[gmx-users] Chemical Potential

[Steven Neumann]

Dear Gmx Users,

I am wondering whether it is possible to obtain in Gromacs chemical
potential e.g. of water in the protein - ligand system?
Please, advise me to do some further reading, suggest method, maybe
tutorial?

Thank you,

Steven
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Re: [gmx-users] mdrun-gpu error

[aiswarya pawar]

Mark,

THe normal mdrun also hangs thus not generating any output.

On Thu, Jan 19, 2012 at 3:09 AM, Mark Abraham wrote:

>  On 19/01/2012 2:59 AM, aiswarya.pa...@gmail.com wrote:
>
> Hi,
>
> Its going into the running mode but gets hang there for long hours which 
> generating any data in the output file. And am not able to figure out the 
> error file_doc. Please anyone knows what's going wrong.
>
>
> No, but you should start trying to simplify what you're doing to see where
> the problem lies. Does normal mdrun work?
>
> Mark
>
>
>  Thanks
> Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!
>
> -Original Message-
> From: Szilárd Páll  
> Sender: gmx-users-boun...@gromacs.org
> Date: Wed, 18 Jan 2012 14:47:59
> To: Discussion list for GROMACS users 
> 
> Reply-To: Discussion list for GROMACS users  
> 
> Subject: Re: [gmx-users] mdrun-gpu error
>
> Hi,
>
> Most of those are just warnings, the only error I see there comes from
> the shell, probably an error in your script.
>
> Cheers,
> --
> Szilárd
>
>
>
> On Wed, Jan 18, 2012 at 12:27 PM, aiswarya pawar 
>  wrote:
>
>  Hi users,
>
> Am running mdrun on gpu . I receive an error such as=
>
> WARNING: This run will generate roughly 38570 Mb of data
>
>
> WARNING: OpenMM does not support leap-frog, will use velocity-verlet
> integrator.
>
>
> WARNING: OpenMM supports only Andersen thermostat with the
> md/md-vv/md-vv-avek integrators.
>
>
> WARNING: OpenMM supports only Monte Carlo barostat for pressure coupling.
>
>
> WARNING: OpenMM provides contraints as a combination of SHAKE, SETTLE and
> CCMA. Accuracy is based on the SHAKE tolerance set by the "shake_tol"
> option.
>
> /bin/cat: file_loc: No such file or directory
>
>
> and the job is running but the nothing written into .xtc, .trr, .edr files .
> What could have gone wrong?
>
> --
> Aiswarya  B Pawar
>
> Bioinformatics Dept,
> Indian Institute of Science
> Bangalore
>
>
>
> --
> gmx-users mailing list
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>
>
>
>
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-- 
Aiswarya  B Pawar

Bioinformatics Dept,
Indian Institute of Science
Bangalore
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Re: [gmx-users] getting rid of PBC, completely

[Chandan Choudhury]

On Thu, Jan 19, 2012 at 12:17 PM, Mark Abraham wrote:

> On 19/01/2012 5:39 PM, Chandan Choudhury wrote:
>
>>
>> Dear gmx-users,
>>
>> I have a simulated a system containing a linear polymer in a cubic box
>> with water molecules.  I need to get rid of PBC effect on the system such
>> that I can execute my own analysis code. I intend to compute the msd of
>> water molecules along the polymer backbone.
>>
>
> You can't "get rid of PBC", you can only manage it. The question reduces
> what you want to see if a molecule diffuses across the periodic boundary
> from near one end of the polymer to the other end.
>
>
>  So, when I execute my own analysis code, I see the msd's are abrupt (i.e
>> very high), this is due to the pbc. So, for getting rid of PBC effect, I
>> performed the suggested trjconv workflow (http://www.gromacs.org/**
>> Documentation/Terminology/**Periodic_Boundary_Conditions).
>>
>>
>> Below are my executed commands :
>>
>> # Made the system whole
>>
>> echo 0 | trjconv_4.5.5 -s md0-4.tpr -f 0-4.xtc -pbc whole -o 0-4_whole.xtc
>>
>> # 0 is the whole system. md0-4.tpr is the initial tpr file containing
>> whole (no broken) polymer inside the cubic box.
>> # Extracted 1st frame from the initial trajectory
>>
>> echo 0 | trjconv_4.5.5 -s md0-4.tpr -f 0-4.xtc -pbc nojump  -o 1st.pdb
>> -dump 0
>>
>> # used the whole trajectory to remove jumps with reference to the 1st
>> frame.
>> echo 0 | trjconv_4.5.5 -s 1st.pdb -f 0-4_whole.xtc -pbc nojump -o
>> 0-4_nojump.xtc
>>
>
> So here you said "let molecules diffuse away from the solute".
>
>
>
>> #system is being centered
>> echo "0 0" | trjconv_4.5.5 -s md0-4.tpr -f 0-4_nojump.xtc -o
>> 0-4_center.xtc -center
>>
>> #putting every atom in the box
>> echo 0 | trjconv -s md0-4.tpr -f 0-4_center.xtc -o 0-4_box.xtc -pbc atom
>>
>
> ... and now you said "take all the atoms and put them back in the box",
> creating jumps whenever one crosses the boundaries.
>
>
>
>> Still when I execute my analysis code, I do see the abrupt behaviour in
>> the msd plot. Can someone guide me how to completely get rid of PBC
>> artifacts.
>>
>
> Don't simulate with them :-P Is your analysis technique sound for the
> periodic case?


No, my analysis code doesnot take care of PBC. As to deal with PBC, I need
to have the box vectors (for atleast NPT simulation) from the trajectory
and I am unable to extract the box vectors (as of date).

Chandan


>
> Mark
>
> --
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--
Chandan kumar Choudhury
NCL, Pune
INDIA
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Re: [gmx-users] getting rid of PBC, completely

[Tsjerk Wassenaar]

Hi Chandan,

The box is accessible from the t_trxframe struct. Assuming you have

t_trxframe *fr

You can access it through

fr->box

But if you remove jumps first, you're fine anyway. Just don't put
things back in the box afterwards. And don't center if your aim is
calculating MSDs.

Hope it helps,

Tsjerk

On Thu, Jan 19, 2012 at 11:14 AM, Chandan Choudhury  wrote:
>
>
> On Thu, Jan 19, 2012 at 12:17 PM, Mark Abraham 
> wrote:
>>
>> On 19/01/2012 5:39 PM, Chandan Choudhury wrote:
>>>
>>>
>>> Dear gmx-users,
>>>
>>> I have a simulated a system containing a linear polymer in a cubic box
>>> with water molecules.  I need to get rid of PBC effect on the system such
>>> that I can execute my own analysis code. I intend to compute the msd of
>>> water molecules along the polymer backbone.
>>
>>
>> You can't "get rid of PBC", you can only manage it. The question reduces
>> what you want to see if a molecule diffuses across the periodic boundary
>> from near one end of the polymer to the other end.
>>
>>
>>> So, when I execute my own analysis code, I see the msd's are abrupt (i.e
>>> very high), this is due to the pbc. So, for getting rid of PBC effect, I
>>> performed the suggested trjconv workflow
>>> (http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions).
>>>
>>> Below are my executed commands :
>>>
>>> # Made the system whole
>>>
>>> echo 0 | trjconv_4.5.5 -s md0-4.tpr -f 0-4.xtc -pbc whole -o
>>> 0-4_whole.xtc
>>>
>>> # 0 is the whole system. md0-4.tpr is the initial tpr file containing
>>> whole (no broken) polymer inside the cubic box.
>>> # Extracted 1st frame from the initial trajectory
>>>
>>> echo 0 | trjconv_4.5.5 -s md0-4.tpr -f 0-4.xtc -pbc nojump  -o 1st.pdb
>>> -dump 0
>>>
>>> # used the whole trajectory to remove jumps with reference to the 1st
>>> frame.
>>> echo 0 | trjconv_4.5.5 -s 1st.pdb -f 0-4_whole.xtc -pbc nojump -o
>>> 0-4_nojump.xtc
>>
>>
>> So here you said "let molecules diffuse away from the solute".
>>
>>
>>>
>>> #system is being centered
>>> echo "0 0" | trjconv_4.5.5 -s md0-4.tpr -f 0-4_nojump.xtc -o
>>> 0-4_center.xtc -center
>>>
>>> #putting every atom in the box
>>> echo 0 | trjconv -s md0-4.tpr -f 0-4_center.xtc -o 0-4_box.xtc -pbc atom
>>
>>
>> ... and now you said "take all the atoms and put them back in the box",
>> creating jumps whenever one crosses the boundaries.
>>
>>
>>>
>>> Still when I execute my analysis code, I do see the abrupt behaviour in
>>> the msd plot. Can someone guide me how to completely get rid of PBC
>>> artifacts.
>>
>>
>> Don't simulate with them :-P Is your analysis technique sound for the
>> periodic case?
>
>
> No, my analysis code doesnot take care of PBC. As to deal with PBC, I need
> to have the box vectors (for atleast NPT simulation) from the trajectory and
> I am unable to extract the box vectors (as of date).
>
> Chandan
>
>>
>>
>> Mark
>>
>> --
>> 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!
>> 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/Support/Mailing_Lists
>
>
>
>
> --
> Chandan kumar Choudhury
> NCL, Pune
> INDIA
>
>
> --
> gmx-users mailing list    gmx-users@gromacs.org
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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] Chemical Potential

[Steven Neumann]

  Does anyone can help?


Dear Gmx Users,

I am wondering whether it is possible to obtain in Gromacs chemical
potential e.g. of water in the protein - ligand system?
Please, advise me to do some further reading, suggest method, maybe
tutorial?

Thank you,

Steven
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Re: [gmx-users] Chemical Potential

[Ivan Gladich]

On 01/19/2012 11:34 AM, Steven Neumann wrote:

Does anyone can help?
Dear Gmx Users,
I am wondering whether it is possible to obtain in Gromacs chemical 
potential e.g. of water in the protein - ligand system?
Please, advise me to do some further reading, suggest method, maybe 
tutorial?

Thank you,
Steven

Dear Steven
I am not an expert of protein - ligand system...
However  the chemical potential of a i-th specie is the derivative of 
the potential energy in function of the number of the i-particles 
present in the system.
As far as I know (and if I am not wrong), in GROMACS the number of 
particle is fixed along all the simulation, i.e., you cannot change the 
number of particles during the simulation.
Therefore, you cannot simply  obtain the chemical potential from one 
single run...
I suggest you to search in literature; maybe you can combine different 
runs to obtain the chemical potential...but I do not want to say you 
something wrong since I do not have experience in such systems.


Good luck
Ivan

--
--
Ivan Gladich, Ph.D.
Postdoctoral Fellow
Academy of Sciences of the Czech Republic
Institute of Organic Chemistry and Biochemistry AS CR, v.v.i.
Flemingovo nám. 2.
166 10 Praha 6
Czech Republic

Tel: +420775504164
e-mail: ivan.glad...@uochb.cas.cz
web page:http://www.molecular.cz/~gladich/
-

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Re: [gmx-users] Chemical Potential

[David van der Spoel]

On 2012-01-19 14:49, Ivan Gladich wrote:

On 01/19/2012 11:34 AM, Steven Neumann wrote:

Does anyone can help?
Dear Gmx Users,
I am wondering whether it is possible to obtain in Gromacs chemical
potential e.g. of water in the protein - ligand system?
Please, advise me to do some further reading, suggest method, maybe
tutorial?
Thank you,
Steven

Dear Steven
I am not an expert of protein - ligand system...
However the chemical potential of a i-th specie is the derivative of the
potential energy in function of the number of the i-particles present in
the system.
As far as I know (and if I am not wrong), in GROMACS the number of
particle is fixed along all the simulation, i.e., you cannot change the
number of particles during the simulation.
Therefore, you cannot simply obtain the chemical potential from one
single run...
I suggest you to search in literature; maybe you can combine different
runs to obtain the chemical potential...but I do not want to say you
something wrong since I do not have experience in such systems.

Good luck
Ivan

Correct me if I'm wrong, but in principle you can just do an 
annihilation simulation in solution and the free energy obtained in this 
manner is the chemical potential. If you do the same in the gas phase 
and subtract that you get the Gibbs energy of hydration.



--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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Re: [gmx-users] Chemical Potential

[René Pool]

Hi,

If I understand the question correctly, you want to know the water 
chemical potential in the water/protein/ligand system.
If so, in principle it should be possible to approximate the water 
chemical potential using test particle insertion. Gromacs has a utility 
for that.


Cheers,
René

=
René Pool

Division of Molecular and Computational Toxicology
Department of Chemistry and Pharmaceutical Sciences
Vrije Universiteit Amsterdam
De Boelelaan 1083
1081HV AMSTERDAM, the Netherlands
-
IBIVU/Bioinformatics
Department of Computer Science
Vrije Universiteit Amsterdam
De Boelelaan 1081a
1081HV AMSTERDAM, the Netherlands

Room P 2.75
E: r.p...@vu.nl
T: +31 20 598 76 12
F: +31 20 598 76 10
=


On 01/19/2012 02:49 PM, Ivan Gladich wrote:

On 01/19/2012 11:34 AM, Steven Neumann wrote:

Does anyone can help?
Dear Gmx Users,
I am wondering whether it is possible to obtain in Gromacs chemical 
potential e.g. of water in the protein - ligand system?
Please, advise me to do some further reading, suggest method, maybe 
tutorial?

Thank you,
Steven

Dear Steven
I am not an expert of protein - ligand system...
However  the chemical potential of a i-th specie is the derivative of 
the potential energy in function of the number of the i-particles 
present in the system.
As far as I know (and if I am not wrong), in GROMACS the number of 
particle is fixed along all the simulation, i.e., you cannot change 
the number of particles during the simulation.
Therefore, you cannot simply  obtain the chemical potential from one 
single run...
I suggest you to search in literature; maybe you can combine different 
runs to obtain the chemical potential...but I do not want to say you 
something wrong since I do not have experience in such systems.


Good luck
Ivan


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Re: [gmx-users] mdrun-gpu error

[Mark Abraham]

On 19/01/2012 8:45 PM, aiswarya pawar wrote:

Mark,

THe normal mdrun also hangs thus not generating any output.


OK. It's your problem to solve... keep simplifying stuff until you can 
isolate a small number of possible causes. Top of the list is file 
system availability.


Mark



On Thu, Jan 19, 2012 at 3:09 AM, Mark Abraham > wrote:


On 19/01/2012 2:59 AM, aiswarya.pa...@gmail.com
 wrote:

Hi,

Its going into the running mode but gets hang there for long hours which 
generating any data in the output file. And am not able to figure out the error 
file_doc. Please anyone knows what's going wrong.


No, but you should start trying to simplify what you're doing to
see where the problem lies. Does normal mdrun work?

Mark



Thanks
Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for 
it!

-Original Message-
From: Szilárd Páll  
Sender:gmx-users-boun...@gromacs.org  
Date: Wed, 18 Jan 2012 14:47:59
To: Discussion list for GROMACS users  

Reply-To: Discussion list for GROMACS users  

Subject: Re: [gmx-users] mdrun-gpu error

Hi,

Most of those are just warnings, the only error I see there comes from
the shell, probably an error in your script.

Cheers,
--
Szilárd



On Wed, Jan 18, 2012 at 12:27 PM, aiswarya pawar
    wrote:

Hi users,

Am running mdrun on gpu . I receive an error such as=

WARNING: This run will generate roughly 38570 Mb of data


WARNING: OpenMM does not support leap-frog, will use velocity-verlet
integrator.


WARNING: OpenMM supports only Andersen thermostat with the
md/md-vv/md-vv-avek integrators.


WARNING: OpenMM supports only Monte Carlo barostat for pressure coupling.


WARNING: OpenMM provides contraints as a combination of SHAKE, SETTLE and
CCMA. Accuracy is based on the SHAKE tolerance set by the "shake_tol"
option.

/bin/cat: file_loc: No such file or directory


and the job is running but the nothing written into .xtc, .trr, .edr files .
What could have gone wrong?

--
Aiswarya  B Pawar

Bioinformatics Dept,
Indian Institute of Science
Bangalore



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--
Aiswarya  B Pawar

Bioinformatics Dept,
Indian Institute of Science
Bangalore






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Re: [gmx-users] getting rid of PBC, completely

[Chandan Choudhury]

On Thu, Jan 19, 2012 at 3:49 PM, Tsjerk Wassenaar  wrote:

> Hi Chandan,
>
> The box is accessible from the t_trxframe struct. Assuming you have
>
> t_trxframe *fr
>
> You can access it through
>
> fr->box
>

Thanks Tsjerk. It (fr.box) did help me to get the box coordinates.

fr.box[XX][XX], fr.box[YY][YY] and fr.box[ZZ][ZZ] gives me the values
but fr.box[XX][YY], fr.box[XX][ZZ] prints 0. Which seems to me that the
origin of the box is at (0,0,0). Then,  fr.box[XX][XX] is the maximum
X-coordinate, fr.box[YY][YY] is the maximum Y-coordinate,fr.box[ZZ][ZZ] is
the maximum Z-coordinate. Am I correct?


> But if you remove jumps first, you're fine anyway. Just don't put
> things back in the box afterwards. And don't center if your aim is
> calculating MSDs.
>

Yeah, you are right.

Chandan

>
> Hope it helps,
>
> Tsjerk
>
> On Thu, Jan 19, 2012 at 11:14 AM, Chandan Choudhury 
> wrote:
> >
> >
> > On Thu, Jan 19, 2012 at 12:17 PM, Mark Abraham 
> > wrote:
> >>
> >> On 19/01/2012 5:39 PM, Chandan Choudhury wrote:
> >>>
> >>>
> >>> Dear gmx-users,
> >>>
> >>> I have a simulated a system containing a linear polymer in a cubic box
> >>> with water molecules.  I need to get rid of PBC effect on the system
> such
> >>> that I can execute my own analysis code. I intend to compute the msd of
> >>> water molecules along the polymer backbone.
> >>
> >>
> >> You can't "get rid of PBC", you can only manage it. The question reduces
> >> what you want to see if a molecule diffuses across the periodic boundary
> >> from near one end of the polymer to the other end.
> >>
> >>
> >>> So, when I execute my own analysis code, I see the msd's are abrupt
> (i.e
> >>> very high), this is due to the pbc. So, for getting rid of PBC effect,
> I
> >>> performed the suggested trjconv workflow
> >>> (
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
> ).
> >>>
> >>> Below are my executed commands :
> >>>
> >>> # Made the system whole
> >>>
> >>> echo 0 | trjconv_4.5.5 -s md0-4.tpr -f 0-4.xtc -pbc whole -o
> >>> 0-4_whole.xtc
> >>>
> >>> # 0 is the whole system. md0-4.tpr is the initial tpr file containing
> >>> whole (no broken) polymer inside the cubic box.
> >>> # Extracted 1st frame from the initial trajectory
> >>>
> >>> echo 0 | trjconv_4.5.5 -s md0-4.tpr -f 0-4.xtc -pbc nojump  -o 1st.pdb
> >>> -dump 0
> >>>
> >>> # used the whole trajectory to remove jumps with reference to the 1st
> >>> frame.
> >>> echo 0 | trjconv_4.5.5 -s 1st.pdb -f 0-4_whole.xtc -pbc nojump -o
> >>> 0-4_nojump.xtc
> >>
> >>
> >> So here you said "let molecules diffuse away from the solute".
> >>
> >>
> >>>
> >>> #system is being centered
> >>> echo "0 0" | trjconv_4.5.5 -s md0-4.tpr -f 0-4_nojump.xtc -o
> >>> 0-4_center.xtc -center
> >>>
> >>> #putting every atom in the box
> >>> echo 0 | trjconv -s md0-4.tpr -f 0-4_center.xtc -o 0-4_box.xtc -pbc
> atom
> >>
> >>
> >> ... and now you said "take all the atoms and put them back in the box",
> >> creating jumps whenever one crosses the boundaries.
> >>
> >>
> >>>
> >>> Still when I execute my analysis code, I do see the abrupt behaviour in
> >>> the msd plot. Can someone guide me how to completely get rid of PBC
> >>> artifacts.
> >>
> >>
> >> Don't simulate with them :-P Is your analysis technique sound for the
> >> periodic case?
> >
> >
> > No, my analysis code doesnot take care of PBC. As to deal with PBC, I
> need
> > to have the box vectors (for atleast NPT simulation) from the trajectory
> and
> > I am unable to extract the box vectors (as of date).
> >
> > Chandan
> >
> >>
> >>
> >> 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/Support/Mailing_Lists/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/Support/Mailing_Lists
> >
> >
> >
> >
> > --
> > Chandan kumar Choudhury
> > NCL, Pune
> > INDIA
> >
> >
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > 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/Support/Mailing_Lists
>
>
>
> --
> 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
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
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> Please don't post (un)sub

Re: [gmx-users] getting rid of PBC, completely

[Tsjerk Wassenaar]

Hi Chandan,

> fr.box[XX][XX], fr.box[YY][YY] and fr.box[ZZ][ZZ] gives me the values
> but fr.box[XX][YY], fr.box[XX][ZZ] prints 0. Which seems to me that the
> origin of the box is at (0,0,0). Then,  fr.box[XX][XX] is the maximum
> X-coordinate, fr.box[YY][YY] is the maximum Y-coordinate,fr.box[ZZ][ZZ] is
> the maximum Z-coordinate. Am I correct?

That's correct if the box is rectangular. If it's triclinic, the
furthest point has (xx+yx+zx,yy+zy,zz), where xx stands for
fr.box[XX][XX].

Cheers,

Tsjerk


-- 
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] getting rid of PBC, completely

[Mark Abraham]

On 19/01/2012 11:27 PM, Chandan Choudhury wrote:
On Thu, Jan 19, 2012 at 3:49 PM, Tsjerk Wassenaar > wrote:


Hi Chandan,

The box is accessible from the t_trxframe struct. Assuming you have

t_trxframe *fr

You can access it through

fr->box


Thanks Tsjerk. It (fr.box) did help me to get the box coordinates.

fr.box[XX][XX], fr.box[YY][YY] and fr.box[ZZ][ZZ] gives me the values 
but fr.box[XX][YY], fr.box[XX][ZZ] prints 0. Which seems to me that 
the origin of the box is at (0,0,0).


The origin is always at (0,0,0) by definition, not by the contents of 
fr.box. There's no magic center of a periodic box, either.


fr.box has the box dimensions, which in general require more than the 3 
pieces of information required for a rectangular solid box.


Then,  fr.box[XX][XX] is the maximum X-coordinate, fr.box[YY][YY] is 
the maximum Y-coordinate,fr.box[ZZ][ZZ] is the maximum Z-coordinate. 
Am I correct?


For some box types, yes.

Mark




But if you remove jumps first, you're fine anyway. Just don't put
things back in the box afterwards. And don't center if your aim is
calculating MSDs.


Yeah, you are right.

Chandan


Hope it helps,

Tsjerk

On Thu, Jan 19, 2012 at 11:14 AM, Chandan Choudhury
mailto:iitd...@gmail.com>> wrote:
>
>
> On Thu, Jan 19, 2012 at 12:17 PM, Mark Abraham
mailto:mark.abra...@anu.edu.au>>
> wrote:
>>
>> On 19/01/2012 5:39 PM, Chandan Choudhury wrote:
>>>
>>>
>>> Dear gmx-users,
>>>
>>> I have a simulated a system containing a linear polymer in a
cubic box
>>> with water molecules.  I need to get rid of PBC effect on the
system such
>>> that I can execute my own analysis code. I intend to compute
the msd of
>>> water molecules along the polymer backbone.
>>
>>
>> You can't "get rid of PBC", you can only manage it. The
question reduces
>> what you want to see if a molecule diffuses across the periodic
boundary
>> from near one end of the polymer to the other end.
>>
>>
>>> So, when I execute my own analysis code, I see the msd's are
abrupt (i.e
>>> very high), this is due to the pbc. So, for getting rid of PBC
effect, I
>>> performed the suggested trjconv workflow
>>>

(http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions).
>>>
>>> Below are my executed commands :
>>>
>>> # Made the system whole
>>>
>>> echo 0 | trjconv_4.5.5 -s md0-4.tpr -f 0-4.xtc -pbc whole -o
>>> 0-4_whole.xtc
>>>
>>> # 0 is the whole system. md0-4.tpr is the initial tpr file
containing
>>> whole (no broken) polymer inside the cubic box.
>>> # Extracted 1st frame from the initial trajectory
>>>
>>> echo 0 | trjconv_4.5.5 -s md0-4.tpr -f 0-4.xtc -pbc nojump  -o
1st.pdb
>>> -dump 0
>>>
>>> # used the whole trajectory to remove jumps with reference to
the 1st
>>> frame.
>>> echo 0 | trjconv_4.5.5 -s 1st.pdb -f 0-4_whole.xtc -pbc nojump -o
>>> 0-4_nojump.xtc
>>
>>
>> So here you said "let molecules diffuse away from the solute".
>>
>>
>>>
>>> #system is being centered
>>> echo "0 0" | trjconv_4.5.5 -s md0-4.tpr -f 0-4_nojump.xtc -o
>>> 0-4_center.xtc -center
>>>
>>> #putting every atom in the box
>>> echo 0 | trjconv -s md0-4.tpr -f 0-4_center.xtc -o 0-4_box.xtc
-pbc atom
>>
>>
>> ... and now you said "take all the atoms and put them back in
the box",
>> creating jumps whenever one crosses the boundaries.
>>
>>
>>>
>>> Still when I execute my analysis code, I do see the abrupt
behaviour in
>>> the msd plot. Can someone guide me how to completely get rid
of PBC
>>> artifacts.
>>
>>
>> Don't simulate with them :-P Is your analysis technique sound
for the
>> periodic case?
>
>
> No, my analysis code doesnot take care of PBC. As to deal with
PBC, I need
> to have the box vectors (for atleast NPT simulation) from the
trajectory and
> I am unable to extract the box vectors (as of date).
>
> Chandan
>
>>
>>
>> Mark
>>
>> --
>> 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!
>> 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/Support/Mailing_Lists
>
>
>
>
> --
> Chandan kumar Choudhury
> NCL, Pune
> INDIA
>
>
> --
> gmx-users mailing list gmx-users@gromacs.org

> http://list

[gmx-users] pdb2gmx -ter with cyclic peptide

[andrea spitaleri]

Hi there,
normally to generate a cyclic peptide I use to edit specbond.dat to force the bond between the N- 
and C-termini and I use the -ter flag into pdb2gmx tool in order to avoid to add hydrogens and 
oxygen to the end of the peptide. This was okay until the gromacs version 4.0.5 with opls ff.


Now using gromacs 4.5.3 with opls ff I get this message:

"There is a dangling bond at at least one of the terminal ends. Select a proper 
terminal entry."

did something change or is is a bug? I have checked in the mailing list and I 
did not find any answer.

thanks in advance for any help

and



--
-
Andrea Spitaleri PhD
Dulbecco Telethon Institute c/o Raffaele Scientific Institute
Biomolecular NMR Laboratory Dibit2 Basilica 3A2
Via Olgettina 58
20132 Milano
Italy
Tel: 0039-0226434348
Fax: 0039-0226434153
http://sites.google.com/site/andreaspitaleri/
http://www.linkedin.com/in/andreaspitaleri
-
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Re: [gmx-users] Chemical Potential

[Steven Neumann]

Thank you very much guys! I will search for some reading. If you can
suggest a tutorial I will appreciate.

On Thu, Jan 19, 2012 at 11:57 AM, René Pool  wrote:

> Hi,
>
> If I understand the question correctly, you want to know the water
> chemical potential in the water/protein/ligand system.
> If so, in principle it should be possible to approximate the water
> chemical potential using test particle insertion. Gromacs has a utility for
> that.
>
> Cheers,
> René
>
> ==**===
> René Pool
>
> Division of Molecular and Computational Toxicology
> Department of Chemistry and Pharmaceutical Sciences
> Vrije Universiteit Amsterdam
> De Boelelaan 1083
> 1081HV AMSTERDAM, the Netherlands
> -
> IBIVU/Bioinformatics
> Department of Computer Science
> Vrije Universiteit Amsterdam
> De Boelelaan 1081a
> 1081HV AMSTERDAM, the Netherlands
>
> Room P 2.75
> E: r.p...@vu.nl
> T: +31 20 598 76 12
> F: +31 20 598 76 10
> ==**===
>
>
>
> On 01/19/2012 02:49 PM, Ivan Gladich wrote:
>
>> On 01/19/2012 11:34 AM, Steven Neumann wrote:
>>
>>> Does anyone can help?
>>> Dear Gmx Users,
>>> I am wondering whether it is possible to obtain in Gromacs chemical
>>> potential e.g. of water in the protein - ligand system?
>>> Please, advise me to do some further reading, suggest method, maybe
>>> tutorial?
>>> Thank you,
>>> Steven
>>>
>> Dear Steven
>> I am not an expert of protein - ligand system...
>> However  the chemical potential of a i-th specie is the derivative of the
>> potential energy in function of the number of the i-particles present in
>> the system.
>> As far as I know (and if I am not wrong), in GROMACS the number of
>> particle is fixed along all the simulation, i.e., you cannot change the
>> number of particles during the simulation.
>> Therefore, you cannot simply  obtain the chemical potential from one
>> single run...
>> I suggest you to search in literature; maybe you can combine different
>> runs to obtain the chemical potential...but I do not want to say you
>> something wrong since I do not have experience in such systems.
>>
>> Good luck
>> Ivan
>>
>> --
>  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!
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[gmx-users] Residue representation

[Steven Neumann]

Dear Gmx Users,

I am simulating (Charmm27 ff) my protein in presence of a tube (made of
atoms). This tube is a representation of a surface of protein. I want to do
an approximation of residues on the surface. I divided amino acids and
represent them as:
- positively charged - I used Na+
[ SOD ]

[ atoms ]

SOD SOD 1.00 0

-negatively charged - I used CL-

[ CLA ]

[ atoms ]

CLA CLA -1.00 0

- hydrophilic - I took Oxygen from Tyrosine OH group

[ TYR ]

[ atoms ]

OH OH1 -0.54 13

- hydrophobic - I want to take Carbon atom - but I have no clue from which
group - I guess somethin positive? Or random Carbon from hydrophobic amino
acids

Please, let me know your opinion for such representation. Would you suggest
representing charged amino acids by atoms taken from charged amino acids
(e.g. N from Arg?)

Do you think its a good approximation?

Thank you

 Steven
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Re: [gmx-users] mdrun-gpu error

[Szilárd Páll]

And sorting out where the /bin/cat error comes from because that is
surely not a Gromacs message!

Cheers,
--
Szilárd



On Thu, Jan 19, 2012 at 1:12 PM, Mark Abraham  wrote:
> On 19/01/2012 8:45 PM, aiswarya pawar wrote:
>
> Mark,
>
> THe normal mdrun also hangs thus not generating any output.
>
>
> OK. It's your problem to solve... keep simplifying stuff until you can
> isolate a small number of possible causes. Top of the list is file system
> availability.
>
> Mark
>
>
>
> On Thu, Jan 19, 2012 at 3:09 AM, Mark Abraham 
> wrote:
>>
>> On 19/01/2012 2:59 AM, aiswarya.pa...@gmail.com wrote:
>>
>> Hi,
>>
>> Its going into the running mode but gets hang there for long hours which
>> generating any data in the output file. And am not able to figure out the
>> error file_doc. Please anyone knows what's going wrong.
>>
>>
>> No, but you should start trying to simplify what you're doing to see where
>> the problem lies. Does normal mdrun work?
>>
>> Mark
>>
>>
>> Thanks
>> Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for
>> it!
>>
>> -Original Message-
>> From: Szilárd Páll 
>> Sender: gmx-users-boun...@gromacs.org
>> Date: Wed, 18 Jan 2012 14:47:59
>> To: Discussion list for GROMACS users
>> Reply-To: Discussion list for GROMACS users 
>> Subject: Re: [gmx-users] mdrun-gpu error
>>
>> Hi,
>>
>> Most of those are just warnings, the only error I see there comes from
>> the shell, probably an error in your script.
>>
>> Cheers,
>> --
>> Szilárd
>>
>>
>>
>> On Wed, Jan 18, 2012 at 12:27 PM, aiswarya pawar
>>  wrote:
>>
>> Hi users,
>>
>> Am running mdrun on gpu . I receive an error such as=
>>
>> WARNING: This run will generate roughly 38570 Mb of data
>>
>>
>> WARNING: OpenMM does not support leap-frog, will use velocity-verlet
>> integrator.
>>
>>
>> WARNING: OpenMM supports only Andersen thermostat with the
>> md/md-vv/md-vv-avek integrators.
>>
>>
>> WARNING: OpenMM supports only Monte Carlo barostat for pressure coupling.
>>
>>
>> WARNING: OpenMM provides contraints as a combination of SHAKE, SETTLE and
>> CCMA. Accuracy is based on the SHAKE tolerance set by the "shake_tol"
>> option.
>>
>> /bin/cat: file_loc: No such file or directory
>>
>>
>> and the job is running but the nothing written into .xtc, .trr, .edr files
>> .
>> What could have gone wrong?
>>
>> --
>> Aiswarya  B Pawar
>>
>> Bioinformatics Dept,
>> Indian Institute of Science
>> Bangalore
>>
>>
>>
>> --
>> 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!
>> 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/Support/Mailing_Lists
>>
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> 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/Support/Mailing_Lists
>>
>>
>>
>>
>>
>> --
>> gmx-users mailing list    gmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
>
> --
> Aiswarya  B Pawar
>
> Bioinformatics Dept,
> Indian Institute of Science
> Bangalore
>
>
>
>
>
>
> --
> gmx-users mailing list    gmx-users@gromacs.org
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Re: [gmx-users] mdrun-gpu error

[aiswarya pawar]

Has the tesla card got to do anything with the error. Am using Nvidia Tesla
S1070 1U server.


On Thu, Jan 19, 2012 at 8:37 PM, Szilárd Páll wrote:

> And sorting out where the /bin/cat error comes from because that is
> surely not a Gromacs message!
>
> Cheers,
> --
> Szilárd
>
>
>
> On Thu, Jan 19, 2012 at 1:12 PM, Mark Abraham 
> wrote:
> > On 19/01/2012 8:45 PM, aiswarya pawar wrote:
> >
> > Mark,
> >
> > THe normal mdrun also hangs thus not generating any output.
> >
> >
> > OK. It's your problem to solve... keep simplifying stuff until you can
> > isolate a small number of possible causes. Top of the list is file system
> > availability.
> >
> > Mark
> >
> >
> >
> > On Thu, Jan 19, 2012 at 3:09 AM, Mark Abraham 
> > wrote:
> >>
> >> On 19/01/2012 2:59 AM, aiswarya.pa...@gmail.com wrote:
> >>
> >> Hi,
> >>
> >> Its going into the running mode but gets hang there for long hours which
> >> generating any data in the output file. And am not able to figure out
> the
> >> error file_doc. Please anyone knows what's going wrong.
> >>
> >>
> >> No, but you should start trying to simplify what you're doing to see
> where
> >> the problem lies. Does normal mdrun work?
> >>
> >> Mark
> >>
> >>
> >> Thanks
> >> Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go
> for
> >> it!
> >>
> >> -Original Message-
> >> From: Szilárd Páll 
> >> Sender: gmx-users-boun...@gromacs.org
> >> Date: Wed, 18 Jan 2012 14:47:59
> >> To: Discussion list for GROMACS users
> >> Reply-To: Discussion list for GROMACS users 
> >> Subject: Re: [gmx-users] mdrun-gpu error
> >>
> >> Hi,
> >>
> >> Most of those are just warnings, the only error I see there comes from
> >> the shell, probably an error in your script.
> >>
> >> Cheers,
> >> --
> >> Szilárd
> >>
> >>
> >>
> >> On Wed, Jan 18, 2012 at 12:27 PM, aiswarya pawar
> >>  wrote:
> >>
> >> Hi users,
> >>
> >> Am running mdrun on gpu . I receive an error such as=
> >>
> >> WARNING: This run will generate roughly 38570 Mb of data
> >>
> >>
> >> WARNING: OpenMM does not support leap-frog, will use velocity-verlet
> >> integrator.
> >>
> >>
> >> WARNING: OpenMM supports only Andersen thermostat with the
> >> md/md-vv/md-vv-avek integrators.
> >>
> >>
> >> WARNING: OpenMM supports only Monte Carlo barostat for pressure
> coupling.
> >>
> >>
> >> WARNING: OpenMM provides contraints as a combination of SHAKE, SETTLE
> and
> >> CCMA. Accuracy is based on the SHAKE tolerance set by the "shake_tol"
> >> option.
> >>
> >> /bin/cat: file_loc: No such file or directory
> >>
> >>
> >> and the job is running but the nothing written into .xtc, .trr, .edr
> files
> >> .
> >> What could have gone wrong?
> >>
> >> --
> >> Aiswarya  B Pawar
> >>
> >> Bioinformatics Dept,
> >> Indian Institute of Science
> >> Bangalore
> >>
> >>
> >>
> >> --
> >> gmx-users mailing listgmx-users@gromacs.org
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> >> 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/Support/Mailing_Lists
> >>
> >> --
> >> gmx-users mailing listgmx-users@gromacs.org
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> >> 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/Support/Mailing_Lists
> >>
> >>
> >>
> >>
> >>
> >> --
> >> gmx-users mailing listgmx-users@gromacs.org
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> >> 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/Support/Mailing_Lists
> >
> >
> >
> >
> > --
> > Aiswarya  B Pawar
> >
> > Bioinformatics Dept,
> > Indian Institute of Science
> > Bangalore
> >
> >
> >
> >
> >
> >
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > 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/Support/Mailing_Lists
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
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Re: [gmx-users] mdrun-gpu error

[aiswarya pawar]

when i tired running it again, i got an error as

Cuda error in file
'/home/staff/sec/secdpal/software/openmm_tesla/platforms/cuda/./src/kernels//
bbsort.cu' in line 176 : unspecified launch failure.
/bin/cat: file_loc: No such file or directory

On Thu, Jan 19, 2012 at 8:45 PM, aiswarya pawar wrote:

> Has the tesla card got to do anything with the error. Am using Nvidia
> Tesla S1070 1U server.
>
>
> On Thu, Jan 19, 2012 at 8:37 PM, Szilárd Páll wrote:
>
>> And sorting out where the /bin/cat error comes from because that is
>> surely not a Gromacs message!
>>
>> Cheers,
>> --
>> Szilárd
>>
>>
>>
>> On Thu, Jan 19, 2012 at 1:12 PM, Mark Abraham 
>> wrote:
>> > On 19/01/2012 8:45 PM, aiswarya pawar wrote:
>> >
>> > Mark,
>> >
>> > THe normal mdrun also hangs thus not generating any output.
>> >
>> >
>> > OK. It's your problem to solve... keep simplifying stuff until you can
>> > isolate a small number of possible causes. Top of the list is file
>> system
>> > availability.
>> >
>> > Mark
>> >
>> >
>> >
>> > On Thu, Jan 19, 2012 at 3:09 AM, Mark Abraham 
>> > wrote:
>> >>
>> >> On 19/01/2012 2:59 AM, aiswarya.pa...@gmail.com wrote:
>> >>
>> >> Hi,
>> >>
>> >> Its going into the running mode but gets hang there for long hours
>> which
>> >> generating any data in the output file. And am not able to figure out
>> the
>> >> error file_doc. Please anyone knows what's going wrong.
>> >>
>> >>
>> >> No, but you should start trying to simplify what you're doing to see
>> where
>> >> the problem lies. Does normal mdrun work?
>> >>
>> >> Mark
>> >>
>> >>
>> >> Thanks
>> >> Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go
>> for
>> >> it!
>> >>
>> >> -Original Message-
>> >> From: Szilárd Páll 
>> >> Sender: gmx-users-boun...@gromacs.org
>> >> Date: Wed, 18 Jan 2012 14:47:59
>> >> To: Discussion list for GROMACS users
>> >> Reply-To: Discussion list for GROMACS users 
>> >> Subject: Re: [gmx-users] mdrun-gpu error
>> >>
>> >> Hi,
>> >>
>> >> Most of those are just warnings, the only error I see there comes from
>> >> the shell, probably an error in your script.
>> >>
>> >> Cheers,
>> >> --
>> >> Szilárd
>> >>
>> >>
>> >>
>> >> On Wed, Jan 18, 2012 at 12:27 PM, aiswarya pawar
>> >>  wrote:
>> >>
>> >> Hi users,
>> >>
>> >> Am running mdrun on gpu . I receive an error such as=
>> >>
>> >> WARNING: This run will generate roughly 38570 Mb of data
>> >>
>> >>
>> >> WARNING: OpenMM does not support leap-frog, will use velocity-verlet
>> >> integrator.
>> >>
>> >>
>> >> WARNING: OpenMM supports only Andersen thermostat with the
>> >> md/md-vv/md-vv-avek integrators.
>> >>
>> >>
>> >> WARNING: OpenMM supports only Monte Carlo barostat for pressure
>> coupling.
>> >>
>> >>
>> >> WARNING: OpenMM provides contraints as a combination of SHAKE, SETTLE
>> and
>> >> CCMA. Accuracy is based on the SHAKE tolerance set by the "shake_tol"
>> >> option.
>> >>
>> >> /bin/cat: file_loc: No such file or directory
>> >>
>> >>
>> >> and the job is running but the nothing written into .xtc, .trr, .edr
>> files
>> >> .
>> >> What could have gone wrong?
>> >>
>> >> --
>> >> Aiswarya  B Pawar
>> >>
>> >> Bioinformatics Dept,
>> >> Indian Institute of Science
>> >> Bangalore
>> >>
>> >>
>> >>
>> >> --
>> >> gmx-users mailing listgmx-users@gromacs.org
>> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> >> Please search the archive at
>> >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> >> 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/Support/Mailing_Lists
>> >>
>> >> --
>> >> gmx-users mailing listgmx-users@gromacs.org
>> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> >> Please search the archive at
>> >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> >> 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/Support/Mailing_Lists
>> >>
>> >>
>> >>
>> >>
>> >>
>> >> --
>> >> gmx-users mailing listgmx-users@gromacs.org
>> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> >> Please search the archive at
>> >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> >> 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/Support/Mailing_Lists
>> >
>> >
>> >
>> >
>> > --
>> > Aiswarya  B Pawar
>> >
>> > Bioinformatics Dept,
>> > Indian Institute of Science
>> > Bangalore
>> >
>> >
>> >
>> >
>> >
>> >
>> > --
>> > gmx-users mailing listgmx-users@gromacs.org
>> > http://lists.gromacs.org/mailman/listinfo/gmx-users
>> > Please search the archive at
>> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> > Please don't post (un)subscribe request

[gmx-users] Problem with Position Restraints (before running SMD)!

[Talal E. AlOtaibi]

Hi guys, When I did my SMD simulation by applying load to a certain group of 
atoms and fixing certain atoms by modifying the topology file, the points that 
i have fixed moved from there original position. I don't know what the problem 
is! Any suggestion!  To make what I was doing clear, I started the equilibrium 
by creating a box and filling it with water. Then I did the energy 
minimization. After that I heated up and pressurized the structure. Every thing 
is good so far. After that, I modified the topology file by adding four points 
that i want to fix as following:; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
 1 1   1000   1000   1000
13301   1000   1000   1000  <-   my 1st 
point
14261   1000   1000   1000  <-   my 2nd 
point
14371   1000   1000   1000  <-my 3rd 
point1548 1 1000 1000 1000  <-my 4th point
#endifThis only what I did to fix the points. The results have shown that the 
fixid points moved from their original position.   Here is my topology file: ;
;   File '3gm1a.top' was generated
;   By user: onbekend (0)
;   On host: onbekend
;   At date: Sat Jul  2 14:03:14 2011
;
;   This is a standalone topology file
;
;   It was generated using program:
;   pdb2gmx - VERSION 4.5.3
;
;   Command line was:
;   pdb2gmx -f 3gm1a.pdb -o 3gm1a.gro -p 3gm1a.top
;
;   Force field data was read from:
;   /opt/apps/pgi7_2/mvapich1_1_0_1/gromacs/4.5.3/share/gromacs/top
;
;   Note:
;   This might be a non-standard force field location. When you use this 
topology, the
;   force field must either be present in the current directory, or the 
location
;   specified in the GMXLIB path variable or with the 'include' mdp file 
option.
; ; Include forcefield parameters
#include "gromos53a6.ff/forcefield.itp" ; Include chain topologies
#include "3gm1a_Protein_chain_A.itp"
#include "3gm1a_Protein_chain_E.itp"
#include "3gm1a_Protein_chain_F.itp" ; Include water topology
#include "gromos53a6.ff/spc.itp"#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
 11   1000   1000   1000
13301   1000   1000   1000
14261   1000   1000   1000
14371   1000   1000   1000
15481   1000   1000   1000
#endif ; Include topology for ions
#include "gromos53a6.ff/ions.itp" [ system ]; Name
PROTEIN TYROSINE KINASE 2 BETA; 5 RESIDUES 861-1009; PAXILLIN in water [ 
molecules ]; Compound#mols
Protein_chain_A 1
Protein_chain_E 1
Protein_chain_F 1
SOL 8788
NA  25
CL  18
 And Here is my mdp file: title   = smd_120 ; 120 pN
; this is loosely based off of the VT pulling tutorial; heavily modified 
; Run parameters
integrator  = md
dt  = 0.002
tinit   = 0
nsteps  = 250   ; 5 ns
; Output parameters
nstxout = 1000  ; every  2 ps
nstvout = 1000
nstfout = 5000
nstxtcout   = 5000  ; every ps
nstenergy   = 1000
; Bond parameters
constraint_algorithm= lincs
constraints = hbonds
lincs_iter  = 1  ; accuracy of LINCS
lincs_order = 4  ; also related to accuracy; Single-range 
cutoff scheme
nstlist = 5
ns_type = grid
rlist   = 1.4
rcoulomb= 1.4
rvdw= 1.4
; PME electrostatics parameters
coulombtype = PME
fourierspacing  = 0.16
pme_order   = 4
ewald_rtol  = 1e-5
optimize_fft= yes
; Berendsen temperature coupling is on in two groups
Tcoupl  = Nose-Hoover
tc_grps = Protein Non-Protein
tau_t   = 0.2 0.2
ref_t   = 310 310
; Pressure coupling is on
Pcoupl  = Parrinello-Rahman
pcoupltype  = isotropic
tau_p   = 1.0
compressibility = 4.5e-5
ref_p   = 1.0
; Generate velocities is off
gen_vel = no
; Periodic boundary conditions are on in all directions
pbc = xyz
; Long-range dispersion correction
DispCorr= EnerPres
; COM motion removal
; These options remove comm motion of the constraint / freeze group
nstcomm = 1
comm_mode   = Linear
comm_grps   = System
; pull parameters
pull= constant_force
pull_geometry   = direction
pull_nstxout= 500 ; will print the c.o.m. coordinates
pull_nstfout= 500 ; forces on group
pull_ngroups= 1
pull_group0 = Protein ;
pull_group1 = group_B ;
pull_pbcatom1   = 100 ; the CA of the 10th residue
pull_vec1   = -2.63 -16.48 -14.95 ; direction of pull, will be normalized
pull_k1 = 72.29 ; pull_k1*1.66 = pN;  units: [kJ / (mol * nm^2)] 
What should I do?  Thanks,Talal  -- 
gmx-users mail

Re: [gmx-users] Problem with Position Restraints (before running SMD)!

[Justin A. Lemkul]

Talal E. AlOtaibi wrote:

Hi guys,
 
When I did my SMD simulation by applying load to a certain group of 
atoms and fixing certain atoms by modifying the topology file, the 
points that i have fixed moved from there original position. I don't 
know what the problem is!
 
Any suggestion!
 


Position restraints disfavor motion, they don't prevent it.  If the pulling 
force is sufficient to overcome the restraint bias, then the atoms move.  Two 
options:


1. Use a stronger position restraint force constant
2. Use freezegrps instead - these don't move

-Justin

 
To make what I was doing clear, I started the equilibrium by creating a 
box and filling it with water. Then I did the energy minimization. After 
that I heated up and pressurized the structure. Every thing is good so 
far. After that, I modified the topology file by adding four points that 
i want to fix as following:

; Position restraint for each water oxygen
[ position_restraints ]
; i funct   fcxfcyfcz
 1 1 1000 1000 1000
1330 1 1000 1000 1000  <-   my 1st point
1426 1 1000 1000 1000  <-   my 2nd point
1437 1 1000 1000 1000  <-   my 3rd point
1548 1 1000 1000 1000  <-   my 4th point
#endif
This only what I did to fix the points.
 
The results have shown that the fixid points moved from their original 
position.
 
 
 
Here is my topology file:
 
;

;   File '3gm1a.top' was generated
;   By user: onbekend (0)
;   On host: onbekend
;   At date: Sat Jul  2 14:03:14 2011
;
;   This is a standalone topology file
;
;   It was generated using program:
;   pdb2gmx - VERSION 4.5.3
;
;   Command line was:
;   pdb2gmx -f 3gm1a.pdb -o 3gm1a.gro -p 3gm1a.top
;
;   Force field data was read from:
;   /opt/apps/pgi7_2/mvapich1_1_0_1/gromacs/4.5.3/share/gromacs/top
;
;   Note:
;   This might be a non-standard force field location. When you use 
this topology, the
;   force field must either be present in the current directory, or 
the location
;   specified in the GMXLIB path variable or with the 'include' mdp 
file option.

;
 
; Include forcefield parameters

#include "gromos53a6.ff/forcefield.itp"
 
; Include chain topologies

#include "3gm1a_Protein_chain_A.itp"
#include "3gm1a_Protein_chain_E.itp"
#include "3gm1a_Protein_chain_F.itp"
 
; Include water topology

#include "gromos53a6.ff/spc.itp"
#ifdef POSRES_WATER

; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
 11   1000   1000   1000
13301   1000   1000   1000
14261   1000   1000   1000
14371   1000   1000   1000
15481   1000   1000   1000

#endif
 
; Include topology for ions

#include "gromos53a6.ff/ions.itp"
 
[ system ]

; Name
PROTEIN TYROSINE KINASE 2 BETA; 5 RESIDUES 861-1009; PAXILLIN in water
 
[ molecules ]

; Compound#mols
Protein_chain_A 1
Protein_chain_E 1
Protein_chain_F 1
SOL 8788
NA  25
CL  18

 
And Here is my mdp file:
 
title   = smd_120 ; 120 pN

; this is loosely based off of the VT pulling tutorial; heavily modified
; Run parameters
integrator  = md
dt  = 0.002
tinit   = 0
nsteps  = 250   ; 5 ns
; Output parameters
nstxout = 1000  ; every  2 ps
nstvout = 1000
nstfout = 5000
nstxtcout   = 5000  ; every ps
nstenergy   = 1000
; Bond parameters
constraint_algorithm= lincs
constraints = hbonds
lincs_iter  = 1  ; accuracy of LINCS
lincs_order = 4  ; also related to accuracy
; Single-range cutoff scheme
nstlist = 5
ns_type = grid
rlist   = 1.4
rcoulomb= 1.4
rvdw= 1.4
; PME electrostatics parameters
coulombtype = PME
fourierspacing  = 0.16
pme_order   = 4
ewald_rtol  = 1e-5
optimize_fft= yes
; Berendsen temperature coupling is on in two groups
Tcoupl  = Nose-Hoover
tc_grps = Protein Non-Protein
tau_t   = 0.2 0.2
ref_t   = 310 310
; Pressure coupling is on
Pcoupl  = Parrinello-Rahman
pcoupltype  = isotropic
tau_p   = 1.0
compressibility = 4.5e-5
ref_p   = 1.0
; Generate velocities is off
gen_vel = no
; Periodic boundary conditions are on in all directions
pbc = xyz
; Long-range dispersion correction
DispCorr= EnerPres
; COM motion removal
; These options remove comm motion of the constraint / freeze group
nstcomm = 1
comm_mode   = Linear
comm_grps   = System
; pull parameters
pull= constant_force
pull_geometry   = direction
pull_nstxout= 500 ; will print the c.o.m. coordinates
pull_nstfout= 500 ; forces on group
pull_ngroups= 1
pull_group0 = Protein ;
pull_group1 = group_B ;
pull_pbcatom1   = 100 ; the CA of

Re: [gmx-users] Problem with Position Restraints (before running SMD)!

[Justin A. Lemkul]

Talal E. AlOtaibi wrote:



; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
 11   1000   1000   1000
13301   1000   1000   1000
14261   1000   1000   1000
14371   1000   1000   1000
15481   1000   1000   1000

#endif


More to the point, this will fail and should have raised a fatal error in 
grompp.  You're putting restraints on atoms that can't possibly exist in water. 
 The numbering is done per [moleculetype] so a position restraint directive for 
water can only have numbers 1, 2, and 3 (OW and the two HW atoms).


If you're trying to restrain atoms in a protein, you have to create a separate 
[position_restraints] directive within the protein's [moleculetype].  See the 
wiki for an example.


-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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Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists

[gmx-users] How to find Hbonding partner

[Sanku M]

Hi,
   I am wondering whether there is any way in GROMACS that one can find which 
groups are the main Hbonding partners in a trajectory. For example, if I 
simulate a peptide in water, I want to know during the simulation, which 
particular atoms in the peptides are making most of the Hbonds with water as a 
function of time. I find g_hbond can tell us the total number of Hbond between 
two groups as a function of time but, can it specify which groups are making 
the Hbonds most of the time ?

Any help will be appreciated.

Sanku-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
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[gmx-users] writing checkpoints

[Dr. Vitaly V. Chaban]

We are running quite a large system with a default checkpoint
intervals (15 minutes). However, in the md.log file, it is written
like below

Writing checkpoint, step 138 at Thu Jan 19 11:00:36 2012
Writing checkpoint, step 1380010 at Thu Jan 19 11:00:41 2012
Writing checkpoint, step 1380020 at Thu Jan 19 11:00:46 2012
Writing checkpoint, step 1380030 at Thu Jan 19 11:00:51 2012
Writing checkpoint, step 1380040 at Thu Jan 19 11:00:55 2012
Writing checkpoint, step 1380050 at Thu Jan 19 11:01:00 2012

Then  after an hour -

Writing checkpoint, step 139 at Thu Jan 19 12:21:18 2012
Writing checkpoint, step 1390010 at Thu Jan 19 12:21:23 2012
Writing checkpoint, step 1390020 at Thu Jan 19 12:21:28 2012
Writing checkpoint, step 1390030 at Thu Jan 19 12:21:32 2012


The job is executed using 4 cores. The version is 4-0-7.

Is this a bug? Just curious.


-- 
Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester, Rochester, New York 14627-0216
THE UNITED STATES OF AMERICA
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
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Re: [gmx-users] mdrun-gpu error

[Szilárd Páll]

That's a generic GPU kernel launch failure which can mean anything,
from faulty hardware to bad driver to messed up installation.

Does the memory test run? Try to compile/install again and see if it works.

--
Szilárd



On Thu, Jan 19, 2012 at 4:18 PM, aiswarya pawar
 wrote:
> when i tired running it again, i got an error as
>
> Cuda error in file
> '/home/staff/sec/secdpal/software/openmm_tesla/platforms/cuda/./src/kernels//bbsort.cu'
> in line 176 : unspecified launch failure.
>
> /bin/cat: file_loc: No such file or directory
>
>
> On Thu, Jan 19, 2012 at 8:45 PM, aiswarya pawar 
> wrote:
>>
>> Has the tesla card got to do anything with the error. Am using Nvidia
>> Tesla S1070 1U server.
>>
>>
>> On Thu, Jan 19, 2012 at 8:37 PM, Szilárd Páll 
>> wrote:
>>>
>>> And sorting out where the /bin/cat error comes from because that is
>>> surely not a Gromacs message!
>>>
>>> Cheers,
>>> --
>>> Szilárd
>>>
>>>
>>>
>>> On Thu, Jan 19, 2012 at 1:12 PM, Mark Abraham 
>>> wrote:
>>> > On 19/01/2012 8:45 PM, aiswarya pawar wrote:
>>> >
>>> > Mark,
>>> >
>>> > THe normal mdrun also hangs thus not generating any output.
>>> >
>>> >
>>> > OK. It's your problem to solve... keep simplifying stuff until you can
>>> > isolate a small number of possible causes. Top of the list is file
>>> > system
>>> > availability.
>>> >
>>> > Mark
>>> >
>>> >
>>> >
>>> > On Thu, Jan 19, 2012 at 3:09 AM, Mark Abraham 
>>> > wrote:
>>> >>
>>> >> On 19/01/2012 2:59 AM, aiswarya.pa...@gmail.com wrote:
>>> >>
>>> >> Hi,
>>> >>
>>> >> Its going into the running mode but gets hang there for long hours
>>> >> which
>>> >> generating any data in the output file. And am not able to figure out
>>> >> the
>>> >> error file_doc. Please anyone knows what's going wrong.
>>> >>
>>> >>
>>> >> No, but you should start trying to simplify what you're doing to see
>>> >> where
>>> >> the problem lies. Does normal mdrun work?
>>> >>
>>> >> Mark
>>> >>
>>> >>
>>> >> Thanks
>>> >> Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go
>>> >> for
>>> >> it!
>>> >>
>>> >> -Original Message-
>>> >> From: Szilárd Páll 
>>> >> Sender: gmx-users-boun...@gromacs.org
>>> >> Date: Wed, 18 Jan 2012 14:47:59
>>> >> To: Discussion list for GROMACS users
>>> >> Reply-To: Discussion list for GROMACS users 
>>> >> Subject: Re: [gmx-users] mdrun-gpu error
>>> >>
>>> >> Hi,
>>> >>
>>> >> Most of those are just warnings, the only error I see there comes from
>>> >> the shell, probably an error in your script.
>>> >>
>>> >> Cheers,
>>> >> --
>>> >> Szilárd
>>> >>
>>> >>
>>> >>
>>> >> On Wed, Jan 18, 2012 at 12:27 PM, aiswarya pawar
>>> >>  wrote:
>>> >>
>>> >> Hi users,
>>> >>
>>> >> Am running mdrun on gpu . I receive an error such as=
>>> >>
>>> >> WARNING: This run will generate roughly 38570 Mb of data
>>> >>
>>> >>
>>> >> WARNING: OpenMM does not support leap-frog, will use velocity-verlet
>>> >> integrator.
>>> >>
>>> >>
>>> >> WARNING: OpenMM supports only Andersen thermostat with the
>>> >> md/md-vv/md-vv-avek integrators.
>>> >>
>>> >>
>>> >> WARNING: OpenMM supports only Monte Carlo barostat for pressure
>>> >> coupling.
>>> >>
>>> >>
>>> >> WARNING: OpenMM provides contraints as a combination of SHAKE, SETTLE
>>> >> and
>>> >> CCMA. Accuracy is based on the SHAKE tolerance set by the "shake_tol"
>>> >> option.
>>> >>
>>> >> /bin/cat: file_loc: No such file or directory
>>> >>
>>> >>
>>> >> and the job is running but the nothing written into .xtc, .trr, .edr
>>> >> files
>>> >> .
>>> >> What could have gone wrong?
>>> >>
>>> >> --
>>> >> Aiswarya  B Pawar
>>> >>
>>> >> Bioinformatics Dept,
>>> >> Indian Institute of Science
>>> >> Bangalore
>>> >>
>>> >>
>>> >>
>>> >> --
>>> >> 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!
>>> >> 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/Support/Mailing_Lists
>>> >>
>>> >> --
>>> >> 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!
>>> >> 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/Support/Mailing_Lists
>>> >>
>>> >>
>>> >>
>>> >>
>>> >>
>>> >> --
>>> >> 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!
>>> >> 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?

Re: [gmx-users] mdrun-gpu error

[aiswarya pawar]

Szilárd,

I did a memory test run yesterday and it went fine but today received an
error. So you mean to say the tesla card version nothing to do with this
right.

Thanks

On Thu, Jan 19, 2012 at 11:09 PM, Szilárd Páll wrote:

> That's a generic GPU kernel launch failure which can mean anything,
> from faulty hardware to bad driver to messed up installation.
>
> Does the memory test run? Try to compile/install again and see if it works.
>
> --
> Szilárd
>
>
>
> On Thu, Jan 19, 2012 at 4:18 PM, aiswarya pawar
>  wrote:
> > when i tired running it again, i got an error as
> >
> > Cuda error in file
> >
> '/home/staff/sec/secdpal/software/openmm_tesla/platforms/cuda/./src/kernels//
> bbsort.cu'
> > in line 176 : unspecified launch failure.
> >
> > /bin/cat: file_loc: No such file or directory
> >
> >
> > On Thu, Jan 19, 2012 at 8:45 PM, aiswarya pawar <
> aiswarya.pa...@gmail.com>
> > wrote:
> >>
> >> Has the tesla card got to do anything with the error. Am using Nvidia
> >> Tesla S1070 1U server.
> >>
> >>
> >> On Thu, Jan 19, 2012 at 8:37 PM, Szilárd Páll 
> >> wrote:
> >>>
> >>> And sorting out where the /bin/cat error comes from because that is
> >>> surely not a Gromacs message!
> >>>
> >>> Cheers,
> >>> --
> >>> Szilárd
> >>>
> >>>
> >>>
> >>> On Thu, Jan 19, 2012 at 1:12 PM, Mark Abraham  >
> >>> wrote:
> >>> > On 19/01/2012 8:45 PM, aiswarya pawar wrote:
> >>> >
> >>> > Mark,
> >>> >
> >>> > THe normal mdrun also hangs thus not generating any output.
> >>> >
> >>> >
> >>> > OK. It's your problem to solve... keep simplifying stuff until you
> can
> >>> > isolate a small number of possible causes. Top of the list is file
> >>> > system
> >>> > availability.
> >>> >
> >>> > Mark
> >>> >
> >>> >
> >>> >
> >>> > On Thu, Jan 19, 2012 at 3:09 AM, Mark Abraham <
> mark.abra...@anu.edu.au>
> >>> > wrote:
> >>> >>
> >>> >> On 19/01/2012 2:59 AM, aiswarya.pa...@gmail.com wrote:
> >>> >>
> >>> >> Hi,
> >>> >>
> >>> >> Its going into the running mode but gets hang there for long hours
> >>> >> which
> >>> >> generating any data in the output file. And am not able to figure
> out
> >>> >> the
> >>> >> error file_doc. Please anyone knows what's going wrong.
> >>> >>
> >>> >>
> >>> >> No, but you should start trying to simplify what you're doing to see
> >>> >> where
> >>> >> the problem lies. Does normal mdrun work?
> >>> >>
> >>> >> Mark
> >>> >>
> >>> >>
> >>> >> Thanks
> >>> >> Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network.
> Go
> >>> >> for
> >>> >> it!
> >>> >>
> >>> >> -Original Message-
> >>> >> From: Szilárd Páll 
> >>> >> Sender: gmx-users-boun...@gromacs.org
> >>> >> Date: Wed, 18 Jan 2012 14:47:59
> >>> >> To: Discussion list for GROMACS users
> >>> >> Reply-To: Discussion list for GROMACS users 
> >>> >> Subject: Re: [gmx-users] mdrun-gpu error
> >>> >>
> >>> >> Hi,
> >>> >>
> >>> >> Most of those are just warnings, the only error I see there comes
> from
> >>> >> the shell, probably an error in your script.
> >>> >>
> >>> >> Cheers,
> >>> >> --
> >>> >> Szilárd
> >>> >>
> >>> >>
> >>> >>
> >>> >> On Wed, Jan 18, 2012 at 12:27 PM, aiswarya pawar
> >>> >>  wrote:
> >>> >>
> >>> >> Hi users,
> >>> >>
> >>> >> Am running mdrun on gpu . I receive an error such as=
> >>> >>
> >>> >> WARNING: This run will generate roughly 38570 Mb of data
> >>> >>
> >>> >>
> >>> >> WARNING: OpenMM does not support leap-frog, will use velocity-verlet
> >>> >> integrator.
> >>> >>
> >>> >>
> >>> >> WARNING: OpenMM supports only Andersen thermostat with the
> >>> >> md/md-vv/md-vv-avek integrators.
> >>> >>
> >>> >>
> >>> >> WARNING: OpenMM supports only Monte Carlo barostat for pressure
> >>> >> coupling.
> >>> >>
> >>> >>
> >>> >> WARNING: OpenMM provides contraints as a combination of SHAKE,
> SETTLE
> >>> >> and
> >>> >> CCMA. Accuracy is based on the SHAKE tolerance set by the
> "shake_tol"
> >>> >> option.
> >>> >>
> >>> >> /bin/cat: file_loc: No such file or directory
> >>> >>
> >>> >>
> >>> >> and the job is running but the nothing written into .xtc, .trr, .edr
> >>> >> files
> >>> >> .
> >>> >> What could have gone wrong?
> >>> >>
> >>> >> --
> >>> >> Aiswarya  B Pawar
> >>> >>
> >>> >> Bioinformatics Dept,
> >>> >> Indian Institute of Science
> >>> >> Bangalore
> >>> >>
> >>> >>
> >>> >>
> >>> >> --
> >>> >> gmx-users mailing listgmx-users@gromacs.org
> >>> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >>> >> Please search the archive at
> >>> >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> >>> >> 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/Support/Mailing_Lists
> >>> >>
> >>> >> --
> >>> >> gmx-users mailing listgmx-users@gromacs.org
> >>> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >>> >> Please search the archive at
> >>> >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> >>> >

Re: [gmx-users] How to find Hbonding partner

[Justin A. Lemkul]

Sanku M wrote:

Hi,
   I am wondering whether there is any way in GROMACS that one can find 
which groups are the main Hbonding partners in a trajectory. For 
example, if I simulate a peptide in water, I want to know during the 
simulation, which particular atoms in the peptides are making most of 
the Hbonds with water as a function of time. I find g_hbond can tell us 
the total number of Hbond between two groups as a function of time but, 
can it specify which groups are making the Hbonds most of the time ?




Use the output of g_hbond -hbn -hbm.

-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] mdrun-gpu error

[Justin A. Lemkul]

aiswarya pawar wrote:

Szilárd,

I did a memory test run yesterday and it went fine but today received an 
error. So you mean to say the tesla card version nothing to do with this 
right.




You're trying to solve multiple problems at once.  You told Mark that the normal 
mdrun executable (which works independently of any GPU components) also hangs, 
so either your filesystem is faulty or your installation procedure produced 
nonfunctional executables.


You're posting bits and pieces of information, which makes it incredibly hard 
for anyone to help you.  Let's recap and try again.  Please provide:


1. The Gromacs version you're using
2. Description of the hardware (GPU and non-GPU components)
3. Installation procedure for Gromacs and any of the prerequisite software and 
libraries that were required, including versions
4. The exact command(s) you're issuing, including the full script that is 
causing a problem


-Justin


Thanks

On Thu, Jan 19, 2012 at 11:09 PM, Szilárd Páll > wrote:


That's a generic GPU kernel launch failure which can mean anything,
from faulty hardware to bad driver to messed up installation.

Does the memory test run? Try to compile/install again and see if it
works.

--
Szilárd



On Thu, Jan 19, 2012 at 4:18 PM, aiswarya pawar
mailto:aiswarya.pa...@gmail.com>> wrote:
 > when i tired running it again, i got an error as
 >
 > Cuda error in file
 >

'/home/staff/sec/secdpal/software/openmm_tesla/platforms/cuda/./src/kernels//bbsort.cu
'
 > in line 176 : unspecified launch failure.
 >
 > /bin/cat: file_loc: No such file or directory
 >
 >
 > On Thu, Jan 19, 2012 at 8:45 PM, aiswarya pawar
mailto:aiswarya.pa...@gmail.com>>
 > wrote:
 >>
 >> Has the tesla card got to do anything with the error. Am
using Nvidia
 >> Tesla S1070 1U server.
 >>
 >>
 >> On Thu, Jan 19, 2012 at 8:37 PM, Szilárd Páll
mailto:szilard.p...@cbr.su.se>>
 >> wrote:
 >>>
 >>> And sorting out where the /bin/cat error comes from because that is
 >>> surely not a Gromacs message!
 >>>
 >>> Cheers,
 >>> --
 >>> Szilárd
 >>>
 >>>
 >>>
 >>> On Thu, Jan 19, 2012 at 1:12 PM, Mark Abraham
mailto:mark.abra...@anu.edu.au>>
 >>> wrote:
 >>> > On 19/01/2012 8:45 PM, aiswarya pawar wrote:
 >>> >
 >>> > Mark,
 >>> >
 >>> > THe normal mdrun also hangs thus not generating any output.
 >>> >
 >>> >
 >>> > OK. It's your problem to solve... keep simplifying stuff
until you can
 >>> > isolate a small number of possible causes. Top of the list is
file
 >>> > system
 >>> > availability.
 >>> >
 >>> > Mark
 >>> >
 >>> >
 >>> >
 >>> > On Thu, Jan 19, 2012 at 3:09 AM, Mark Abraham
mailto:mark.abra...@anu.edu.au>>
 >>> > wrote:
 >>> >>
 >>> >> On 19/01/2012 2:59 AM, aiswarya.pa...@gmail.com
 wrote:
 >>> >>
 >>> >> Hi,
 >>> >>
 >>> >> Its going into the running mode but gets hang there for long
hours
 >>> >> which
 >>> >> generating any data in the output file. And am not able to
figure out
 >>> >> the
 >>> >> error file_doc. Please anyone knows what's going wrong.
 >>> >>
 >>> >>
 >>> >> No, but you should start trying to simplify what you're
doing to see
 >>> >> where
 >>> >> the problem lies. Does normal mdrun work?
 >>> >>
 >>> >> Mark
 >>> >>
 >>> >>
 >>> >> Thanks
 >>> >> Sent from my BlackBerry® on Reliance Mobile, India's No. 1
Network. Go
 >>> >> for
 >>> >> it!
 >>> >>
 >>> >> -Original Message-
 >>> >> From: Szilárd Páll mailto:szilard.p...@cbr.su.se>>
 >>> >> Sender: gmx-users-boun...@gromacs.org

 >>> >> Date: Wed, 18 Jan 2012 14:47:59
 >>> >> To: Discussion list for GROMACS usersmailto:gmx-users@gromacs.org>>
 >>> >> Reply-To: Discussion list for GROMACS users
mailto:gmx-users@gromacs.org>>
 >>> >> Subject: Re: [gmx-users] mdrun-gpu error
 >>> >>
 >>> >> Hi,
 >>> >>
 >>> >> Most of those are just warnings, the only error I see there
comes from
 >>> >> the shell, probably an error in your script.
 >>> >>
 >>> >> Cheers,
 >>> >> --
 >>> >> Szilárd
 >>> >>
 >>> >>
 >>> >>
 >>> >> On Wed, Jan 18, 2012 at 12:27 PM, aiswarya pawar
 >>> >> mailto:aiswarya.pa...@gmail.com>>
wrote:
 >>> >>
 >>> >> Hi users,
 >>> >>
 >>> >> Am running mdrun on gpu . I receive an error such as=
 >>> >>
 >>> >> WARNING: This run will generate roughly 38570 Mb of data
 >>> >>
 >>> >>
 >>> >> WARNING: OpenMM does not support leap-frog, will use
velocity-verlet
 >>> >> integrator.
 >>> >>
 >>> >>
 >>> >> WARN

[gmx-users] Reg: Number of nodes in REMD

[Rohit Farmer]

Hi there,

I am trying to run REMD using the following command

 mdrun_mpi -s run_.tpr -multi 8 -replex 100

and i am getting the following error

Fatal error:
The number of nodes (1) is not a multiple of the number of simulations (8)

i tried using -np option to give the number of nodes but it is also not 
working.


I installed gromacs_mpich using synaptics in ubuntu.

Any help please.

Thanks

Rohit

--
Rohit Farmer
PhD Biosciences (2011-2014)
Center for Systems Biology
University of Birmingham
Birmingham B152TT
United Kingdom
Email : rohit.far...@gmail.com

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Re: [gmx-users] Reg: Number of nodes in REMD

[Justin A. Lemkul]

Rohit Farmer wrote:

Hi there,

I am trying to run REMD using the following command

 mdrun_mpi -s run_.tpr -multi 8 -replex 100

and i am getting the following error

Fatal error:
The number of nodes (1) is not a multiple of the number of simulations (8)

i tried using -np option to give the number of nodes but it is also not 
working.




The mdrun_mpi -np option is not used; the parallel job needs to be initiated via 
mpirun, e.g.:


mpirun -np 8 mdrun_mpi ...

Otherwise, install Gromacs yourself to make use of threading rather than MPI.

-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] Problem with Position Restraints (before running SMD)!

[Justin A. Lemkul]

Talal E. AlOtaibi wrote:

Thank you so much Justin,
 
I made some changes and the SMD run was fine with no errors but I 
still have the same problem (the fixed points moved away from their 
original position).
 


How great is the displacement?  Recall what I said before - position restraints 
are simply a bias against change, they do not prevent the change in position. 
If your pulling force is stronger than the restraining force, motion occurs and 
Newton was right ;)


I mentioned two possible fixes before.  If the displacement is unacceptably 
large, try those suggestions.


I made index file for the atoms that i want to fix. Then, I use 
'genrestr' to generate 'posre.itp' file that contains the 
[position_restraints] points. After that, I add the following to the 
Topology file:

#ifdef POSRES
#include "posre.itp"
#endif

Then, I run my SMD simulation. But, I get the same problem. Could you 
please tell me what is my problem. I really try to do my best.
BTW, I didn't find any example in wiki that could help me to run SMD 
simulation that contains both fix points and points under load.
 


There is no such example.  I was pointing you to the proper method for 
#including position restraints directives in a complex topology.


http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds

-Justin


Thanks alot,
Talal
 > Date: Thu, 19 Jan 2012 10:39:30 -0500
 > From: jalem...@vt.edu
 > To: gmx-users@gromacs.org
 > Subject: Re: [gmx-users] Problem with Position Restraints (before 
running SMD)!

 >
 >
 >
 > Talal E. AlOtaibi wrote:
 >
 > >
 > > ; Position restraint for each water oxygen
 > > [ position_restraints ]
 > > ; i funct   fcxfcyfcz
 > > 1 1 1000 1000 1000
 > > 1330 1 1000 1000 1000
 > > 1426 1 1000 1000 1000
 > > 1437 1 1000 1000 1000
 > > 1548 1 1000 1000 1000
 > >
 > > #endif
 >
 > More to the point, this will fail and should have raised a fatal 
error in
 > grompp. You're putting restraints on atoms that can't possibly exist 
in water.
 > The numbering is done per [moleculetype] so a position restraint 
directive for

 > water can only have numbers 1, 2, and 3 (OW and the two HW atoms).
 >
 > If you're trying to restrain atoms in a protein, you have to create a 
separate
 > [position_restraints] directive within the protein's [moleculetype]. 
See the

 > wiki for an example.
 >
 > -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/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/Support/Mailing_Lists


--


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] sudden jumps in RMSD etc.

[Yun Shi]

Hi all,

I am doing duplicate MD simulations with a protein-ligand system.

After processing one trajectory by trjconv with the optioin -pbc nojump, I
still find abrupt jumps (on the scale of nm) in RMSDs and COM distances.

Then I tried -pbc mol -ur compact, which did not work. And then -fit
progressive on protein atoms, which again did not completely eliminate
those jumps in protein atom RMSDs.

I wonder if I have not used the right option?

Thanks for any advice,

Yun
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[gmx-users] query on g_sorient

[Sanku M]

Hi,

  I am trying to understand what are the angles g_sorient plans to compute. 
The manual says that the theta1 is "the angle with the vector from the first 
atom of the solvent molecule
to the midpoint between atoms 2 and 3" .  But, I wonder what is the reference 
position of this angle  ? In other words, what is the 3rd atom that one needs 
for the calculation angle ( the first atom being the water-oxygen, second atom 
being the  
midpoint of two water-hydrogen) ?  Is the 3rd atom any solute atom or their 
center of mass ?


Thanks
Sanku-- 
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Re: [gmx-users] sudden jumps in RMSD etc.

[Mark Abraham]

On 20/01/2012 7:55 AM, Yun Shi wrote:

Hi all,

I am doing duplicate MD simulations with a protein-ligand system.

After processing one trajectory by trjconv with the optioin -pbc 
nojump, I still find abrupt jumps (on the scale of nm) in RMSDs and 
COM distances.


Then I tried -pbc mol -ur compact, which did not work. And then -fit 
progressive on protein atoms, which again did not completely eliminate 
those jumps in protein atom RMSDs.


I wonder if I have not used the right option?


There's a suggested workflow here 
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions 
which you can adapt to your needs.


Mark
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Re: [gmx-users] query on g_sorient

[Justin A. Lemkul]

Sanku M wrote:

Hi,

  I am trying to understand what are the angles g_sorient plans to compute. 
The manual says that the theta1 is "the angle with the vector from the 
first atom of the solvent molecule
to the midpoint between atoms 2 and 3" .  But, I wonder what is the 
reference position of this angle  ? In other words, what is the 3rd atom 
that one needs for the calculation angle ( the first atom being the 
water-oxygen, second atom being the  
midpoint of two water-hydrogen) ?  Is the 3rd atom any solute atom or 
their center of mass ?




Keep reading g_sorient -h, the reference group is explained.

-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] Lincs warnings

[Ben Porebski]

Hi all,

I've been working on some structures between 2.5A and 3.4A in resolution
and all of my structures suffer from lincs warnings.
>From reading the page about lincs warnings, I've performed a more lengthy
equilibration:

I'm using gromacs 4.0.7 single precision and the G53a6 force field with spc
water model.

- Genbox, add ions.
- EM until converges
- Positional restraints at 2,000 kJ/mol, 200, 20 and 2 for 100ps each at
100K
- Followed by simulated annealing with the following parameters:

; Simulated annealing @ positional restraint of 2 kJ/mol
annealing = single  single
annealing_npoints   = 3   3
annealing_time = 0 50 2500 50 250
annealing_temp = 100 100 300 100 100 300

- This then undergoes 750ps of md at 300K.

Once done. I continue the run in my production MD.
Sometimes my structures will crash within 5 ns, sometimes it will run out
for 60 ns before I start seeing any lincs warnings.

I've attempted to further refine the structures and they behave a little
better, but still crash, just less often.
To continue the simulation, I will not use the .trr output from the
previous simulation. If this doesn't work, I'll run the simulation using
shake for 2 ns, but this is significantly slower.

I'm a little concerned that these crashes may be introducing some sort of
error into the simulation and I'm not sure of the right way to get around
this problem.
I've played around with changing the lincs order and lincs iteration
parameters, which appear to reduce the number of lincs warnings and slows
down the simulation slightly.

Another thing I've played with was the constraints. Changing this from
all-bonds to hbonds.
This stopped my crashes, but a co-worker thought that it may not be
accurately modelling the system, or would introduce anomalies into the
simulation.
My impression was that changing from all-bonds to hbonds would improve the
accuracy of the system... But I could be wrong.

If anyone has experience with dealing with lincs warnings or simulating low
resolution structures, help would be amazing.
I've been stuck on this for quite some time now.


Cheers, Ben
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Re: [gmx-users] Lincs warnings

[Mark Abraham]

On 20/01/12, Ben Porebski  wrote:

> Hi all, 
> 
> 
> I've been working on some structures between 2.5A and 3.4A in resolution and 
> all of my structures suffer from lincs warnings.
> From reading the page about lincs warnings, I've performed a more lengthy 
> equilibration:
> 
> 
> I'm using gromacs 4.0.7 single precision and the G53a6 force field with spc 
> water model.
> 
> 
> - Genbox, add ions.
> - EM until converges
> - Positional restraints at 2,000 kJ/mol, 200, 20 and 2 for 100ps each at 100K
> - Followed by simulated annealing with the following parameters:
> 
> 
> 
> ; Simulated annealing @ positional restraint of 2 kJ/mol
> annealing = single  single
> annealing_npoints   = 3   3
> annealing_time = 0 50 2500 50 250
> annealing_temp = 100 100 300 100 100 300
> 
> 
> 
> - This then undergoes 750ps of md at 300K.
> 
> 
> Once done. I continue the run in my production MD.
> Sometimes my structures will crash within 5 ns, sometimes it will run out for 
> 60 ns before I start seeing any lincs warnings.
> 

 
An important trouble-shooting stage is to observe in a visualization program 
what happens in your simulation immediately before a crash, and look also at 
the variation in the energy terms. That might mean saving output more often. 
This could clue you in to a region of structure that is problematic, either 
atomic clashes that persist through EM+SA, or a malformed topology. See 
http://www.gromacs.org/Documentation/Terminology/Blowing_Up. Note also that 
restraining atoms to positions that are of low resolution can be problematic - 
you apparently don't want large rearrangements during equilibration, but it 
seems you need to permit more. Note what grompp -h has to say about position 
restraints.
 

> 
>  I've attempted to further refine the structures and they behave a little 
> better, but still crash, just less often.
> To continue the simulation, I will not use the .trr output from the previous 
> simulation. If this doesn't work, I'll run the simulation using shake for 2 
> ns, but this is significantly slower.
> 
> 
> I'm a little concerned that these crashes may be introducing some sort of 
> error into the simulation and I'm not sure of the right way to get around 
> this problem.
> I've played around with changing the lincs order and lincs iteration 
> parameters, which appear to reduce the number of lincs warnings and slows 
> down the simulation slightly.
> 

 
The constraint algorithms are normally not the problem, they're just the 
machinery most prone to breaking when something else goes wrong. As such, 
tweaking them is not productive.
 

> 
> Another thing I've played with was the constraints. Changing this from 
> all-bonds to hbonds.
> This stopped my crashes, but a co-worker thought that it may not be 
> accurately modelling the system, or would introduce anomalies into the 
> simulation.
> My impression was that changing from all-bonds to hbonds would improve the 
> accuracy of the system... But I could be wrong.
> 

 
The accuracy of the numerical integration is strongly tied to the size of the 
time step and the kinds of constraints you are using. See manual section 6.5. 
One strategy in your case is a lengthy equilibration period with a short time 
step (say 0.5fs) and no constraints or restraints at all. Monitor the trends in 
the energy terms over this period to see if changes are occurring.
 
Mark 
 

> 
> 
> If anyone has experience with dealing with lincs warnings or simulating low 
> resolution structures, help would be amazing.
> I've been stuck on this for quite some time now.
> 
> 
> 
> 
> Cheers, Ben
> 
> 

 
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Re: [gmx-users] mdrun-gpu error

[aiswarya pawar]

Justin,

Sorry for not giving the correct information.

Gromacs version 4.5.5
Tesla card- Nvidia Tesla S1070 (Tesla T10 Processor)
Cuda version 3.1
CMake 2.8

I installed the OpenMM from the source using commands=

ccmake -i .
make
make test
make install

everything went fine and set the paths

export OPENMM_ROOT_DIR=path_to_custom_openmm_installation
cmake -DGMX_OPENMM=ON

then
make
make install

The submission script used is=

#!/bin/csh
#PBS -l gpu=1
#PBS -l ncpus=1
#PBS -o /global/utemp/cuda-out2.out
#PBS -e /global/utemp/cuda-err2.out
/home/staff/software/gromacs_gpu_t/bin/mdrun-gpu -device
"OpenMM:platform=Cuda,DeviceID=0,Memtest=15,**,force-device=yes"  -v
-deffnm /global/utemp/md

for this i receive an error such as
Cuda error in file
'/home/staff/software/openmm_tesla/platforms/cuda/./src/kernels//bbsort.cu'
in line 176 : unspecified launch failure.
/bin/cat: file_loc: No such file or directory




On Thu, Jan 19, 2012 at 11:41 PM, Justin A. Lemkul  wrote:

>
>
> aiswarya pawar wrote:
>
>> Szilárd,
>>
>> I did a memory test run yesterday and it went fine but today received an
>> error. So you mean to say the tesla card version nothing to do with this
>> right.
>>
>>
> You're trying to solve multiple problems at once.  You told Mark that the
> normal mdrun executable (which works independently of any GPU components)
> also hangs, so either your filesystem is faulty or your installation
> procedure produced nonfunctional executables.
>
> You're posting bits and pieces of information, which makes it incredibly
> hard for anyone to help you.  Let's recap and try again.  Please provide:
>
> 1. The Gromacs version you're using
> 2. Description of the hardware (GPU and non-GPU components)
> 3. Installation procedure for Gromacs and any of the prerequisite software
> and libraries that were required, including versions
> 4. The exact command(s) you're issuing, including the full script that is
> causing a problem
>
> -Justin
>
>  Thanks
>>
>>
>> On Thu, Jan 19, 2012 at 11:09 PM, Szilárd Páll 
>> > szilard.p...@cbr.su.se**>> wrote:
>>
>>That's a generic GPU kernel launch failure which can mean anything,
>>from faulty hardware to bad driver to messed up installation.
>>
>>Does the memory test run? Try to compile/install again and see if it
>>works.
>>
>>--
>>Szilárd
>>
>>
>>
>>On Thu, Jan 19, 2012 at 4:18 PM, aiswarya pawar
>>> >
>> wrote:
>> > when i tired running it again, i got an error as
>> >
>> > Cuda error in file
>> >
>>'/home/staff/sec/secdpal/**software/openmm_tesla/**
>> platforms/cuda/./src/kernels//**bbsort.cu 
>>'
>>
>> > in line 176 : unspecified launch failure.
>> >
>> > /bin/cat: file_loc: No such file or directory
>> >
>> >
>> > On Thu, Jan 19, 2012 at 8:45 PM, aiswarya pawar
>>> > >>
>>
>> > wrote:
>> >>
>> >> Has the tesla card got to do anything with the error. Am
>>using Nvidia
>> >> Tesla S1070 1U server.
>> >>
>> >>
>> >> On Thu, Jan 19, 2012 at 8:37 PM, Szilárd Páll
>>mailto:szilard.p...@cbr.su.se**>>
>>
>> >> wrote:
>> >>>
>> >>> And sorting out where the /bin/cat error comes from because that
>> is
>> >>> surely not a Gromacs message!
>> >>>
>> >>> Cheers,
>> >>> --
>> >>> Szilárd
>> >>>
>> >>>
>> >>>
>> >>> On Thu, Jan 19, 2012 at 1:12 PM, Mark Abraham
>>> > >>
>>
>> >>> wrote:
>> >>> > On 19/01/2012 8:45 PM, aiswarya pawar wrote:
>> >>> >
>> >>> > Mark,
>> >>> >
>> >>> > THe normal mdrun also hangs thus not generating any output.
>> >>> >
>> >>> >
>> >>> > OK. It's your problem to solve... keep simplifying stuff
>>until you can
>> >>> > isolate a small number of possible causes. Top of the list is
>>file
>> >>> > system
>> >>> > availability.
>> >>> >
>> >>> > Mark
>> >>> >
>> >>> >
>> >>> >
>> >>> > On Thu, Jan 19, 2012 at 3:09 AM, Mark Abraham
>>> > >>
>>
>> >>> > wrote:
>> >>> >>
>> >>> >> On 19/01/2012 2:59 AM, aiswarya.pa...@gmail.com
>> wrote:
>> >>> >>
>> >>> >> Hi,
>> >>> >>
>> >>> >> Its going into the running mode but gets hang there for long
>>hours
>> >>> >> which
>> >>> >> generating any data in the output file. And am not able to
>>figure out
>> >>> >> the
>> >>> >> error file_doc. Please anyone knows what's going wrong.
>> >>> >>
>> >>> >>
>> >>> >> No, but you should start trying to simplify what you're
>>doing to see
>> >>> >> where
>> >>> >> the problem lies. Does normal mdrun work?
>> >>> >>
>> >>> >> Mark
>> >>> >>
>> >>> >>
>> >>> >> Thanks
>> >>> >> Sent from my BlackBerryŽ on Reliance Mobile, I

[gmx-users] Regarding ngmx with double precision

[Ravi Kumar Venkatraman]

Dear All,
  While installing Gromacs in double precision, I am not able
to make ngmx run. Is it because of lack of X libraries. I want to run ngmx
trajectory viewer. So I kindly request you to suggest me to make ngmx run.

Thank you in Advance

*With Regards,
Ravi Kumar Venkatraman,
IPC Dept., IISc,
Bangalore, INDIA.

+91-9686933963.*
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[gmx-users] How to balance charge for modeling N2 molecules

[Kiwoong Kim]

Hi,

I asked this question before.
Thanks to Justin, he did reply as follows.

Kiwoong Kim wrote:

Hi,

I'm getting better to use Gromacs owing to many posts on this sites :) .

I have several questions about adding the counter-ions.


My system has a number of N2 molecules which has charge, -0.40484(for single
N) X 2.

Thus, I have to add some counter-ions to make the system neutral.


However, because I'm newbie on Gromacs, I thought of several clumsy ways
myself.

#1. Add virtual sites (virtual atoms) which has counter-ions like below.

[ atomtypes ]
; name  mass   charge  ptype  sigma  epsilon
DUM 00.80968 V0.00.0


I set the coordinates of each virtual DUM atoms to the center of N2
molecules.

#2. using genion in Gromacs.


But, I have no idea on this. What molecules do I have to designate to charge
plus ion using genion ??

I typed below line.

genion -s md_0_1.tpr -n index.ndx -o ton_genion.pdb -g md_0_1_genion.log -p
topol_genion.top -np 322 -pname dum -pq 0.80968

and selected N2 molecules which is diffusing particle.


It results that the name of half of N2 molecules is changed as DUM. (maybe
the system become neutral)

The number of N2 molecules should be fixed.

Do I have additional N2 molecule for charging using genion?? Then, what are
the initial coordinates???

please help me

any advises would be helpful.

How can I do that???

I see no reason why you should do either. For dinitrogen, which has no
net dipole,
it seems intuitive to me that both N atoms should have zero charge.

-Justin


I made linear rigid model (CO2) by introducing virtual interaction.
However, I have troubles in modelling N2 molecules.

I want to model N2 with quadrupole moment according to the paper
(Adsorption (2007) 13: 469-476).

In the paper, the charge N2 model (originally developed by Murthy et
al. (1980) can be described as follows.

N (-0.40484), Dummy (N2, +0.80968).


Actually, I don't know how to model N2 molecules with dummy. Please
let me know any advises.


Thx. Have a great day. :)
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Re: [gmx-users] Regarding ngmx with double precision

[Mark Abraham]

On 20/01/2012 5:05 PM, Ravi Kumar Venkatraman wrote:

Dear All,
  While installing Gromacs in double precision, I am not 
able to make ngmx run. Is it because of lack of X libraries. I want to 
run ngmx trajectory viewer. So I kindly request you to suggest me to 
make ngmx run.


You need X libraries and headers, and maybe Motif/Lesstif also. I forget 
the details. Do search the archives.


Mark
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Re: [gmx-users] How to balance charge for modeling N2 molecules

[Mark Abraham]

On 20/01/2012 5:51 PM, Kiwoong Kim wrote:

Hi,

I asked this question before.
Thanks to Justin, he did reply as follows.

Kiwoong Kim wrote:

Hi,

I'm getting better to use Gromacs owing to many posts on this sites :) .

I have several questions about adding the counter-ions.


My system has a number of N2 molecules which has charge,
-0.40484(for single N) X 2.

Thus, I have to add some counter-ions to make the system neutral.


However, because I'm newbie on Gromacs, I thought of several
clumsy ways myself.

#1. Add virtual sites (virtual atoms) which has counter-ions like below.

[ atomtypes ]
; name  mass   charge  ptype  sigma  epsilon
DUM 00.80968 V0.00.0


I set the coordinates of each virtual DUM atoms to the center of
N2 molecules.

#2. using genion in Gromacs.


But, I have no idea on this. What molecules do I have to designate
to charge plus ion using genion ??

I typed below line.

genion -s md_0_1.tpr -n index.ndx -o ton_genion.pdb -g
md_0_1_genion.log -p topol_genion.top -np 322 -pname dum -pq 0.80968

and selected N2 molecules which is diffusing particle.


It results that the name of half of N2 molecules is changed as
DUM. (maybe the system become neutral)

The number of N2 molecules should be fixed.

Do I have additional N2 molecule for charging using genion?? Then,
what are the initial coordinates???

please help me

any advises would be helpful.

How can I do that??? 

I see no reason why you should do either. For dinitrogen, which has no 
net dipole, it seems intuitive to me that both N atoms should have 
zero charge.

-Justin

I made linear rigid model (CO2) by introducing virtual interaction. However, I 
have troubles in modelling N2 molecules.
I want to model N2 with quadrupole moment according to the paper (Adsorption 
(2007) 13: 469-476).
In the paper, the charge N2 model (originally developed by Murthy et al. (1980) 
can be described as follows.
N (-0.40484), Dummy (N2, +0.80968).


Right... that's totally different from N2 with charged N atoms :)



Actually, I don't know how to model N2 molecules with dummy. Please let me know 
any advises.


Sounds like virtual site type 2 is perfect - and didn't you already use 
that for CO2? See section 4.7 and somewhere in chapter 5.


Mark

  



Thx. Have a great day. :)




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