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

2012-01-19 Thread 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

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

2012-01-19 Thread 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
--
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

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

2012-01-19 Thread 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
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)sub

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

2012-01-19 Thread 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
> 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 
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

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

2012-01-19 Thread 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
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-requ...@gromacs.org.
> 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

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

2012-01-18 Thread Mark Abraham 

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?


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

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

2012-01-18 Thread Tsjerk Wassenaar 
Hi Chadan,

You should stop after your second step, removing jumps. Don't center.
And definitely don't put the system in the box, as that exactly undoes
removal of jumps.

Cheers,

Tsjerk

On Thu, Jan 19, 2012 at 7:39 AM, 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. 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
>
> #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
>
> 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.
>
> Chadan
>
> --
> Chandan kumar Choudhury
> NCL, Pune
> INDIA
>
> --
> 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



-- 
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 
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] getting rid of PBC, completely

2012-01-18 Thread Chandan Choudhury 
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. 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

#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

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.

Chadan

--
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