Re: [gmx-users] last line in .gro file

2010-02-02 Thread Vishal Agarwal 
Hi Tsjerk,

Thanks for replying. I was going through the pdb format dcoument on the PDB
webpage. I found that the box corresponds to the following:

 a   b(cos(gama))  c(cos(beta))
 0   b(sin(gama))   c(cos(alpha) - cos(beta) cos(gama) / sin(gama)
 00  V/(ab sin(gama))
where V = abc(1 - (cos(alpha))^2 - (cos(beta))^2 - (cos(gama))^2+
2cos(alpha) cos(beta) cos(gama))^1/2

This corresponds to general form in representing these vectors.  The
following code also desolves to this form.

Thank you again.

Best,
Vishal

P.S. I thank all who have replied to this mail.

On Tue, Feb 2, 2010 at 3:44 PM, Tsjerk Wassenaar  wrote:

> Hi Vishal,
>
> Here is  a python function that generates a triclinic representation
> given a definition with lengths and angles. The argument L is a tuple
> or list containing the lengths and angles.
>
> def triclinic(L):
>B = [[0,0,0],[0,0,0],[0,0,0]]
>
>x, y, z, a, b, c = L[:6]
>
>B[0][0] = x
>if a == 90 and b == 90 and c == 90:
>B[1][1] = y
>B[2][2] = z
>else:
>a = a*pi/180
>b = b*pi/180
>c = c*pi/180
>B[1][0] = y*cos(c)
>B[1][1] = y*sin(c)
>B[2][0] = z*cos(b)
>B[2][1] = z*(cos(a)-cos(b)*cos(c))/sin(c)
>B[2][2] = sqrt(z*z-B[2][0]**2-B[2][1]**2)
>
>return B
>
> Hope it helps,
>
> Tsjerk
>
> On Tue, Feb 2, 2010 at 9:23 PM, Erik Marklund 
> wrote:
> > Hi,
> >
> > Since any unit cell can be formulated as a triclinic cell, the monoclinic
> > cell is indeed supported. By definition it has two 90 degree angles and
> one
> > that is not 90 degrees.  The box vectors can be of different lengths.
> You'll
> > have to do the math and reading yourself to find out how this translates
> to
> > a .gro box. The manual is your friend here.
> >
> > Good luck,
> >
> > Erik
> >
> > Vishal Agarwal skrev:
> >>
> >> Dear Justin,
> >>
> >> Thanks for replying. The table mentions only a few unit cell type. I am
> >> using a monclinic unit cell. Do you know how these box vectors have been
> >> derived.
> >>
> >> thanks
> >> vishal
> >>
> >> On Tue, Feb 2, 2010 at 11:26 AM, Justin A. Lemkul  >> > wrote:
> >>
> >>
> >>
> >>Vishal Agarwal wrote:
> >>
> >>Dear gmx-users,
> >>
> >>I am new to GROMACS. Can anyone tell me what does the last
> >>line in .gro file stands for ?
> >>
> >>The manual mentions
> >>"box[X][X],box[Y][Y],box[Z][Z],
> >>box[X][Y],box[X][Z],box[Y][X],box[Y][Z],box[Z][X],box[Z][Y]"
> >>
> >>Can anyone explain what each of these mean in terms of cell
> >>parameters ?
> >>
> >>
> >>The last line contains the box vectors.  Specifics in terms of
> >>unit cell geometry are given in the manual, Table 3.1 and section
> >>3.2.1.
> >>
> >>-Justin
> >>
> >>Thanks,
> >>vishal
> >>
> >>
> >>--
> >>
> >>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 [email protected]
> >>
> >>http://lists.gromacs.org/mailman/listinfo/gmx-users
> >>Please search the archive at http://www.gromacs.org/search before
> >>posting!
> >>Please don't post (un)subscribe requests to the list. Use the www
> >>interface or send it to [email protected]
> >>.
> >>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >>
> >>
> >>
> >>
> >> --
> >> Regards
> >>
> >> ***
> >> Vishal Agarwal
> >> Research Scholar
> >> University of Massachusetts, Amherst
> >> ***
> >> 'Your only obligation in any lifetime is to be true to yourself."
> >>---Richard Bach
> >
> >
> > --
> > ---
> > Erik Marklund, PhD student
> > Laboratory of Molecular Biophysics,
> > Dept. of Cell and Molecular Biology, Uppsala University.
> > Husargatan 3, Box 596,75124 Uppsala, Sweden
> > phone:+46 18 471 4537fax: +46 18 511 755
> > [email protected]://xray.bmc.uu.se/molbiophys
> >
> > --
> > gmx-users mailing [email protected]
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before
> posting!
> > Please don't post (un)subscribe requests to the list. Use the www
> interface
> > or send it to [email protected].
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> Computational Chemist
> Medicina

Re: [gmx-users] last line in .gro file

2010-02-02 Thread Tsjerk Wassenaar 
Hi Vishal,

Here is  a python function that generates a triclinic representation
given a definition with lengths and angles. The argument L is a tuple
or list containing the lengths and angles.

def triclinic(L):
B = [[0,0,0],[0,0,0],[0,0,0]]

x, y, z, a, b, c = L[:6]

B[0][0] = x
if a == 90 and b == 90 and c == 90:
B[1][1] = y
B[2][2] = z
else:
a = a*pi/180
b = b*pi/180
c = c*pi/180
B[1][0] = y*cos(c)
B[1][1] = y*sin(c)
B[2][0] = z*cos(b)
B[2][1] = z*(cos(a)-cos(b)*cos(c))/sin(c)
B[2][2] = sqrt(z*z-B[2][0]**2-B[2][1]**2)

return B

Hope it helps,

Tsjerk

On Tue, Feb 2, 2010 at 9:23 PM, Erik Marklund  wrote:
> Hi,
>
> Since any unit cell can be formulated as a triclinic cell, the monoclinic
> cell is indeed supported. By definition it has two 90 degree angles and one
> that is not 90 degrees.  The box vectors can be of different lengths. You'll
> have to do the math and reading yourself to find out how this translates to
> a .gro box. The manual is your friend here.
>
> Good luck,
>
> Erik
>
> Vishal Agarwal skrev:
>>
>> Dear Justin,
>>
>> Thanks for replying. The table mentions only a few unit cell type. I am
>> using a monclinic unit cell. Do you know how these box vectors have been
>> derived.
>>
>> thanks
>> vishal
>>
>> On Tue, Feb 2, 2010 at 11:26 AM, Justin A. Lemkul > > wrote:
>>
>>
>>
>>    Vishal Agarwal wrote:
>>
>>        Dear gmx-users,
>>
>>        I am new to GROMACS. Can anyone tell me what does the last
>>        line in .gro file stands for ?
>>
>>        The manual mentions
>>        "box[X][X],box[Y][Y],box[Z][Z],
>>        box[X][Y],box[X][Z],box[Y][X],box[Y][Z],box[Z][X],box[Z][Y]"
>>
>>        Can anyone explain what each of these mean in terms of cell
>>        parameters ?
>>
>>
>>    The last line contains the box vectors.  Specifics in terms of
>>    unit cell geometry are given in the manual, Table 3.1 and section
>>    3.2.1.
>>
>>    -Justin
>>
>>        Thanks,
>>        vishal
>>
>>
>>    --    
>>
>>    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 list    [email protected]
>>    
>>    http://lists.gromacs.org/mailman/listinfo/gmx-users
>>    Please search the archive at http://www.gromacs.org/search before
>>    posting!
>>    Please don't post (un)subscribe requests to the list. Use the www
>>    interface or send it to [email protected]
>>    .
>>    Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
>>
>>
>> --
>> Regards
>>
>> ***
>> Vishal Agarwal
>> Research Scholar
>> University of Massachusetts, Amherst
>> ***
>> 'Your only obligation in any lifetime is to be true to yourself."
>>            ---Richard Bach
>
>
> --
> ---
> Erik Marklund, PhD student
> Laboratory of Molecular Biophysics,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,    75124 Uppsala, Sweden
> phone:    +46 18 471 4537        fax: +46 18 511 755
> [email protected]    http://xray.bmc.uu.se/molbiophys
>
> --
> gmx-users mailing list    [email protected]
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to [email protected].
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>



-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist
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Re: [gmx-users] last line in .gro file

2010-02-02 Thread Erik Marklund 

Hi,

Since any unit cell can be formulated as a triclinic cell, the 
monoclinic cell is indeed supported. By definition it has two 90 degree 
angles and one that is not 90 degrees.  The box vectors can be of 
different lengths. You'll have to do the math and reading yourself to 
find out how this translates to a .gro box. The manual is your friend here.


Good luck,

Erik

Vishal Agarwal skrev:

Dear Justin,

Thanks for replying. The table mentions only a few unit cell type. I 
am using a monclinic unit cell. Do you know how these box vectors have 
been derived.


thanks
vishal

On Tue, Feb 2, 2010 at 11:26 AM, Justin A. Lemkul > wrote:




Vishal Agarwal wrote:

Dear gmx-users,

I am new to GROMACS. Can anyone tell me what does the last
line in .gro file stands for ?

The manual mentions
"box[X][X],box[Y][Y],box[Z][Z],
box[X][Y],box[X][Z],box[Y][X],box[Y][Z],box[Z][X],box[Z][Y]"

Can anyone explain what each of these mean in terms of cell
parameters ?


The last line contains the box vectors.  Specifics in terms of
unit cell geometry are given in the manual, Table 3.1 and section
3.2.1.

-Justin

Thanks,
vishal


-- 



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 [email protected]


http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before
posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to [email protected]
.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php




--
Regards

***
Vishal Agarwal
Research Scholar
University of Massachusetts, Amherst
***
'Your only obligation in any lifetime is to be true to yourself."
---Richard Bach



--
---
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
[email protected]://xray.bmc.uu.se/molbiophys

--
gmx-users mailing [email protected]
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Please search the archive at http://www.gromacs.org/search before posting!
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Re: [gmx-users] last line in .gro file

2010-02-02 Thread Vishal Agarwal 
Dear Justin,

Thanks for replying. You mentioned that gromacs supports triclinic
structure. Can you tell me what will be the box parameters for triclinic
structure of cell parameters a, b, c and angles alpha, beta and gama.

Thanks in advance
Vishal

On Tue, Feb 2, 2010 at 12:30 PM, Justin A. Lemkul  wrote:

>
>
> Vishal Agarwal wrote:
>
>> Dear Justin,
>>
>> I am trying to set up calculations for a cellulose structure. The
>> allomorph of cellulose which I want to study has a monoclinic structure. I
>> have a .cif file of the XRD structure. I think the better question to ask is
>> how can I make input files using that.
>>
>>
> That is a far more complex question.  There are numerous posts in the list
> archive regarding preparing input for polymeric systems, so please do search
> the list archive.  I helped one user set up a polyethylene system some time
> ago, so that may help out.  You'll have to familiarize yourself with .rtp
> entry construction, specbond.dat (maybe), and the ins and outs of pdb2gmx to
> get it to work though.  There are lots of resources in the manual and on the
> Gromacs wiki pages to get you started.
>
> -Justin
>
>  thanks
>> vishal
>>
>>
>> On Tue, Feb 2, 2010 at 11:52 AM, Justin A. Lemkul > [email protected]>> wrote:
>>
>>
>>
>>Vishal Agarwal wrote:
>>
>>Dear Justin,
>>
>>Thanks for replying. The table mentions only a few unit cell
>>type. I am using a monclinic unit cell. Do you know how these
>>box vectors have been derived.
>>
>>
>>Are you talking about your unit cell type, or the structure of the
>>species you wish to simulate?  I see no mention of monoclinic box
>>support in Gromacs, nor is it listed as a type of box that can be
>>defined with editconf, so you need to clarify what it is you're
>>trying to do.  In any case, the last line of the .gro file
>>corresponds to the box vectors of the unit cell you specify with
>>editconf.  If you don't specify anything explicitly, the default is
>>to build a triclinic unit cell.
>>
>>-Justin
>>
>>thanks
>>vishal
>>
>>
>>On Tue, Feb 2, 2010 at 11:26 AM, Justin A. Lemkul
>>mailto:[email protected]>
>>>> wrote:
>>
>>
>>
>>   Vishal Agarwal wrote:
>>
>>   Dear gmx-users,
>>
>>   I am new to GROMACS. Can anyone tell me what does the
>>last line
>>   in .gro file stands for ?
>>
>>   The manual mentions
>>   "box[X][X],box[Y][Y],box[Z][Z],
>>   box[X][Y],box[X][Z],box[Y][X],box[Y][Z],box[Z][X],box[Z][Y]"
>>
>>   Can anyone explain what each of these mean in terms of cell
>>   parameters ?
>>
>>
>>   The last line contains the box vectors.  Specifics in terms
>>of unit
>>   cell geometry are given in the manual, Table 3.1 and section
>>3.2.1.
>>
>>   -Justin
>>
>>   Thanks,
>>   vishal
>>
>>
>>   --
>>
>>   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 [email protected]
>>
>>   >
>>
>>
>>   http://lists.gromacs.org/mailman/listinfo/gmx-users
>>   Please search the archive at http://www.gromacs.org/searchbefore
>>   posting!
>>   Please don't post (un)subscribe requests to the list. Use the
>> www
>>   interface or send it to [email protected]
>>
>>   >>.
>>
>>   Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
>>
>>
>>--Regards
>>
>>***
>>Vishal Agarwal
>>Research Scholar
>>University of Massachusetts, Amherst
>>***
>>'Your only obligation in any lifetime is to be true to yourself."
>>   ---Richard Bach
>>
>>
>>--
>>
>>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/Per

Re: [gmx-users] last line in .gro file

2010-02-02 Thread Justin A. Lemkul 



Vishal Agarwal wrote:

Dear Justin,

I am trying to set up calculations for a cellulose structure. The 
allomorph of cellulose which I want to study has a monoclinic structure. 
I have a .cif file of the XRD structure. I think the better question to 
ask is how can I make input files using that.




That is a far more complex question.  There are numerous posts in the list 
archive regarding preparing input for polymeric systems, so please do search the 
list archive.  I helped one user set up a polyethylene system some time ago, so 
that may help out.  You'll have to familiarize yourself with .rtp entry 
construction, specbond.dat (maybe), and the ins and outs of pdb2gmx to get it to 
work though.  There are lots of resources in the manual and on the Gromacs wiki 
pages to get you started.


-Justin


thanks
vishal

On Tue, Feb 2, 2010 at 11:52 AM, Justin A. Lemkul > wrote:




Vishal Agarwal wrote:

Dear Justin,

Thanks for replying. The table mentions only a few unit cell
type. I am using a monclinic unit cell. Do you know how these
box vectors have been derived.


Are you talking about your unit cell type, or the structure of the
species you wish to simulate?  I see no mention of monoclinic box
support in Gromacs, nor is it listed as a type of box that can be
defined with editconf, so you need to clarify what it is you're
trying to do.  In any case, the last line of the .gro file
corresponds to the box vectors of the unit cell you specify with
editconf.  If you don't specify anything explicitly, the default is
to build a triclinic unit cell.

-Justin

thanks
vishal


On Tue, Feb 2, 2010 at 11:26 AM, Justin A. Lemkul
mailto:[email protected]>
>> wrote:



   Vishal Agarwal wrote:

   Dear gmx-users,

   I am new to GROMACS. Can anyone tell me what does the
last line
   in .gro file stands for ?

   The manual mentions
   "box[X][X],box[Y][Y],box[Z][Z],
   box[X][Y],box[X][Z],box[Y][X],box[Y][Z],box[Z][X],box[Z][Y]"

   Can anyone explain what each of these mean in terms of cell
   parameters ?


   The last line contains the box vectors.  Specifics in terms
of unit
   cell geometry are given in the manual, Table 3.1 and section
3.2.1.

   -Justin

   Thanks,
   vishal


   --

   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 [email protected]

   >

   http://lists.gromacs.org/mailman/listinfo/gmx-users
   Please search the archive at http://www.gromacs.org/search before
   posting!
   Please don't post (un)subscribe requests to the list. Use the www
   interface or send it to [email protected]

   >.

   Can't post? Read http://www.gromacs.org/mailing_lists/users.php




-- 
Regards


***
Vishal Agarwal
Research Scholar
University of Massachusetts, Amherst
***
'Your only obligation in any lifetime is to be true to yourself."
   ---Richard Bach


-- 



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 [email protected]


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Please search the archive at http://www.gromacs.org/search before
posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to [email protected]
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Can't post? Read http://www.gromacs.org/mailing_lists/users.php




--
Regards

*

Re: [gmx-users] last line in .gro file

2010-02-02 Thread Vishal Agarwal 
Dear Justin,

I am trying to set up calculations for a cellulose structure. The allomorph
of cellulose which I want to study has a monoclinic structure. I have a .cif
file of the XRD structure. I think the better question to ask is how can I
make input files using that.

thanks
vishal

On Tue, Feb 2, 2010 at 11:52 AM, Justin A. Lemkul  wrote:

>
>
> Vishal Agarwal wrote:
>
>> Dear Justin,
>>
>> Thanks for replying. The table mentions only a few unit cell type. I am
>> using a monclinic unit cell. Do you know how these box vectors have been
>> derived.
>>
>>
> Are you talking about your unit cell type, or the structure of the species
> you wish to simulate?  I see no mention of monoclinic box support in
> Gromacs, nor is it listed as a type of box that can be defined with
> editconf, so you need to clarify what it is you're trying to do.  In any
> case, the last line of the .gro file corresponds to the box vectors of the
> unit cell you specify with editconf.  If you don't specify anything
> explicitly, the default is to build a triclinic unit cell.
>
> -Justin
>
>  thanks
>> vishal
>>
>>
>> On Tue, Feb 2, 2010 at 11:26 AM, Justin A. Lemkul > [email protected]>> wrote:
>>
>>
>>
>>Vishal Agarwal wrote:
>>
>>Dear gmx-users,
>>
>>I am new to GROMACS. Can anyone tell me what does the last line
>>in .gro file stands for ?
>>
>>The manual mentions
>>"box[X][X],box[Y][Y],box[Z][Z],
>>box[X][Y],box[X][Z],box[Y][X],box[Y][Z],box[Z][X],box[Z][Y]"
>>
>>Can anyone explain what each of these mean in terms of cell
>>parameters ?
>>
>>
>>The last line contains the box vectors.  Specifics in terms of unit
>>cell geometry are given in the manual, Table 3.1 and section 3.2.1.
>>
>>-Justin
>>
>>Thanks,
>>vishal
>>
>>
>>--
>>
>>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 [email protected]
>>
>>
>>http://lists.gromacs.org/mailman/listinfo/gmx-users
>>Please search the archive at http://www.gromacs.org/search before
>>posting!
>>Please don't post (un)subscribe requests to the list. Use the www
>>interface or send it to [email protected]
>>.
>>
>>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
>>
>>
>> --
>> Regards
>>
>> ***
>> Vishal Agarwal
>> Research Scholar
>> University of Massachusetts, Amherst
>> ***
>> 'Your only obligation in any lifetime is to be true to yourself."
>>---Richard Bach
>>
>
> --
> 
>
> 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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-- 
Regards

***
Vishal Agarwal
Research Scholar
University of Massachusetts, Amherst
***
'Your only obligation in any lifetime is to be true to yourself."
---Richard Bach
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Re: [gmx-users] last line in .gro file

2010-02-02 Thread Justin A. Lemkul 



Vishal Agarwal wrote:

Dear Justin,

Thanks for replying. The table mentions only a few unit cell type. I am 
using a monclinic unit cell. Do you know how these box vectors have been 
derived.




Are you talking about your unit cell type, or the structure of the species you 
wish to simulate?  I see no mention of monoclinic box support in Gromacs, nor is 
it listed as a type of box that can be defined with editconf, so you need to 
clarify what it is you're trying to do.  In any case, the last line of the .gro 
file corresponds to the box vectors of the unit cell you specify with editconf. 
 If you don't specify anything explicitly, the default is to build a triclinic 
unit cell.


-Justin


thanks
vishal

On Tue, Feb 2, 2010 at 11:26 AM, Justin A. Lemkul > wrote:




Vishal Agarwal wrote:

Dear gmx-users,

I am new to GROMACS. Can anyone tell me what does the last line
in .gro file stands for ?

The manual mentions
"box[X][X],box[Y][Y],box[Z][Z],
box[X][Y],box[X][Z],box[Y][X],box[Y][Z],box[Z][X],box[Z][Y]"

Can anyone explain what each of these mean in terms of cell
parameters ?


The last line contains the box vectors.  Specifics in terms of unit
cell geometry are given in the manual, Table 3.1 and section 3.2.1.

-Justin

Thanks,
vishal


-- 



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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posting!
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--
Regards

***
Vishal Agarwal
Research Scholar
University of Massachusetts, Amherst
***
'Your only obligation in any lifetime is to be true to yourself."
---Richard Bach


--


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] last line in .gro file

2010-02-02 Thread Vishal Agarwal 
Dear Justin,

Thanks for replying. The table mentions only a few unit cell type. I am
using a monclinic unit cell. Do you know how these box vectors have been
derived.

thanks
vishal

On Tue, Feb 2, 2010 at 11:26 AM, Justin A. Lemkul  wrote:

>
>
> Vishal Agarwal wrote:
>
>> Dear gmx-users,
>>
>> I am new to GROMACS. Can anyone tell me what does the last line in .gro
>> file stands for ?
>>
>> The manual mentions
>> "box[X][X],box[Y][Y],box[Z][Z],
>> box[X][Y],box[X][Z],box[Y][X],box[Y][Z],box[Z][X],box[Z][Y]"
>>
>> Can anyone explain what each of these mean in terms of cell parameters ?
>>
>>
> The last line contains the box vectors.  Specifics in terms of unit cell
> geometry are given in the manual, Table 3.1 and section 3.2.1.
>
> -Justin
>
>  Thanks,
>> vishal
>>
>>
> --
> 
>
> 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 [email protected]
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to [email protected].
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>



-- 
Regards

***
Vishal Agarwal
Research Scholar
University of Massachusetts, Amherst
***
'Your only obligation in any lifetime is to be true to yourself."
---Richard Bach
-- 
gmx-users mailing [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
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Re: [gmx-users] last line in .gro file

2010-02-02 Thread Justin A. Lemkul 



Vishal Agarwal wrote:

Dear gmx-users,

I am new to GROMACS. Can anyone tell me what does the last line in .gro 
file stands for ?


The manual mentions
"box[X][X],box[Y][Y],box[Z][Z],
box[X][Y],box[X][Z],box[Y][X],box[Y][Z],box[Z][X],box[Z][Y]"

Can anyone explain what each of these mean in terms of cell parameters ?



The last line contains the box vectors.  Specifics in terms of unit cell 
geometry are given in the manual, Table 3.1 and section 3.2.1.


-Justin


Thanks,
vishal



--


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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