Re: [gmx-users] I can't figure out what is wrong with my .gro

[Justin Lemkul]

On 1/9/13 8:06 PM, Xu Dong Huang wrote:

Dear Justin Lemkul,

I had a correspondence with you several times in January about .gro file
formatting and I remember you suggested to me that there is a code you can use
in C to automate the spacing format in .gro file generation. I can no longer
locate that specific email and I was wondering if you could be kind and
enlighten me again on this format automation procedure in C environment.



http://manual.gromacs.org/online/gro.html

-Justin


Thanks,


Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering
xudo...@eden.rutgers.edu 

On Jan 9, 2013, at 8:04 PM, Justin Lemkul mailto:jalem...@vt.edu>> wrote:




On 1/9/13 8:02 PM, Xu Dong Huang wrote:

Oh, you have an Additional line after vector size box…. I thought you said to
remove that blank line



There is no additional line.  The last line in the file must be the box vectors.

-Justin


Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering
xudo...@eden.rutgers.edu 

On Jan 9, 2013, at 7:58 PM, Xu Dong Huang mailto:xudo...@eden.rutgers.edu>> wrote:


@Justin,

I did that, and it still says I have 103.

Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering
xudo...@eden.rutgers.edu 

On Jan 9, 2013, at 7:49 PM, Xu Dong Huang  wrote:


@Justin,

I did what you suggested, and I still can't load my molecule in VMD. Maybe
I am still doing something wrong with the new line character thing.


Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering
xudo...@eden.rutgers.edu

On Jan 9, 2013, at 7:22 PM, Xu Dong Huang  wrote:


@ Justin,

I laughed. :) Thank you. I can't believe I miss the smallest and most
rudimentary things.
Thanks again,
Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering
xudo...@eden.rutgers.edu

On Jan 9, 2013, at 7:20 PM, Justin Lemkul  wrote:




On 1/9/13 7:16 PM, Xu Dong Huang wrote:

@ Justin,

Thanks for always saving me from my mistakes. But I don't quite
understand what is a new line character?



The thing you get when you press enter.

http://en.wikipedia.org/wiki/Newline#In_programming_languages

Note that Google has plenty more to say ;)

There should not be a blank line at the end of the .gro file, though, but
to be correctly parsed by VMD, the line must terminate with a '\n'
character.  So at the end of your box vector line, hit return then backspace.

-Justin

--


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


--
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


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


--
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

Re: [gmx-users] I can't figure out what is wrong with my .gro

[Xu Dong Huang]

Must be something wrong with my editor program (BBEdit), because when I open 
the file you sent me, it shows me there an additional blank line. Ok, time to 
switch to regular text editor… 


Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering 
xudo...@eden.rutgers.edu 

On Jan 9, 2013, at 8:04 PM, Justin Lemkul  wrote:

> 
> 
> On 1/9/13 8:02 PM, Xu Dong Huang wrote:
>> Oh, you have an Additional line after vector size box…. I thought you said 
>> to remove that blank line
>> 
> 
> There is no additional line.  The last line in the file must be the box 
> vectors.
> 
> -Justin
> 
>> Xu Dong Huang
>> Chemical & Biochemical Engineering
>> Rutgers School of Engineering
>> xudo...@eden.rutgers.edu
>> 
>> On Jan 9, 2013, at 7:58 PM, Xu Dong Huang  wrote:
>> 
>>> @Justin,
>>> 
>>> I did that, and it still says I have 103.
>>> 
>>> Xu Dong Huang
>>> Chemical & Biochemical Engineering
>>> Rutgers School of Engineering
>>> xudo...@eden.rutgers.edu
>>> 
>>> On Jan 9, 2013, at 7:49 PM, Xu Dong Huang  wrote:
>>> 
 @Justin,
 
 I did what you suggested, and I still can't load my molecule in VMD. Maybe 
 I am still doing something wrong with the new line character thing.
 
 
 Xu Dong Huang
 Chemical & Biochemical Engineering
 Rutgers School of Engineering
 xudo...@eden.rutgers.edu
 
 On Jan 9, 2013, at 7:22 PM, Xu Dong Huang  wrote:
 
> @ Justin,
> 
> I laughed. :) Thank you. I can't believe I miss the smallest and most 
> rudimentary things.
> Thanks again,
> Xu Dong Huang
> Chemical & Biochemical Engineering
> Rutgers School of Engineering
> xudo...@eden.rutgers.edu
> 
> On Jan 9, 2013, at 7:20 PM, Justin Lemkul  wrote:
> 
>> 
>> 
>> On 1/9/13 7:16 PM, Xu Dong Huang wrote:
>>> @ Justin,
>>> 
>>> Thanks for always saving me from my mistakes. But I don't quite 
>>> understand what is a new line character?
>>> 
>> 
>> The thing you get when you press enter.
>> 
>> http://en.wikipedia.org/wiki/Newline#In_programming_languages
>> 
>> Note that Google has plenty more to say ;)
>> 
>> There should not be a blank line at the end of the .gro file, though, 
>> but to be correctly parsed by VMD, the line must terminate with a '\n' 
>> character.  So at the end of your box vector line, hit return then 
>> backspace.
>> 
>> -Justin
>> 
>> --
>> 
>> 
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>> 
>> 
>> --
>> 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
>>> 
>>> --
>>> 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.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> 
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-u

Re: [gmx-users] I can't figure out what is wrong with my .gro

[Justin Lemkul]

On 1/9/13 8:02 PM, Xu Dong Huang wrote:

Oh, you have an Additional line after vector size box…. I thought you said to 
remove that blank line



There is no additional line.  The last line in the file must be the box vectors.

-Justin


Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering
xudo...@eden.rutgers.edu

On Jan 9, 2013, at 7:58 PM, Xu Dong Huang  wrote:


@Justin,

I did that, and it still says I have 103.

Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering
xudo...@eden.rutgers.edu

On Jan 9, 2013, at 7:49 PM, Xu Dong Huang  wrote:


@Justin,

I did what you suggested, and I still can't load my molecule in VMD. Maybe I am 
still doing something wrong with the new line character thing.


Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering
xudo...@eden.rutgers.edu

On Jan 9, 2013, at 7:22 PM, Xu Dong Huang  wrote:


@ Justin,

I laughed. :) Thank you. I can't believe I miss the smallest and most 
rudimentary things.
Thanks again,
Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering
xudo...@eden.rutgers.edu

On Jan 9, 2013, at 7:20 PM, Justin Lemkul  wrote:




On 1/9/13 7:16 PM, Xu Dong Huang wrote:

@ Justin,

Thanks for always saving me from my mistakes. But I don't quite understand what 
is a new line character?



The thing you get when you press enter.

http://en.wikipedia.org/wiki/Newline#In_programming_languages

Note that Google has plenty more to say ;)

There should not be a blank line at the end of the .gro file, though, but to be 
correctly parsed by VMD, the line must terminate with a '\n' character.  So at 
the end of your box vector line, hit return then backspace.

-Justin

--


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


--
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


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


--
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] I can't figure out what is wrong with my .gro

[Xu Dong Huang]

Oh, you have an Additional line after vector size box…. I thought you said to 
remove that blank line

Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering 
xudo...@eden.rutgers.edu 

On Jan 9, 2013, at 7:58 PM, Xu Dong Huang  wrote:

> @Justin,
> 
> I did that, and it still says I have 103. 
> 
> Xu Dong Huang
> Chemical & Biochemical Engineering
> Rutgers School of Engineering 
> xudo...@eden.rutgers.edu 
> 
> On Jan 9, 2013, at 7:49 PM, Xu Dong Huang  wrote:
> 
>> @Justin,
>> 
>> I did what you suggested, and I still can't load my molecule in VMD. Maybe I 
>> am still doing something wrong with the new line character thing. 
>> 
>> 
>> Xu Dong Huang
>> Chemical & Biochemical Engineering
>> Rutgers School of Engineering 
>> xudo...@eden.rutgers.edu 
>> 
>> On Jan 9, 2013, at 7:22 PM, Xu Dong Huang  wrote:
>> 
>>> @ Justin,
>>> 
>>> I laughed. :) Thank you. I can't believe I miss the smallest and most 
>>> rudimentary things. 
>>> Thanks again,
>>> Xu Dong Huang
>>> Chemical & Biochemical Engineering
>>> Rutgers School of Engineering 
>>> xudo...@eden.rutgers.edu 
>>> 
>>> On Jan 9, 2013, at 7:20 PM, Justin Lemkul  wrote:
>>> 
 
 
 On 1/9/13 7:16 PM, Xu Dong Huang wrote:
> @ Justin,
> 
> Thanks for always saving me from my mistakes. But I don't quite 
> understand what is a new line character?
> 
 
 The thing you get when you press enter.
 
 http://en.wikipedia.org/wiki/Newline#In_programming_languages
 
 Note that Google has plenty more to say ;)
 
 There should not be a blank line at the end of the .gro file, though, but 
 to be correctly parsed by VMD, the line must terminate with a '\n' 
 character.  So at the end of your box vector line, hit return then 
 backspace.
 
 -Justin
 
 -- 
 
 
 Justin A. Lemkul, Ph.D.
 Research Scientist
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
 
 
 -- 
 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
> 
> --
> 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

Re: [gmx-users] I can't figure out what is wrong with my .gro

[Justin Lemkul]

On 1/9/13 7:58 PM, Xu Dong Huang wrote:

@Justin,

I did that, and it still says I have 103.



I will send you a fixed file off-list so you can compare with what you've got. 
I don't know what text editor you're using, but I can produce a correct file 
using two different methods in vi.  It's very important to be using a plain text 
editor when manipulating any Gromacs file.


-Justin

--


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


--
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] I can't figure out what is wrong with my .gro

[Xu Dong Huang]

@Justin,

I did that, and it still says I have 103. 

Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering 
xudo...@eden.rutgers.edu 

On Jan 9, 2013, at 7:49 PM, Xu Dong Huang  wrote:

> @Justin,
> 
> I did what you suggested, and I still can't load my molecule in VMD. Maybe I 
> am still doing something wrong with the new line character thing. 
> 
> 
> Xu Dong Huang
> Chemical & Biochemical Engineering
> Rutgers School of Engineering 
> xudo...@eden.rutgers.edu 
> 
> On Jan 9, 2013, at 7:22 PM, Xu Dong Huang  wrote:
> 
>> @ Justin,
>> 
>> I laughed. :) Thank you. I can't believe I miss the smallest and most 
>> rudimentary things. 
>> Thanks again,
>> Xu Dong Huang
>> Chemical & Biochemical Engineering
>> Rutgers School of Engineering 
>> xudo...@eden.rutgers.edu 
>> 
>> On Jan 9, 2013, at 7:20 PM, Justin Lemkul  wrote:
>> 
>>> 
>>> 
>>> On 1/9/13 7:16 PM, Xu Dong Huang wrote:
 @ Justin,
 
 Thanks for always saving me from my mistakes. But I don't quite understand 
 what is a new line character?
 
>>> 
>>> The thing you get when you press enter.
>>> 
>>> http://en.wikipedia.org/wiki/Newline#In_programming_languages
>>> 
>>> Note that Google has plenty more to say ;)
>>> 
>>> There should not be a blank line at the end of the .gro file, though, but 
>>> to be correctly parsed by VMD, the line must terminate with a '\n' 
>>> character.  So at the end of your box vector line, hit return then 
>>> backspace.
>>> 
>>> -Justin
>>> 
>>> -- 
>>> 
>>> 
>>> Justin A. Lemkul, Ph.D.
>>> Research Scientist
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu | (540) 231-9080
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>> 
>>> 
>>> -- 
>>> 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

--
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] I can't figure out what is wrong with my .gro

[Justin Lemkul]

On 1/9/13 7:49 PM, Xu Dong Huang wrote:

@Justin,

I did what you suggested, and I still can't load my molecule in VMD. Maybe I am 
still doing something wrong with the new line character thing.



Go to the last line and go to the end of it.  Hit enter.  Hit backspace (brings 
you back up to the vectors line and removes the blank line).  Save the file. 
That's all I did.  If you run 'wc -l star.gro' you should get 104 in the 
terminal instead of 103.


-Justin

--


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


--
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] I can't figure out what is wrong with my .gro

[Xu Dong Huang]

@Justin,

I did what you suggested, and I still can't load my molecule in VMD. Maybe I am 
still doing something wrong with the new line character thing. 


Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering 
xudo...@eden.rutgers.edu 

On Jan 9, 2013, at 7:22 PM, Xu Dong Huang  wrote:

> @ Justin,
> 
> I laughed. :) Thank you. I can't believe I miss the smallest and most 
> rudimentary things. 
> Thanks again,
> Xu Dong Huang
> Chemical & Biochemical Engineering
> Rutgers School of Engineering 
> xudo...@eden.rutgers.edu 
> 
> On Jan 9, 2013, at 7:20 PM, Justin Lemkul  wrote:
> 
>> 
>> 
>> On 1/9/13 7:16 PM, Xu Dong Huang wrote:
>>> @ Justin,
>>> 
>>> Thanks for always saving me from my mistakes. But I don't quite understand 
>>> what is a new line character?
>>> 
>> 
>> The thing you get when you press enter.
>> 
>> http://en.wikipedia.org/wiki/Newline#In_programming_languages
>> 
>> Note that Google has plenty more to say ;)
>> 
>> There should not be a blank line at the end of the .gro file, though, but to 
>> be correctly parsed by VMD, the line must terminate with a '\n' character.  
>> So at the end of your box vector line, hit return then backspace.
>> 
>> -Justin
>> 
>> -- 
>> 
>> 
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>> 
>> 
>> -- 
>> 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

Re: [gmx-users] I can't figure out what is wrong with my .gro

[Xu Dong Huang]

@ Justin,

I laughed. :) Thank you. I can't believe I miss the smallest and most 
rudimentary things. 
Thanks again,
Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering 
xudo...@eden.rutgers.edu 

On Jan 9, 2013, at 7:20 PM, Justin Lemkul  wrote:

> 
> 
> On 1/9/13 7:16 PM, Xu Dong Huang wrote:
>> @ Justin,
>> 
>> Thanks for always saving me from my mistakes. But I don't quite understand 
>> what is a new line character?
>> 
> 
> The thing you get when you press enter.
> 
> http://en.wikipedia.org/wiki/Newline#In_programming_languages
> 
> Note that Google has plenty more to say ;)
> 
> There should not be a blank line at the end of the .gro file, though, but to 
> be correctly parsed by VMD, the line must terminate with a '\n' character.  
> So at the end of your box vector line, hit return then backspace.
> 
> -Justin
> 
> -- 
> 
> 
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> 
> -- 
> 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

Re: [gmx-users] I can't figure out what is wrong with my .gro

[Justin Lemkul]

On 1/9/13 7:16 PM, Xu Dong Huang wrote:

@ Justin,

Thanks for always saving me from my mistakes. But I don't quite understand what 
is a new line character?



The thing you get when you press enter.

http://en.wikipedia.org/wiki/Newline#In_programming_languages

Note that Google has plenty more to say ;)

There should not be a blank line at the end of the .gro file, though, but to be 
correctly parsed by VMD, the line must terminate with a '\n' character.  So at 
the end of your box vector line, hit return then backspace.


-Justin

--


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


--
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] I can't figure out what is wrong with my .gro

[Xu Dong Huang]

@ Justin,

Thanks for always saving me from my mistakes. But I don't quite understand what 
is a new line character? 

Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering 
xudo...@eden.rutgers.edu 

On Jan 9, 2013, at 7:12 PM, Justin Lemkul  wrote:

> 
> 
> On 1/9/13 7:07 PM, Xu Dong Huang wrote:
>> Dear all,
>> 
>> I created this .gro file following the gromacs format. But when I load it 
>> into VMD, it doesn't show the structure or molecule, and I have made many 
>> .gro before this one, and learned from many mistakes, but for this one, I 
>> don't know what I did wrong. I still proceeded to do simulation anyway and 
>> when I do energy minimization, I get an error of infinite normal force and 
>> etc (which I read past gmx list question that an atom is severely 
>> overlapping and causing the complication). Since I can't even view the .gro 
>> structure i made in VMD, I'm going to go ahead and assume there is something 
>> wrong with my initial structure to begin with, but I don't know where.
>> 
>> Here is the link to my .gro file + topology
>> 
>> https://docs.google.com/open?id=0BwQvutOxRUqkNFMtSmVDanlwRFE
>> https://docs.google.com/open?id=0BwQvutOxRUqkRkNQR2RYS0d6aDA
>> https://docs.google.com/open?id=0BwQvutOxRUqkaXV4ZmJaTks5Zzg
>> 
> 
> The last line of the .gro file (box vectors) does not end in a newline 
> character.  I discovered this by running:
> 
> wc -l star.gro
> 
> which returned 103, which would indicate that there should be 100 atoms in 
> addition to a title line, number of atoms, and box vectors.  Since there are 
> 101 listed atoms, I knew there was a problem, likely with the last line.  
> Adding a newline character allows the structure to be opened in VMD.
> 
> -Justin
> 
> -- 
> 
> 
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> 
> -- 
> 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

Re: [gmx-users] I can't figure out what is wrong with my .gro

[Justin Lemkul]

On 1/9/13 7:07 PM, Xu Dong Huang wrote:

Dear all,

I created this .gro file following the gromacs format. But when I load it into 
VMD, it doesn't show the structure or molecule, and I have made many .gro 
before this one, and learned from many mistakes, but for this one, I don't know 
what I did wrong. I still proceeded to do simulation anyway and when I do 
energy minimization, I get an error of infinite normal force and etc (which I 
read past gmx list question that an atom is severely overlapping and causing 
the complication). Since I can't even view the .gro structure i made in VMD, 
I'm going to go ahead and assume there is something wrong with my initial 
structure to begin with, but I don't know where.

Here is the link to my .gro file + topology

https://docs.google.com/open?id=0BwQvutOxRUqkNFMtSmVDanlwRFE
https://docs.google.com/open?id=0BwQvutOxRUqkRkNQR2RYS0d6aDA
https://docs.google.com/open?id=0BwQvutOxRUqkaXV4ZmJaTks5Zzg



The last line of the .gro file (box vectors) does not end in a newline 
character.  I discovered this by running:


wc -l star.gro

which returned 103, which would indicate that there should be 100 atoms in 
addition to a title line, number of atoms, and box vectors.  Since there are 101 
listed atoms, I knew there was a problem, likely with the last line.  Adding a 
newline character allows the structure to be opened in VMD.


-Justin

--


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


--
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] I can't figure out what is wrong with my .gro

[Xu Dong Huang]

Dear all, 

I created this .gro file following the gromacs format. But when I load it into 
VMD, it doesn't show the structure or molecule, and I have made many .gro 
before this one, and learned from many mistakes, but for this one, I don't know 
what I did wrong. I still proceeded to do simulation anyway and when I do 
energy minimization, I get an error of infinite normal force and etc (which I 
read past gmx list question that an atom is severely overlapping and causing 
the complication). Since I can't even view the .gro structure i made in VMD, 
I'm going to go ahead and assume there is something wrong with my initial 
structure to begin with, but I don't know where. 

Here is the link to my .gro file + topology

https://docs.google.com/open?id=0BwQvutOxRUqkNFMtSmVDanlwRFE
https://docs.google.com/open?id=0BwQvutOxRUqkRkNQR2RYS0d6aDA
https://docs.google.com/open?id=0BwQvutOxRUqkaXV4ZmJaTks5Zzg

Thanks for any input.

Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering 
xudo...@eden.rutgers.edu 

--
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