jiao wrote:


Hi Gromacs users,

I was trying to compute minimum distance between groups in a cubic water
box with g_mindist using periodic boundary condition. In order to test
this, I added one more "atom" which is far away from any of the other
atoms in the pdb file. The mindist between that atom and all the waters
were computed. The output of g_mindist is 3.089281e+00. (the unit is nm,
right?)


You haven't said how big your box is, or how far "far away" is, so we
can't tell whether you think 3nm is too big, too small, etc.


The manual shows that pbc is one of the option of g_mindist, but isn't
the default "yes"? I even tried with "-pbc" in the command, still did
not work. Can anyone tell me how to turn on PBC in g_mindist?


See g_mindist -h. The -pbc flag turns PBC on, -nopbc turns it off.

Mark
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Re: [gmx-users] g_mindist periodic boundary condition

[Tsjerk Wassenaar]

Hi Dian,

Which version of gromacs are you using? Can you assert that the pdb
file has the correct box? It should have a line starting with CRYST1
(grep "^CRYST1" file.pdb). Some versions of gromacs (3.3.2  I think)
didn't write the CRYST1 record, and thus disallow PBC related
operations.

Cheers,

Tsjerk

On Thu, Mar 4, 2010 at 8:08 AM, Dian Jiao  wrote:
> The box is 24X24X24 (Angstrom). The dummy atom I added at the end is about
> 31 A away from the closest water in the box. But if it is periodic,
> shouldn't there be waters near the dummy too?
>
> On Wed, Mar 3, 2010 at 10:29 PM, Mark Abraham 
> wrote:
>>
>> On 4/03/2010 11:30 AM, Dian Jiao wrote:
>>>
>>> Hi Gromacs users,
>>>
>>> I was trying to compute minimum distance between groups in a cubic water
>>> box with g_mindist using periodic boundary condition. In order to test
>>> this, I added one more "atom" which is far away from any of the other
>>> atoms in the pdb file. The mindist between that atom and all the waters
>>> were computed. The output of g_mindist is 3.089281e+00. (the unit is nm,
>>> right?)
>>
>> You haven't said how big your box is, or how far "far away" is, so we
>> can't tell whether you think 3nm is too big, too small, etc.
>>
>>> The manual shows that pbc is one of the option of g_mindist, but isn't
>>> the default "yes"? I even tried with "-pbc" in the command, still did
>>> not work. Can anyone tell me how to turn on PBC in g_mindist?
>>
>> See g_mindist -h. The -pbc flag turns PBC on, -nopbc turns it off.
>>
>> Mark
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Computational Chemist
Medicinal Chemist
Neuropharmacologist
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Re: [gmx-users] g_mindist periodic boundary condition

[Dian Jiao]

The box is 24X24X24 (Angstrom). The dummy atom I added at the end is about
31 A away from the closest water in the box. But if it is periodic,
shouldn't there be waters near the dummy too?

On Wed, Mar 3, 2010 at 10:29 PM, Mark Abraham wrote:

> On 4/03/2010 11:30 AM, Dian Jiao wrote:
>
>> Hi Gromacs users,
>>
>> I was trying to compute minimum distance between groups in a cubic water
>> box with g_mindist using periodic boundary condition. In order to test
>> this, I added one more "atom" which is far away from any of the other
>> atoms in the pdb file. The mindist between that atom and all the waters
>> were computed. The output of g_mindist is 3.089281e+00. (the unit is nm,
>> right?)
>>
>
> You haven't said how big your box is, or how far "far away" is, so we can't
> tell whether you think 3nm is too big, too small, etc.
>
>
>  The manual shows that pbc is one of the option of g_mindist, but isn't
>> the default "yes"? I even tried with "-pbc" in the command, still did
>> not work. Can anyone tell me how to turn on PBC in g_mindist?
>>
>
> See g_mindist -h. The -pbc flag turns PBC on, -nopbc turns it off.
>
>
> Mark
> --
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Re: [gmx-users] g_mindist periodic boundary condition

[Mark Abraham]

On 4/03/2010 11:30 AM, Dian Jiao wrote:

Hi Gromacs users,

I was trying to compute minimum distance between groups in a cubic water
box with g_mindist using periodic boundary condition. In order to test
this, I added one more "atom" which is far away from any of the other
atoms in the pdb file. The mindist between that atom and all the waters
were computed. The output of g_mindist is 3.089281e+00. (the unit is nm,
right?)


You haven't said how big your box is, or how far "far away" is, so we 
can't tell whether you think 3nm is too big, too small, etc.



The manual shows that pbc is one of the option of g_mindist, but isn't
the default "yes"? I even tried with "-pbc" in the command, still did
not work. Can anyone tell me how to turn on PBC in g_mindist?


See g_mindist -h. The -pbc flag turns PBC on, -nopbc turns it off.

Mark
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[gmx-users] g_mindist periodic boundary condition

[Dian Jiao]

Hi Gromacs users,

I was trying to compute minimum distance between groups in a cubic water box
with g_mindist using periodic boundary condition. In order to test this, I
added one more "atom" which is far away from any of the other atoms in the
pdb file. The mindist between that atom and all the waters were computed.
The output of g_mindist is 3.089281e+00. (the unit is nm, right?)

The manual shows that pbc is one of the option of g_mindist, but isn't the
default "yes"? I even tried with "-pbc" in the command, still did not work.
Can anyone tell me how to turn on PBC in g_mindist?

Thanks

Dian
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RE: [gmx-users] g_mindist -or inconsistencies with atom-pairs

[Shay Amram]

Thank you very much Ran,
Will do.
-Shay

-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Ran Friedman
Sent: Tuesday, December 22, 2009 16:53
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] g_mindist -or inconsistencies with atom-pairs

Dear Shay,

What do you get when -or is present? Do the atoms always belong to the
same residues?
I suspect that since the calculation of the minimal distance is made for
all residues, what you get at the end is the atoms at minimal distance
between the last two residues. This seems like a bug and I suggest you
submit a bugzilla.

As a side note I think that the output will be given only for the last
two groups in case there are more than two. You may want to check this
as well if you submit a bug report.

It should be too difficult to fix, but would involve changes in a few
places in the code.

Best regards,
Ran.

shaya...@post.tau.ac.il wrote:
> Dear Gromacs users,
>
> We used g_mindist analysis as follows:
> g_mindist -f *.xtc -s *.tpr -o atom-pairs.out -od mindist.xvg -or
> res_mindist.xvg
>
> and surprisingly in the atom-pairs.out only several atoms in one
> residue (from group 1) were at minimum distance from group 2
> throughout the entire simulation. Checking this output manually showed
> it to be incorrect.
> res_mindist.xvg seems to hold the correct data.
>
> When running the same analysis, only omitting the -or flag, we get a
> *correct* atom-pairs.out.
> g_mindist -f *.xtc -s *.tpr -o atom-pairs.out -od mindist.xvg
>
> Comparing mindist.xvg from both scenarios shows no difference (files
> are identical).
>
> Is the -or flag supposed to affect the other output files of the
> g_mindist function?
>
> Supplementary details:
> 1. The same thing happened when g_mindist -s was supplied with either
> .gro, .pdb or .tpr files.
> 2. Index-groups 1 and 2 consisted upon full molecules with no
> ommisions (full protein and not only C-alpha).
> 3. We ruled out PBC by using -nopi
> 4. This is common with the following Gromacs versions: 3.3.3., 4.0.5,
> 4.0.7.
>
> Regards,
> -Shay
>
> --gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] g_mindist -or inconsistencies with atom-pairs

[Ran Friedman]

Dear Shay,

What do you get when -or is present? Do the atoms always belong to the
same residues?
I suspect that since the calculation of the minimal distance is made for
all residues, what you get at the end is the atoms at minimal distance
between the last two residues. This seems like a bug and I suggest you
submit a bugzilla.

As a side note I think that the output will be given only for the last
two groups in case there are more than two. You may want to check this
as well if you submit a bug report.

It should be too difficult to fix, but would involve changes in a few
places in the code.

Best regards,
Ran.

shaya...@post.tau.ac.il wrote:
> Dear Gromacs users,
>
> We used g_mindist analysis as follows:
> g_mindist -f *.xtc -s *.tpr -o atom-pairs.out -od mindist.xvg -or
> res_mindist.xvg
>
> and surprisingly in the atom-pairs.out only several atoms in one
> residue (from group 1) were at minimum distance from group 2
> throughout the entire simulation. Checking this output manually showed
> it to be incorrect.
> res_mindist.xvg seems to hold the correct data.
>
> When running the same analysis, only omitting the -or flag, we get a
> *correct* atom-pairs.out.
> g_mindist -f *.xtc -s *.tpr -o atom-pairs.out -od mindist.xvg
>
> Comparing mindist.xvg from both scenarios shows no difference (files
> are identical).
>
> Is the -or flag supposed to affect the other output files of the
> g_mindist function?
>
> Supplementary details:
> 1. The same thing happened when g_mindist -s was supplied with either
> .gro, .pdb or .tpr files.
> 2. Index-groups 1 and 2 consisted upon full molecules with no
> ommisions (full protein and not only C-alpha).
> 3. We ruled out PBC by using -nopi
> 4. This is common with the following Gromacs versions: 3.3.3., 4.0.5,
> 4.0.7.
>
> Regards,
> -Shay
>
> --gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before
> posting!
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[gmx-users] g_mindist -or inconsistencies with atom-pairs

[shayamra]

Dear Gromacs users,

We used g_mindist analysis as follows:
g_mindist -f *.xtc -s *.tpr -o atom-pairs.out -od mindist.xvg -or  
res_mindist.xvg


and surprisingly in the atom-pairs.out only several atoms in one  
residue (from group 1) were at minimum distance from group 2  
throughout the entire simulation. Checking this output manually showed  
it to be incorrect.

res_mindist.xvg seems to hold the correct data.

When running the same analysis, only omitting the -or flag, we get a  
*correct* atom-pairs.out.

g_mindist -f *.xtc -s *.tpr -o atom-pairs.out -od mindist.xvg

Comparing mindist.xvg from both scenarios shows no difference (files  
are identical).


Is the -or flag supposed to affect the other output files of the  
g_mindist function?


Supplementary details:
1. The same thing happened when g_mindist -s was supplied with either  
.gro, .pdb or .tpr files.
2. Index-groups 1 and 2 consisted upon full molecules with no  
ommisions (full protein and not only C-alpha).

3. We ruled out PBC by using -nopi
4. This is common with the following Gromacs versions: 3.3.3., 4.0.5, 4.0.7.

Regards,
-Shay

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Re: [gmx-users] g_mindist after trjconv -fit give different results

[Tsjerk Wassenaar]

Hi Elad,

You can't count on operations that involve PBC after fitting. In your
case, you can use

trjconv -fit translation

to remove translational degrees of freedom only, keeping the system
consistent with PBC.

Hope it helps,

Tsjerk

On Sun, Dec 6, 2009 at 8:50 PM,   wrote:
> Hi Tsjerk,
> thanks for the reply.
>
> Will the MSD of the molecule also be affected by the fitting.
> I'm trying to calculate the relative diffusion coefficient of an ion near a
> protein. For this I thought to first fix the system according to the protein
> and then calculate the msd of the ion.
> I noticed in the g_msd code that periodicity is taken into account (as
> expected). However, in g_msd the interest of the periodicity handling
> regards regards the atom position relative to itself in previous frames.
> Will this relative movement (of the atom in relation to itself in the
> previous frame) be kept after doing "trjconv -fit".
>
> Thanks.
>
>>
>> Hi Elad,
>>
>> This has been mentioned several times before, in a different context.
>> But fitting only affects coordinates, and not the PBC. So after
>> fitting the coordinates and the PBC don't match any more and any
>> analysis requiring PBC, such as calculating minimal distances, will
>> give garbled results. Always do such things on untransformed
>> trajectories.
>>
>> Cheers,
>>
>> Tsjerk
>>
>> On Fri, Dec 4, 2009 at 7:43 PM,   wrote:
>>>
>>> Hi all,
>>>
>>> I have a system of protein+water+ions.
>>> I measured the minimum distance between one of the ions to the protein.
>>>
>>> Afterwards I fitted the trajectory using g_trjconv -fit rot+trans
>>>
>>> Did the same mindist again and the graphs are not always identical.
>>>
>>> Any suggestions?
>>>
>>> I use gromacs 4.0.5 with an octahedron box.
>>> same problem happens when I do trjconv -fit rot but does not happen when
>>> -fit trans.
>>>
>>> In VMD I do see a difference in the position of the ion relative to the
>>> protein.
>>>
>>> Thanks.
>>> Elad P.
>>>
>
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist
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[gmx-users] g_mindist after trjconv -fit give different results

[eladp]

Hi Tsjerk,
thanks for the reply.

Will the MSD of the molecule also be affected by the fitting.
I'm trying to calculate the relative diffusion coefficient of an ion  
near a protein. For this I thought to first fix the system according  
to the protein and then calculate the msd of the ion.
I noticed in the g_msd code that periodicity is taken into account (as  
expected). However, in g_msd the interest of the periodicity handling  
regards regards the atom position relative to itself in previous  
frames. Will this relative movement (of the atom in relation to itself  
in the previous frame) be kept after doing "trjconv -fit".


Thanks.



Hi Elad,

This has been mentioned several times before, in a different context.
But fitting only affects coordinates, and not the PBC. So after
fitting the coordinates and the PBC don't match any more and any
analysis requiring PBC, such as calculating minimal distances, will
give garbled results. Always do such things on untransformed
trajectories.

Cheers,

Tsjerk

On Fri, Dec 4, 2009 at 7:43 PM,   wrote:

Hi all,

I have a system of protein+water+ions.
I measured the minimum distance between one of the ions to the protein.

Afterwards I fitted the trajectory using g_trjconv -fit rot+trans

Did the same mindist again and the graphs are not always identical.

Any suggestions?

I use gromacs 4.0.5 with an octahedron box.
same problem happens when I do trjconv -fit rot but does not happen when
-fit trans.

In VMD I do see a difference in the position of the ion relative to the
protein.

Thanks.
Elad P.





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Re: [gmx-users] g_mindist after trjconv -fit give different results

[Tsjerk Wassenaar]

Hi Elad,

This has been mentioned several times before, in a different context.
But fitting only affects coordinates, and not the PBC. So after
fitting the coordinates and the PBC don't match any more and any
analysis requiring PBC, such as calculating minimal distances, will
give garbled results. Always do such things on untransformed
trajectories.

Cheers,

Tsjerk

On Fri, Dec 4, 2009 at 7:43 PM,   wrote:
> Hi all,
>
> I have a system of protein+water+ions.
> I measured the minimum distance between one of the ions to the protein.
>
> Afterwards I fitted the trajectory using g_trjconv -fit rot+trans
>
> Did the same mindist again and the graphs are not always identical.
>
> Any suggestions?
>
> I use gromacs 4.0.5 with an octahedron box.
> same problem happens when I do trjconv -fit rot but does not happen when
> -fit trans.
>
> In VMD I do see a difference in the position of the ion relative to the
> protein.
>
> Thanks.
> Elad P.
>
> --
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>



-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist
--
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[gmx-users] g_mindist after trjconv -fit give different results

[eladp]

Hi all,

I have a system of protein+water+ions.
I measured the minimum distance between one of the ions to the protein.

Afterwards I fitted the trajectory using g_trjconv -fit rot+trans

Did the same mindist again and the graphs are not always identical.

Any suggestions?

I use gromacs 4.0.5 with an octahedron box.
same problem happens when I do trjconv -fit rot but does not happen  
when -fit trans.


In VMD I do see a difference in the position of the ion relative to  
the protein.


Thanks.
Elad P.

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Re: [gmx-users] g_mindist , trajectory only CA atoms, to small values?

[Tsjerk Wassenaar]

Hi Peter,

> Instead of the pairs with the shortest distance a much further pair is 
> selected. Although the output pair from "atm-pair.out" has a distance of more 
> then 100 Angstrom the value in  the file "mindist.xvg" is smaller then one 
> Angstrom.

Periodic Boundary Conditions?

You mention in another post that removing the header solves your
'bug'. The way you express yourself indicates you haven't got a clue
what you've removed. Dangerous... Bad idea. You've probably removed a
line which started with CRYST1, preceded by a line REMARK This is a
simulation box, or something along those lines. Sure, if you remove
PBC that way, no gromacs utility will ever see that things should be
close to each other. But you're the one that's mistaken, not the
program. Don't let yourself be mislead by visualization programs.

Hope it helps,

Tsjerk

-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist
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RE: [gmx-users] g_mindist , trajectory only CA atoms, to small values?

[Shay Amram]

Bad choice of words. Did not mean to suggests there's actual program bug.
-Shay

-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Justin A. Lemkul
Sent: Wednesday, December 02, 2009 00:46
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] g_mindist , trajectory only CA atoms, to small
values?



t.peter.muel...@gmx.net wrote:
> Dear Shay, dear Gromacians
> 
>> For purposes of debugging this bug you can also use the flag of g_mindist
>> that gives out atom pairs and see which atom pairs is it that gromacs
>> thinks are less the 1 angstrom.
> I used the  "-o  atm-pair.out" option to get the atom pairs with the
minimal
> distance. For the all atom trajectory the correct atom pairs are selected.
> But for the CA trajectory the wrong atom pairs are selected. Instead of
the
> pairs with the shortest distance a much further pair is selected. Although

Can you post some of this output?

> the output pair from "atm-pair.out" has a distance of more then 100
Angstrom
> the value in  the file "mindist.xvg" is smaller then one Angstrom.
> 

Is this for the CA-only trajectory?

> I think the "g_mindist" command has a bug. In the trajectory each residue
is
> only represented by a single CA atom (to reduce storage footprint and
> increase speed), can it be that g_mindist requires that the atoms have to
> "connected" (no broken bonds)? But for calculating the minimal distance of
> two groups this should really not be required.
> 

Before we jump to the bug conclusion, can you post the command line you're 
using, groups you're selecting (are they custom? simply the default
"C-alpha"?) 
and relevant snippets from the output and/or coordinate files that
demonstrate a 
bit better what's going on.  If, based on this information, things look
weird, 
then file a bugzilla with files that reproduce the problem.  I would
disagree 
that g_mindist requires bond information, since a .tpr file is not strictly 
required for its function.

-Justin

-- 


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] g_mindist , trajectory only CA atoms, to small values?

[Justin A. Lemkul]

t.peter.muel...@gmx.net wrote:

Dear Shay, dear Justin, dear Gromacians

My problem is solved. I used following command

$ g_mindist -f system_onlyCa.xtc -s system_onlyCa.pdb -n system_onlyCa.ndx -o
atm-pair.out

The PDB file "system_onlyCa.pdb" had a header which seems to have confused
the counting of the "g_mindist" command. After deleting the the PDB header/
comments, I get the correct results.


Was this .pdb file a product of a Gromacs utility?  If so, it will be of 
interest in case there needs to be a fix.  If not, it would still also be nice 
to know what lines were confusing g_mindist so others who search for this 
problem might find the solution :)


-Justin



Thanks for your feedback Peter


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ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
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[gmx-users] g_mindist , trajectory only CA atoms, to small values?

[t . peter . Mueller]

Dear Shay, dear Justin, dear Gromacians

My problem is solved. I used following command   

$ g_mindist -f system_onlyCa.xtc -s system_onlyCa.pdb -n system_onlyCa.ndx -o 
atm-pair.out 

The PDB file "system_onlyCa.pdb" had a header which seems to have confused the 
counting of the "g_mindist" command. After deleting the the PDB header/ 
comments, I get the correct results.

Thanks for your feedback
Peter
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Re: [gmx-users] g_mindist , trajectory only CA atoms, to small values?

[Justin A. Lemkul]

t.peter.muel...@gmx.net wrote:

Dear Shay, dear Gromacians


For purposes of debugging this bug you can also use the flag of g_mindist
that gives out atom pairs and see which atom pairs is it that gromacs
thinks are less the 1 angstrom.

I used the  "-o  atm-pair.out" option to get the atom pairs with the minimal
distance. For the all atom trajectory the correct atom pairs are selected.
But for the CA trajectory the wrong atom pairs are selected. Instead of the
pairs with the shortest distance a much further pair is selected. Although


Can you post some of this output?


the output pair from "atm-pair.out" has a distance of more then 100 Angstrom
the value in  the file "mindist.xvg" is smaller then one Angstrom.



Is this for the CA-only trajectory?


I think the "g_mindist" command has a bug. In the trajectory each residue is
only represented by a single CA atom (to reduce storage footprint and
increase speed), can it be that g_mindist requires that the atoms have to
"connected" (no broken bonds)? But for calculating the minimal distance of
two groups this should really not be required.



Before we jump to the bug conclusion, can you post the command line you're 
using, groups you're selecting (are they custom? simply the default "C-alpha"?) 
and relevant snippets from the output and/or coordinate files that demonstrate a 
bit better what's going on.  If, based on this information, things look weird, 
then file a bugzilla with files that reproduce the problem.  I would disagree 
that g_mindist requires bond information, since a .tpr file is not strictly 
required for its function.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] g_mindist , trajectory only CA atoms, to small values?

[t . peter . Mueller]

Dear Shay, dear Gromacians

>For purposes of debugging this bug you can also use
>the flag of g_mindist that gives out atom pairs and
>see which atom pairs is it that gromacs thinks are
> less the 1 angstrom.
I used the  "-o  atm-pair.out" option to get the atom pairs with the minimal 
distance.
For the all atom trajectory the correct atom pairs are selected. But for the CA 
trajectory the wrong atom pairs are selected.
Instead of the pairs with the shortest distance a much further pair is 
selected. Although the output pair from "atm-pair.out" has a distance of more 
then 100 Angstrom the value in  the file "mindist.xvg" is smaller then one 
Angstrom.

I think the "g_mindist" command has a bug. In the trajectory each residue is 
only represented by a single CA atom (to reduce storage footprint and increase 
speed), can it be that g_mindist requires that the atoms have to "connected" 
(no broken bonds)?
But for calculating the minimal distance of two groups this should really not 
be required.

Thanks
Peter
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Re: [gmx-users] g_mindist , trajectory only CA atoms, to small values?

[shayamra]

Dear Peter,

For purposes of debugging this bug you can also use the flag of  
g_mindist that gives out atom pairs and see which atom pairs is it  
that gromacs thinks are less the 1 angstrom.


Another suggestion would be using the backbone and seeing if it matters any.

Regards,
-Shay

Quoting t.peter.muel...@gmx.net:


Dear Gromacs users,

my system consist of two parts, which are not connected. My system  
has around 10 atoms. To make the trajectory handling and the  
analysis more feasible I store only the CA atoms in the xtc  
trajectory.


I want to use the "g_mindist" command to calculate the minimal  
distance between the two parts of my system from the xtc trajectory.  
I created a index file, where I added the atoms of each parts of my  
system.


   $ g_mindist -f system_onlyCa.xtc -s system_onlyCa.pdb -n system_onlyCa.ndx
   $ g_mindist -f system_all.xtc -s system_all.pdb -n system_all.ndx

If I calculate the minimal distance from the XTC trajectory which  
contains only the CA atoms I get a too small values (much smaller  
then 1 Aengstroem).
For testing I calculated the minimal distance from a small part of  
the XTC trajectory which contains all atoms I get the correct value  
(around 100 Aengstroem).


What is the reason for this error? It should not matter if the  
trajectory has all atoms (connected via bonds) or only the CA (not  
connected). "g_mindist" has two sets of atoms. It will calculate the  
distance between all possible pairs of atoms from both groups. For  
every frame it will give out the smallest distance.
If there are broken molecules in the trajectory file (trajectory  
only CA) should not have any influence on the result.


Thanks for answering
Peter
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[gmx-users] g_mindist , trajectory only CA atoms, to small values?

[t . peter . Mueller]

Dear Gromacs users,

my system consist of two parts, which are not connected. My system has around 
10 atoms. To make the trajectory handling and the analysis more feasible I 
store only the CA atoms in the xtc trajectory.

I want to use the "g_mindist" command to calculate the minimal distance between 
the two parts of my system from the xtc trajectory. I created a index file, 
where I added the atoms of each parts of my system.

   $ g_mindist -f system_onlyCa.xtc -s system_onlyCa.pdb -n system_onlyCa.ndx
   $ g_mindist -f system_all.xtc -s system_all.pdb -n system_all.ndx

If I calculate the minimal distance from the XTC trajectory which contains only 
the CA atoms I get a too small values (much smaller then 1 Aengstroem).
For testing I calculated the minimal distance from a small part of the XTC 
trajectory which contains all atoms I get the correct value (around 100 
Aengstroem).

What is the reason for this error? It should not matter if the trajectory has 
all atoms (connected via bonds) or only the CA (not connected). "g_mindist" has 
two sets of atoms. It will calculate the distance between all possible pairs of 
atoms from both groups. For every frame it will give out the smallest distance.
If there are broken molecules in the trajectory file (trajectory only CA) 
should not have any influence on the result.

Thanks for answering
Peter
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RE: [gmx-users] g_mindist

[Berk Hess]

Hi,

If you use -pi with g_mindist, all the other output options are ignored.

Berk

> Date: Fri, 9 Oct 2009 14:24:00 +0200
> From: cseif...@bph.ruhr-uni-bochum.de
> To: gmx-users@gromacs.org
> Subject: [gmx-users] g_mindist
> 
> Dear Mr. Gromacs, ;-)
> and hello to everybody!
> 
> When I use g_mindist with a Syntax like this:
> g_mindist -f ./prot.xtc -s ./prot.tpr -n ./prot.ndx
> -od ./protein_self.xvg -o prot.out -pi
> 
> Then I just get the xvg file with the distance of the group (I selected
> C-alphas) with its periodic image. The xvg file look familiar and
> correct, but the prot.out file is not created. There is no warning or
> error.
> 
> I used g_mindist v4.0.5.
> 
> Greetings,
> Christian
> 
> -- 
> M.Sc. Christian Seifert
> Department of Biophysics
> University of Bochum
> ND 04/67
> 44780 Bochum
> Germany
> Tel: +49 (0)234 32 28363
> Fax: +49 (0)234 32 14626
> E-Mail: cseif...@bph.rub.de
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> 
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[gmx-users] g_mindist

[Christian Seifert]

Dear Mr. Gromacs, ;-)
and hello to everybody!

When I use g_mindist with a Syntax like this:
g_mindist -f ./prot.xtc -s ./prot.tpr -n ./prot.ndx
-od ./protein_self.xvg -o prot.out -pi

Then I just get the xvg file with the distance of the group (I selected
C-alphas) with its periodic image. The xvg file look familiar and
correct, but the prot.out file is not created. There is no warning or
error.

I used g_mindist v4.0.5.

Greetings,
Christian

-- 
M.Sc. Christian Seifert
Department of Biophysics
University of Bochum
ND 04/67
44780 Bochum
Germany
Tel: +49 (0)234 32 28363
Fax: +49 (0)234 32 14626
E-Mail: cseif...@bph.rub.de
Web: http://www.bph.rub.de

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Re: [gmx-users] g_mindist -pi gives segfault in 3.3.3 and 4.0.2 but not 3.3.1

[Florian Dommert]

* Chris Neale  [2009-01-17 10:11:34 -0500]:


Hello,

For my systems, I have been unable to get g_mindist -pi to function unless I 
roll back to gmx 3.3.1. Would somebody please test their 4.0.2 (and perhaps 
3.3.3) installations to see if the error is repeatable or perhaps is somehow 
related to my installation?


Hi,

 I tested it with my version and it gives the same error. As gromacs
 version I have the cvs branch gmx-4-0-patches head 1.4 used for
 testing.


Related output from 3.3.3 when g_mindist -f file.gro -n file.ndx -pi

Selected 3: 'a_1'
Reading frames from gro file 'test', 140634 atoms.
Reading frame   0 time0.000  Back Off! I just backed up mindist.xvg 
to ./#mindist.xvg.9#

Segmentation fault

Note that non -pi g_mindist still works fine for me in all versions.

Thanks,
CHris.
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RE: [gmx-users] g_mindist -pi gives segfault in 3.3.3 and 4.0.2 but not 3.3.1

[Berk Hess]

Hi,

I never noticed this because I always used -s.
Supply a tpr file with -s in addition to -n and it will work.
I fixed this for 4.0.3 such that with -pi it automatically uses -s as well.

Berk

> Date: Sat, 17 Jan 2009 10:11:34 -0500
> From: chris.ne...@utoronto.ca
> To: gmx-users@gromacs.org
> Subject: [gmx-users] g_mindist -pi gives segfault in 3.3.3 and 4.0.2 but not  
> 3.3.1
> 
> Hello,
> 
> For my systems, I have been unable to get g_mindist -pi to function 
> unless I roll back to gmx 3.3.1. Would somebody please test their 4.0.2 
> (and perhaps 3.3.3) installations to see if the error is repeatable or 
> perhaps is somehow related to my installation?
> 
> Related output from 3.3.3 when g_mindist -f file.gro -n file.ndx -pi
> 
> Selected 3: 'a_1'
> Reading frames from gro file 'test', 140634 atoms.
> Reading frame   0 time0.000  
> Back Off! I just backed up mindist.xvg to ./#mindist.xvg.9#
> Segmentation fault
> 
> Note that non -pi g_mindist still works fine for me in all versions.
> 
> Thanks,
> CHris.
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[gmx-users] g_mindist -pi gives segfault in 3.3.3 and 4.0.2 but not 3.3.1

[Chris Neale]

Hello,

For my systems, I have been unable to get g_mindist -pi to function 
unless I roll back to gmx 3.3.1. Would somebody please test their 4.0.2 
(and perhaps 3.3.3) installations to see if the error is repeatable or 
perhaps is somehow related to my installation?


Related output from 3.3.3 when g_mindist -f file.gro -n file.ndx -pi

Selected 3: 'a_1'
Reading frames from gro file 'test', 140634 atoms.
Reading frame   0 time0.000  
Back Off! I just backed up mindist.xvg to ./#mindist.xvg.9#

Segmentation fault

Note that non -pi g_mindist still works fine for me in all versions.

Thanks,
CHris.
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[gmx-users] g_mindist possible bug - missing a frame

[shayamra]

Dear Gromacs users,
I used g_mindist in order to generate minimum distance between a  
certain protein and a ligand. I invoked -od (to generate xvg) and -o  
(to generate atom-pairs list).
Following that, I aligned the atom-pairs columns next to the distance  
columns so to have a list of [protein index] [ligand index] and  
[distance] for each frame.

Oddly enough I got one frame that had mindist but no corresponding atom-pairs.
I checked the .out file and indeed the list just skips to the next  
frame/atom-pair in the list.

Is there any particular reason this might happen?

Regards,
-Shay



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Re: [gmx-users] g_mindist -pi option

[Tsjerk Wassenaar]

Hi Andrea,

You shouldn't fit before analysis involving PBC. Fitting changes the
orientation of the molecule with respect to the lattice. Image an
elongated molecule in a rectangular box, which rotates along its short
axis. Because of fitting, you'd miss it running into its own image...

Cheers,

Tsjerk

On 6/12/07, andrea spitaleri <[EMAIL PROTECTED]> wrote:

Just to keep the post upgraded, I have tried:
trjconv -pbc nojump -o test.xtc
then
trjconv -fit rot+trans -f test.xtc -o test1.xtc
and then run g_mindist on test1.xtc.
The results of -pi is more or less the same that I obtain using vmd program.

Probably it might help other people with the same problem,

Regards

andrea

Yang Ye wrote:
> On 6/12/2007 7:15 PM, Miguel Machuqueiro wrote:
>> At 08:00 AM 6/12/2007, you wrote:
>>> Hi again,
>>> since I did not get answer I double checked my trr file. In case I
>>> calculate the minimum distance of
>>> the periodic image for each component of my complex, I get reasonable
>>> value of it (3.0 and 2.9 nm),
>>> whereas if I consider the whole system (protein) I get this strange
>>> result of 0.17 nm.
>>> Any clue?
>>> thanks again
>>> Regards
>>
>> Hi Andrea,
>>
>> When you have a multi-chain protein (or a protein + peptide) it can
>> happen that when making protein whole (removing pbc) sometimes the two
>> chains can be placed in two different adjacent boxes, so... when doing
>> the "g_mindist -pi" setup, the closest distance is when they are
>> together in the same box at a distance of ~1.7 Angstrom.
>>
>> Point 1 - This is an artifact, but it doesn't exclude the possibility
>> that there are structures seeing their periodic images. As it was
>> suggested by Mark Abraham, you should check these structures just to
>> be sure.
>>
>> Point 2 - If someone knows how to trick trjconv -pbc in order to avoid
>> doing this... it would be appreciated.
> Yes. I got such "separated chain" trajectory with dsDNA as well. I have
> a script to move them back manually frame per frame by comparing minimal
> distance and real distance.
>>
>> Miguel
>>
>>
>> 
>> Miguel Machuqueiro
>> ITQB-Instituto de Tecnologia Química e Biológica
>> Universidade Nova de Lisboa
>> Molecular Simulation Group - 6º Floor (Room 601)
>> Av. da República, EAN, Apartado 127
>> 2781-901 Oeiras, Portugal
>> Tel. : +351 214469618 /Mobile: +351 96 7562285
>> E-mail: machuque at itqb.unl.pt
>> _
>>
>> ___
>> gmx-users mailing listgmx-users@gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
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--
---
Andrea Spitaleri PhD
Dulbecco Telethon Institute
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
http://biomolecularnmr.ihsr.dom/
---


Sostieni la ricerca del San Raffaele con il 5permille!
E' SEMPLICE E NON COSTA NULLA.
Basta indicare nell'apposito riquadro della dichiarazione dei
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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Re: [gmx-users] g_mindist -pi option

[andrea spitaleri]

Just to keep the post upgraded, I have tried:
trjconv -pbc nojump -o test.xtc
then
trjconv -fit rot+trans -f test.xtc -o test1.xtc
and then run g_mindist on test1.xtc.
The results of -pi is more or less the same that I obtain using vmd program.

Probably it might help other people with the same problem,

Regards

andrea

Yang Ye wrote:
> On 6/12/2007 7:15 PM, Miguel Machuqueiro wrote:
>> At 08:00 AM 6/12/2007, you wrote:
>>> Hi again,
>>> since I did not get answer I double checked my trr file. In case I
>>> calculate the minimum distance of
>>> the periodic image for each component of my complex, I get reasonable
>>> value of it (3.0 and 2.9 nm),
>>> whereas if I consider the whole system (protein) I get this strange
>>> result of 0.17 nm.
>>> Any clue?
>>> thanks again
>>> Regards
>>
>> Hi Andrea,
>>
>> When you have a multi-chain protein (or a protein + peptide) it can
>> happen that when making protein whole (removing pbc) sometimes the two
>> chains can be placed in two different adjacent boxes, so... when doing
>> the "g_mindist -pi" setup, the closest distance is when they are
>> together in the same box at a distance of ~1.7 Angstrom.
>>
>> Point 1 - This is an artifact, but it doesn't exclude the possibility
>> that there are structures seeing their periodic images. As it was
>> suggested by Mark Abraham, you should check these structures just to
>> be sure.
>>
>> Point 2 - If someone knows how to trick trjconv -pbc in order to avoid
>> doing this... it would be appreciated.
> Yes. I got such "separated chain" trajectory with dsDNA as well. I have
> a script to move them back manually frame per frame by comparing minimal
> distance and real distance.
>>
>> Miguel
>>
>>
>> 
>> Miguel Machuqueiro
>> ITQB-Instituto de Tecnologia Química e Biológica
>> Universidade Nova de Lisboa
>> Molecular Simulation Group - 6º Floor (Room 601)
>> Av. da República, EAN, Apartado 127
>> 2781-901 Oeiras, Portugal
>> Tel. : +351 214469618 /Mobile: +351 96 7562285
>> E-mail: machuque at itqb.unl.pt
>> _
>>
>> ___
>> gmx-users mailing listgmx-users@gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
>> posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to [EMAIL PROTECTED]
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>>
> 
> ___
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-- 
---
Andrea Spitaleri PhD
Dulbecco Telethon Institute
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
http://biomolecularnmr.ihsr.dom/
---


Sostieni la ricerca del San Raffaele con il 5permille!
E' SEMPLICE E NON COSTA NULLA.
Basta indicare nell'apposito riquadro della dichiarazione dei
redditi ("Ricerca sanitaria") 
il codice fiscale della 
Fondazione Centro S. Raffaele del Monte Tabor:
03 06 42 80 153 e ricordarsi di firmare.
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Re: [gmx-users] g_mindist -pi option

[andrea spitaleri]

Hi Miguel,
that's it. Visualizing the system in vmd I see that at the point the two 
peptides are in two
different boxes.
I was almost sure that there were no interaction between two periodic images 
from the energy
profile. In fact, the energy profile (Coul and LJ) did not show any weird 
behaviour. Besides this,
it sounds very strange that the minimum distance goes from 3.0 nm to 0.17 nm 
and then up to 3.0 in 2
ps ...
Therefore vmd and energy profile seem to be consistent with a proper simulation 
(till now ..) :)
Thanks,

Regards

andrea

Miguel Machuqueiro wrote:
> At 08:00 AM 6/12/2007, you wrote:
>> Hi again,
>> since I did not get answer I double checked my trr file. In case I
>> calculate the minimum distance of
>> the periodic image for each component of my complex, I get reasonable
>> value of it (3.0 and 2.9 nm),
>> whereas if I consider the whole system (protein) I get this strange
>> result of 0.17 nm.
>> Any clue?
>> thanks again
>> Regards
> 
> Hi Andrea,
> 
> When you have a multi-chain protein (or a protein + peptide) it can
> happen that when making protein whole (removing pbc) sometimes the two
> chains can be placed in two different adjacent boxes, so... when doing
> the "g_mindist -pi" setup, the closest distance is when they are
> together in the same box at a distance of ~1.7 Angstrom.
> 
> Point 1 - This is an artifact, but it doesn't exclude the possibility
> that there are structures seeing their periodic images. As it was
> suggested by Mark Abraham, you should check these structures just to be
> sure.
> 
> Point 2 - If someone knows how to trick trjconv -pbc in order to avoid
> doing this... it would be appreciated.
> 
> Miguel
> 
> 
> 
> Miguel Machuqueiro
> ITQB-Instituto de Tecnologia Química e Biológica
> Universidade Nova de Lisboa
> Molecular Simulation Group - 6º Floor (Room 601)
> Av. da República, EAN, Apartado 127
> 2781-901 Oeiras, Portugal
> Tel. : +351 214469618 /Mobile: +351 96 7562285
> E-mail: machuque at itqb.unl.pt
> _
> 
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
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> 

-- 
---
Andrea Spitaleri PhD
Dulbecco Telethon Institute
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
http://biomolecularnmr.ihsr.dom/
---


Sostieni la ricerca del San Raffaele con il 5permille!
E' SEMPLICE E NON COSTA NULLA.
Basta indicare nell'apposito riquadro della dichiarazione dei
redditi ("Ricerca sanitaria") 
il codice fiscale della 
Fondazione Centro S. Raffaele del Monte Tabor:
03 06 42 80 153 e ricordarsi di firmare.
Se vuoi saperne di piu' scrivi a [EMAIL PROTECTED] o vai sul sito
w w w . 5 x m i l l e . o r g
___
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Re: [gmx-users] g_mindist -pi option

[Yang Ye]

On 6/12/2007 7:15 PM, Miguel Machuqueiro wrote:

At 08:00 AM 6/12/2007, you wrote:

Hi again,
since I did not get answer I double checked my trr file. In case I 
calculate the minimum distance of
the periodic image for each component of my complex, I get reasonable 
value of it (3.0 and 2.9 nm),
whereas if I consider the whole system (protein) I get this strange 
result of 0.17 nm.

Any clue?
thanks again
Regards


Hi Andrea,

When you have a multi-chain protein (or a protein + peptide) it can 
happen that when making protein whole (removing pbc) sometimes the two 
chains can be placed in two different adjacent boxes, so... when doing 
the "g_mindist -pi" setup, the closest distance is when they are 
together in the same box at a distance of ~1.7 Angstrom.


Point 1 - This is an artifact, but it doesn't exclude the possibility 
that there are structures seeing their periodic images. As it was 
suggested by Mark Abraham, you should check these structures just to 
be sure.


Point 2 - If someone knows how to trick trjconv -pbc in order to avoid 
doing this... it would be appreciated.
Yes. I got such "separated chain" trajectory with dsDNA as well. I have 
a script to move them back manually frame per frame by comparing minimal 
distance and real distance.


Miguel



Miguel Machuqueiro
ITQB-Instituto de Tecnologia Química e Biológica
Universidade Nova de Lisboa
Molecular Simulation Group - 6º Floor (Room 601)
Av. da República, EAN, Apartado 127
2781-901 Oeiras, Portugal
Tel. : +351 214469618 /Mobile: +351 96 7562285
E-mail: machuque at itqb.unl.pt
_

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Re: [gmx-users] g_mindist -pi option

[Miguel Machuqueiro]

At 08:00 AM 6/12/2007, you wrote:

Hi again,
since I did not get answer I double checked my trr file. In case I 
calculate the minimum distance of
the periodic image for each component of my complex, I get 
reasonable value of it (3.0 and 2.9 nm),
whereas if I consider the whole system (protein) I get this strange 
result of 0.17 nm.

Any clue?
thanks again
Regards


Hi Andrea,

When you have a multi-chain protein (or a protein + peptide) it can 
happen that when making protein whole (removing pbc) sometimes the 
two chains can be placed in two different adjacent boxes, so... when 
doing the "g_mindist -pi" setup, the closest distance is when they 
are together in the same box at a distance of ~1.7 Angstrom.


Point 1 - This is an artifact, but it doesn't exclude the possibility 
that there are structures seeing their periodic images. As it was 
suggested by Mark Abraham, you should check these structures just to be sure.


Point 2 - If someone knows how to trick trjconv -pbc in order to 
avoid doing this... it would be appreciated.


Miguel



Miguel Machuqueiro
ITQB-Instituto de Tecnologia Química e Biológica
Universidade Nova de Lisboa
Molecular Simulation Group - 6º Floor (Room 601)
Av. da República, EAN, Apartado 127
2781-901 Oeiras, Portugal
Tel. : +351 214469618 /Mobile: +351 96 7562285
E-mail: machuque at itqb.unl.pt
_

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Re: [gmx-users] g_mindist -pi option

[Mark Abraham]

andrea spitaleri wrote:

Hi again,
since I did not get answer I double checked my trr file. In case I calculate 
the minimum distance of
the periodic image for each component of my complex, I get reasonable value of 
it (3.0 and 2.9 nm),
whereas if I consider the whole system (protein) I get this strange result of 
0.17 nm.
Any clue?


Have you looked at your structures? g_mindist just might be right :-)

Mark
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Re: [gmx-users] g_mindist -pi option

[andrea spitaleri]

Hi again,
since I did not get answer I double checked my trr file. In case I calculate 
the minimum distance of
the periodic image for each component of my complex, I get reasonable value of 
it (3.0 and 2.9 nm),
whereas if I consider the whole system (protein) I get this strange result of 
0.17 nm.
Any clue?

thanks again

Regards

andrea

andrea spitaleri wrote:
> Hi there,
> I have a complex protein-peptide in a box 6.5 6.5 6.5 with a starting 
> periodic image of 3.0 nm,
> using PME and rlist=rvdw=rcoulomb=0.9.
> Now, I use to check the pi dist during my simulation in order to make sure 
> that the box is larger
> enough. After 6ns I get this result:
> 03.018  4.711  6.555  6.555  6.555
> 30   2.791  4.514  6.557  6.557  6.557
> 60   2.721  4.270  6.555  6.555  6.555
> 90   2.762  4.378  6.554  6.554  6.554
> 
>   4620 3.017  4.042  6.558  6.558  6.558
> 4650 0.173  9.080  6.548  6.548  6.548
> 4680 2.700  3.949  6.561  6.561  6.561
> 4710 2.881  4.113  6.560  6.560  6.560
> ...
> 6000 2.939  4.049  6.556  6.556  6.556
> 
> So it seems that there is a "spike" around 4650 ps of a very low distance 
> (quite worrying me).
> Any hints? is it true this value or is it pbc artefact?
> Thanks in advance
> 
> Regards,
> 
> and
> 
> ps. gmx3-3-1 compiled on suse-10.2 gcc-v 4.1.2
> 
>  --
> ---
> Andrea Spitaleri PhD
> Dulbecco Telethon Institute
> c/o DIBIT Scientific Institute
> Biomolecular NMR, 1B4
> Via Olgettina 58
> 20132 Milano (Italy)
> http://biomolecularnmr.ihsr.dom/
> ---
> 
> 
> Sostieni la ricerca del San Raffaele con il 5permille!
> E' SEMPLICE E NON COSTA NULLA.
> Basta indicare nell'apposito riquadro della dichiarazione dei
> redditi ("Ricerca sanitaria") 
> il codice fiscale della 
> Fondazione Centro S. Raffaele del Monte Tabor:
> 03 06 42 80 153 e ricordarsi di firmare.
> Se vuoi saperne di piu' scrivi a [EMAIL PROTECTED] o vai sul sito
> w w w . 5 x m i l l e . o r g
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to [EMAIL PROTECTED]
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 

-- 
---
Andrea Spitaleri PhD
Dulbecco Telethon Institute
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
http://biomolecularnmr.ihsr.dom/
---


Sostieni la ricerca del San Raffaele con il 5permille!
E' SEMPLICE E NON COSTA NULLA.
Basta indicare nell'apposito riquadro della dichiarazione dei
redditi ("Ricerca sanitaria") 
il codice fiscale della 
Fondazione Centro S. Raffaele del Monte Tabor:
03 06 42 80 153 e ricordarsi di firmare.
Se vuoi saperne di piu' scrivi a [EMAIL PROTECTED] o vai sul sito
w w w . 5 x m i l l e . o r g
___
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[gmx-users] g_mindist -pi option

[andrea spitaleri]

Hi there,
I have a complex protein-peptide in a box 6.5 6.5 6.5 with a starting periodic 
image of 3.0 nm,
using PME and rlist=rvdw=rcoulomb=0.9.
Now, I use to check the pi dist during my simulation in order to make sure that 
the box is larger
enough. After 6ns I get this result:
03.018  4.711  6.555  6.555  6.555
30   2.791  4.514  6.557  6.557  6.557
60   2.721  4.270  6.555  6.555  6.555
90   2.762  4.378  6.554  6.554  6.554

4620 3.017  4.042  6.558  6.558  6.558
4650 0.173  9.080  6.548  6.548  6.548
4680 2.700  3.949  6.561  6.561  6.561
4710 2.881  4.113  6.560  6.560  6.560
...
6000 2.939  4.049  6.556  6.556  6.556

So it seems that there is a "spike" around 4650 ps of a very low distance 
(quite worrying me).
Any hints? is it true this value or is it pbc artefact?
Thanks in advance

Regards,

and

ps. gmx3-3-1 compiled on suse-10.2 gcc-v 4.1.2

 --
---
Andrea Spitaleri PhD
Dulbecco Telethon Institute
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
http://biomolecularnmr.ihsr.dom/
---


Sostieni la ricerca del San Raffaele con il 5permille!
E' SEMPLICE E NON COSTA NULLA.
Basta indicare nell'apposito riquadro della dichiarazione dei
redditi ("Ricerca sanitaria") 
il codice fiscale della 
Fondazione Centro S. Raffaele del Monte Tabor:
03 06 42 80 153 e ricordarsi di firmare.
Se vuoi saperne di piu' scrivi a [EMAIL PROTECTED] o vai sul sito
w w w . 5 x m i l l e . o r g
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Re: [gmx-users] g_mindist

[Tsjerk Wassenaar]

Hi Ozge,

'sidechain' indicates all side chains present in your system, i.e.
everything designated 'protein' based on residue names, excluding
everything taken to be 'backbone' based on atom names.

You'll probably have to run the program three times to get the
combinations of minimal distances between your side chains, using
appropriate index groups.

Best,

Tsjerk

On 3/16/07, OZGE ENGIN <[EMAIL PROTECTED]> wrote:

Hi,

I forgot to ask  my other question :) When I use the g_mindist command, it asks 
me to select two groups for which the distance will be calculated. I am 
confused for the following: I want to calculate the minimum distance among 
three side chains of my molecule in all combinations. So, if I choose the side 
chain (system 8) option for this command twice, which side chains will be taken 
into consideration?

Thanks in advance

Ozge Engin



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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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[gmx-users] g_mindist

[OZGE ENGIN]

Hi,

I forgot to ask  my other question :) When I use the g_mindist command, it asks 
me to select two groups for which the distance will be calculated. I am 
confused for the following: I want to calculate the minimum distance among 
three side chains of my molecule in all combinations. So, if I choose the side 
chain (system 8) option for this command twice, which side chains will be taken 
into consideration?

Thanks in advance

Ozge Engin



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[gmx-users] g_mindist and g_mdmat

[SUSAN VARNUM]

Dear gmx users,

I'm fairly new to gmx and I'm using the analysis tools to understand the 
persistent features of a large ensemble of conformers of an unstructured 
protein restrained with PRE NMR data.

I generated a contact map over the ensemble using the following command

g_mdmat -f fname.pdb -s fname.pdb -mean

Viewing the map after converting with xpm2ps, I found a few persistent contacts.

I then tried to look at the minimum distance distribution for the residue pairs 
that gave the closest contacts in the average contact map.
I used make_ndx to create selections of all atoms of the residues of interest, 
then used the g_mindist with a pair of residues selected.

g_mindist -f fname.pdb -s fname.pdb -n myindexfile.ndx

If I average over the output of g_mindist, I do not get a value that is near 
the discrete value in the g_mdmat contact map representation.  Should these 
values be the same?  If not, why not?

Thanks,
David Lowry___
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Re: [gmx-users] g_mindist

[Mark Abraham]

mahbubeh zarrabi wrote:

Dear all
I want to analyze the electrostatic interaction in
md.I used g_mindist . in this command how can i select
distsnce for contact(-d)?


You select a value with g_mindist -d 1.0

Choosing the value is where your understanding of your scientific 
problem comes in.


Mark
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[gmx-users] g_mindist

[mahbubeh zarrabi]

Dear all
I want to analyze the electrostatic interaction in
md.I used g_mindist . in this command how can i select
distsnce for contact(-d)?
thanks


 

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[gmx-users] g_mindist -pi (minimum periodic) and dodecahedron

[chris . neale]

I have an alanine dipeptide in a box (gromacs-3.3.1). When that box is  
cubic (3. 3. 3.), g_mindist -pi works as I expect it to (i.e.  
selecting Protein yields 2.3nm, which is what I would expect for box  
length minus end to end peptide distance; and selecting a single atom  
yields 3.0nm).


However, when the box type is a rhombic dodecahedron, I get the same  
g_mindist -pi minimum periodic distance output whether I select  
"Protein" or just a single atom of that protein. When that box is  
created by editconf -bt dodecahedron -d 1.110755, I get a box =  
{3.0   3.0   2.12132   0.0   0.0   0.0   0.0
1.5   1.5}, and I get a g_mindist -pi minimum periodic  
distance of 2.12132 for a selection of the entire protein of just a  
single atom (or backbone, C-alpha, etc.)


For clarification, my protein is not entirely linear and I therefore  
suggest that this is some type of error.


When I further solvate the system and select SOL for g_mindist, the  
result is 0.136nm. When I select only a single SOL (4 atoms) or only  
the OW atom within that SOL molecule, I again get 2.12132nm. When I  
select two solvent residues (8 atoms) I again get 2.12132nm.


Thanks for any insight that anybody can offer. One reason that I can't  
figure this out any further myself is that I don't really understand  
the transformations involved in triclinic box PBC and VMD won't render  
all 3 axis positions correctly in periodic display (i.e. there is  
always an offset in at least one dimension, even when using trjconv -ur)


My commands were like this:
1. pdb2gmx -f a.pdb -o a.gro -p a.top -ff oplsaa -water tip4p
2. editconf -f a.gro -o b.gro [(-bt cubic -box 3. 3. 3.) ~OR~ (-bt  
dodecahedron -d 1.)]

3. make_ndx -f b.gro -o b.ndx < file_selecting_a_single_protein_atom
4. g_mindist -f b.gro -n b.ndx -pi

The input pdb file that I used was:

ATOM 13  C   ALA 2   1.199   4.163  -0.186  1.00  0.00   C
ATOM 14  CA  ALA 2   1.936   3.140  -1.094  1.00  0.00   C
ATOM 15  CB  ALA 2   1.931   3.622  -2.546  1.00  0.00   C
ATOM 16  H   ALA 2   1.473   1.194  -1.741  1.00  0.00   H
ATOM 17  HA  ALA 2   2.957   3.060  -0.751  1.00  0.00   H
ATOM 18  N   ALA 2   1.315   1.824  -1.006  1.00  0.00   N
ATOM 19  O   ALA 2   0.786   3.836   0.926  1.00  0.00   O
ATOM 20 1HB  ALA 2   2.493   4.541  -2.623  1.00  0.00   H
ATOM 21 2HB  ALA 2   0.913   3.796  -2.865  1.00  0.00   H
ATOM 22 3HB  ALA 2   2.381   2.871  -3.177  1.00  0.00   H
ATOM 23  C   ALA 3  -0.332   7.289  -1.163  1.00  0.00   C
ATOM 24  CA  ALA 3   0.299   6.426  -0.037  1.00  0.00   C
ATOM 25  CB  ALA 3   1.277   7.267   0.787  1.00  0.00   C
ATOM 26  H   ALA 3   1.377   5.531  -1.610  1.00  0.00   H
ATOM 27  HA  ALA 3  -0.451   6.044   0.639  1.00  0.00   H
ATOM 28  N   ALA 3   1.015   5.356  -0.716  1.00  0.00   N
ATOM 29  O   ALA 3   0.349   8.097  -1.795  1.00  0.00   O
ATOM 30 1HB  ALA 3   1.003   8.309   0.718  1.00  0.00   H
ATOM 31 2HB  ALA 3   2.278   7.132   0.405  1.00  0.00   H
ATOM 32 3HB  ALA 3   1.240   6.953   1.819  1.00  0.00   H
END







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