Re: [gmx-users] Which .tpr file to use for g_rms?

2010-12-04 Thread Mark Abraham 

On 4/12/2010 6:45 PM, Anirban Ghosh wrote:

Thanks a lot for the reply.
But I am getting different results with the two .tpr files (first and 
last) using the following commands:


trjconv -s *first.tpr *-f test.xtc -o str.gro -dump 1 -pbc nojump
trjconv -s *last.tpr* -f test.xtc -o str.gro -dump 1 -pbc nojump


Did you read trjconv -h about -pbc nojump? Notice how when you didn't 
give your command lines last time, you didn't get a very useful answer.



So which .tpr file should I use?


You're trying to measure a membrane thickness. So you want all the 
membrane residues in the same box, and don't care about anything else. 
There's various ways to use -pbc and -center to achieve this, depending 
on what the simulation has done.


Mark



Thanks,

Anirban

On Sat, Dec 4, 2010 at 12:29 PM, Mark Abraham > wrote:


On 4/12/2010 4:33 PM, Anirban Ghosh wrote:

Thanks a lot for the reply.
Actually I am running a protein in lipid bilayer. Now I want to
calculate the thickness of the bilayer at the end of the
simulation.
So for that I want the last structure (.gro) file. So I am
trying to
dump the last structure using trjconv (with -pbc option). So to do
this which .tpr file should I supply to trjconv, the first one
or the
last one?


Since you're not using the coordinates in the .tpr file to extract
the last frame and map its coordinates onto the .tpr's atom names,
it can't matter what they are.

Mark


Thanks again.

Anirban

On 12/4/10, Justin A. Lemkulmailto:jalem...@vt.edu>>  wrote:


Anirban Ghosh wrote:

Thanks a lot Justin for the reply. Yes, I understand
that. But ideally
which structure should be used as the reference, in a
general, the
starting structure or the end structure?

That's up to you to decide based on what you need to
measure.  Do you want
the
RMSD relative to your starting (i.e. crystal/NMR)
structure, or are you
trying
to study how a protein folds, in which case you'd use the
native (end)
state?

like when I an using trjconv to dump my last frame
(with "-pbc nojump"),
which .tpr file should I use to get the exact picture
of what has
happened to my protein at the end of the simulation.
Should I use the
first .tpr file or the last .tpr file?

I don't understand what you mean.  "What has happened" is
an entire
trajectory,
not a snapshot.

-Justin

Thanks a lot again.

Anirban

On Fri, Dec 3, 2010 at 7:35 PM, Justin A.
Lemkulmailto:jalem...@vt.edu>
>>  wrote:



Anirban Ghosh wrote:

Hi ALL,

Its a very basic question but still...
When we calculate RMSD (or any other
parameter) using the g_rms
command, we need to supply the .tpr file with
-s option. Now
suppose if I have a total 20 ns simulation
with 4 breaks (i.e 5
ns in each run), then there will be 4 .tpr
files. So at the end
of 20 ns if I wish to calculate RMSD, then
which .tpr file
should I suppy to g_rms, the first one or the
last one? We I run
g_rms with the two .tpr files, I get different
results. So which
one should be used? Any suggestion is welcome.


Use the one that contains the structure you wish
to serve as your
reference.

-Justin


Thanks,

Anirban


--


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 gmx-users@gromacs.org

Re: [gmx-users] Which .tpr file to use for g_rms?

2010-12-03 Thread Anirban Ghosh 
Thanks a lot for the reply.
But I am getting different results with the two .tpr files (first and last)
using the following commands:

trjconv -s *first.tpr *-f test.xtc -o str.gro -dump 1 -pbc nojump
trjconv -s *last.tpr* -f test.xtc -o str.gro -dump 1 -pbc nojump

So which .tpr file should I use?

Thanks,

Anirban

On Sat, Dec 4, 2010 at 12:29 PM, Mark Abraham wrote:

> On 4/12/2010 4:33 PM, Anirban Ghosh wrote:
>
>> Thanks a lot for the reply.
>> Actually I am running a protein in lipid bilayer. Now I want to
>> calculate the thickness of the bilayer at the end of the simulation.
>> So for that I want the last structure (.gro) file. So I am trying to
>> dump the last structure using trjconv (with -pbc option). So to do
>> this which .tpr file should I supply to trjconv, the first one or the
>> last one?
>>
>
> Since you're not using the coordinates in the .tpr file to extract the last
> frame and map its coordinates onto the .tpr's atom names, it can't matter
> what they are.
>
> Mark
>
>
>  Thanks again.
>>
>> Anirban
>>
>> On 12/4/10, Justin A. Lemkul  wrote:
>>
>>>
>>> Anirban Ghosh wrote:
>>>
 Thanks a lot Justin for the reply. Yes, I understand that. But ideally
 which structure should be used as the reference, in a general, the
 starting structure or the end structure?

>>> That's up to you to decide based on what you need to measure.  Do you
>>> want
>>> the
>>> RMSD relative to your starting (i.e. crystal/NMR) structure, or are you
>>> trying
>>> to study how a protein folds, in which case you'd use the native (end)
>>> state?
>>>
>>>  like when I an using trjconv to dump my last frame (with "-pbc nojump"),
 which .tpr file should I use to get the exact picture of what has
 happened to my protein at the end of the simulation. Should I use the
 first .tpr file or the last .tpr file?

  I don't understand what you mean.  "What has happened" is an entire
>>> trajectory,
>>> not a snapshot.
>>>
>>> -Justin
>>>
>>>  Thanks a lot again.

 Anirban

 On Fri, Dec 3, 2010 at 7:35 PM, Justin A. Lemkul>>> >  wrote:



 Anirban Ghosh wrote:

 Hi ALL,

 Its a very basic question but still...
 When we calculate RMSD (or any other parameter) using the g_rms
 command, we need to supply the .tpr file with -s option. Now
 suppose if I have a total 20 ns simulation with 4 breaks (i.e 5
 ns in each run), then there will be 4 .tpr files. So at the end
 of 20 ns if I wish to calculate RMSD, then which .tpr file
 should I suppy to g_rms, the first one or the last one? We I run
 g_rms with the two .tpr files, I get different results. So which
 one should be used? Any suggestion is welcome.


 Use the one that contains the structure you wish to serve as your
 reference.

 -Justin


 Thanks,

 Anirban


 --
 

 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
>>>
>>> 
>>> --
>>> 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.o

Re: [gmx-users] Which .tpr file to use for g_rms?

2010-12-03 Thread Mark Abraham 

On 4/12/2010 4:33 PM, Anirban Ghosh wrote:

Thanks a lot for the reply.
Actually I am running a protein in lipid bilayer. Now I want to
calculate the thickness of the bilayer at the end of the simulation.
So for that I want the last structure (.gro) file. So I am trying to
dump the last structure using trjconv (with -pbc option). So to do
this which .tpr file should I supply to trjconv, the first one or the
last one?


Since you're not using the coordinates in the .tpr file to extract the 
last frame and map its coordinates onto the .tpr's atom names, it can't 
matter what they are.


Mark


Thanks again.

Anirban

On 12/4/10, Justin A. Lemkul  wrote:


Anirban Ghosh wrote:

Thanks a lot Justin for the reply. Yes, I understand that. But ideally
which structure should be used as the reference, in a general, the
starting structure or the end structure?

That's up to you to decide based on what you need to measure.  Do you want
the
RMSD relative to your starting (i.e. crystal/NMR) structure, or are you
trying
to study how a protein folds, in which case you'd use the native (end)
state?


like when I an using trjconv to dump my last frame (with "-pbc nojump"),
which .tpr file should I use to get the exact picture of what has
happened to my protein at the end of the simulation. Should I use the
first .tpr file or the last .tpr file?


I don't understand what you mean.  "What has happened" is an entire
trajectory,
not a snapshot.

-Justin


Thanks a lot again.

Anirban

On Fri, Dec 3, 2010 at 7:35 PM, Justin A. Lemkulmailto:jalem...@vt.edu>>  wrote:



 Anirban Ghosh wrote:

 Hi ALL,

 Its a very basic question but still...
 When we calculate RMSD (or any other parameter) using the g_rms
 command, we need to supply the .tpr file with -s option. Now
 suppose if I have a total 20 ns simulation with 4 breaks (i.e 5
 ns in each run), then there will be 4 .tpr files. So at the end
 of 20 ns if I wish to calculate RMSD, then which .tpr file
 should I suppy to g_rms, the first one or the last one? We I run
 g_rms with the two .tpr files, I get different results. So which
 one should be used? Any suggestion is welcome.


 Use the one that contains the structure you wish to serve as your
 reference.

 -Justin


 Thanks,

 Anirban


 --
 

 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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Re: [gmx-users] Which .tpr file to use for g_rms?

2010-12-03 Thread Anirban Ghosh 
Thanks a lot for the reply.
Actually I am running a protein in lipid bilayer. Now I want to
calculate the thickness of the bilayer at the end of the simulation.
So for that I want the last structure (.gro) file. So I am trying to
dump the last structure using trjconv (with -pbc option). So to do
this which .tpr file should I supply to trjconv, the first one or the
last one?

Thanks again.

Anirban

On 12/4/10, Justin A. Lemkul  wrote:
>
>
> Anirban Ghosh wrote:
>> Thanks a lot Justin for the reply. Yes, I understand that. But ideally
>> which structure should be used as the reference, in a general, the
>> starting structure or the end structure?
>
> That's up to you to decide based on what you need to measure.  Do you want
> the
> RMSD relative to your starting (i.e. crystal/NMR) structure, or are you
> trying
> to study how a protein folds, in which case you'd use the native (end)
> state?
>
>> like when I an using trjconv to dump my last frame (with "-pbc nojump"),
>> which .tpr file should I use to get the exact picture of what has
>> happened to my protein at the end of the simulation. Should I use the
>> first .tpr file or the last .tpr file?
>>
>
> I don't understand what you mean.  "What has happened" is an entire
> trajectory,
> not a snapshot.
>
> -Justin
>
>> Thanks a lot again.
>>
>> Anirban
>>
>> On Fri, Dec 3, 2010 at 7:35 PM, Justin A. Lemkul > > wrote:
>>
>>
>>
>> Anirban Ghosh wrote:
>>
>> Hi ALL,
>>
>> Its a very basic question but still...
>> When we calculate RMSD (or any other parameter) using the g_rms
>> command, we need to supply the .tpr file with -s option. Now
>> suppose if I have a total 20 ns simulation with 4 breaks (i.e 5
>> ns in each run), then there will be 4 .tpr files. So at the end
>> of 20 ns if I wish to calculate RMSD, then which .tpr file
>> should I suppy to g_rms, the first one or the last one? We I run
>> g_rms with the two .tpr files, I get different results. So which
>> one should be used? Any suggestion is welcome.
>>
>>
>> Use the one that contains the structure you wish to serve as your
>> reference.
>>
>> -Justin
>>
>>
>> Thanks,
>>
>> Anirban
>>
>>
>> --
>> 
>>
>> 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
>
> 
> --
> 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
>
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Re: [gmx-users] Which .tpr file to use for g_rms?

2010-12-03 Thread Justin A. Lemkul 



Anirban Ghosh wrote:
Thanks a lot Justin for the reply. Yes, I understand that. But ideally 
which structure should be used as the reference, in a general, the 
starting structure or the end structure?


That's up to you to decide based on what you need to measure.  Do you want the 
RMSD relative to your starting (i.e. crystal/NMR) structure, or are you trying 
to study how a protein folds, in which case you'd use the native (end) state?


like when I an using trjconv to dump my last frame (with "-pbc nojump"), 
which .tpr file should I use to get the exact picture of what has 
happened to my protein at the end of the simulation. Should I use the 
first .tpr file or the last .tpr file?




I don't understand what you mean.  "What has happened" is an entire trajectory, 
not a snapshot.


-Justin


Thanks a lot again.

Anirban
 
On Fri, Dec 3, 2010 at 7:35 PM, Justin A. Lemkul > wrote:




Anirban Ghosh wrote:

Hi ALL,

Its a very basic question but still...
When we calculate RMSD (or any other parameter) using the g_rms
command, we need to supply the .tpr file with -s option. Now
suppose if I have a total 20 ns simulation with 4 breaks (i.e 5
ns in each run), then there will be 4 .tpr files. So at the end
of 20 ns if I wish to calculate RMSD, then which .tpr file
should I suppy to g_rms, the first one or the last one? We I run
g_rms with the two .tpr files, I get different results. So which
one should be used? Any suggestion is welcome.


Use the one that contains the structure you wish to serve as your
reference.

-Justin


Thanks,

Anirban


-- 



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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.
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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Re: [gmx-users] Which .tpr file to use for g_rms?

2010-12-03 Thread Anirban Ghosh 
Thanks a lot Justin for the reply. Yes, I understand that. But ideally which
structure should be used as the reference, in a general, the starting
structure or the end structure?
like when I an using trjconv to dump my last frame (with "-pbc nojump"),
which .tpr file should I use to get the exact picture of what has happened
to my protein at the end of the simulation. Should I use the first .tpr file
or the last .tpr file?

Thanks a lot again.

Anirban

On Fri, Dec 3, 2010 at 7:35 PM, Justin A. Lemkul  wrote:

>
>
> Anirban Ghosh wrote:
>
>> Hi ALL,
>>
>> Its a very basic question but still...
>> When we calculate RMSD (or any other parameter) using the g_rms command,
>> we need to supply the .tpr file with -s option. Now suppose if I have a
>> total 20 ns simulation with 4 breaks (i.e 5 ns in each run), then there will
>> be 4 .tpr files. So at the end of 20 ns if I wish to calculate RMSD, then
>> which .tpr file should I suppy to g_rms, the first one or the last one? We I
>> run g_rms with the two .tpr files, I get different results. So which one
>> should be used? Any suggestion is welcome.
>>
>>
> Use the one that contains the structure you wish to serve as your
> reference.
>
> -Justin
>
>
>> Thanks,
>>
>> Anirban
>>
>>
> --
> 
>
> 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
>
-- 
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Re: [gmx-users] Which .tpr file to use for g_rms?

2010-12-03 Thread Justin A. Lemkul 



Anirban Ghosh wrote:

Hi ALL,

Its a very basic question but still...
When we calculate RMSD (or any other parameter) using the g_rms command, 
we need to supply the .tpr file with -s option. Now suppose if I have a 
total 20 ns simulation with 4 breaks (i.e 5 ns in each run), then there 
will be 4 .tpr files. So at the end of 20 ns if I wish to calculate 
RMSD, then which .tpr file should I suppy to g_rms, the first one or the 
last one? We I run g_rms with the two .tpr files, I get different 
results. So which one should be used? Any suggestion is welcome.




Use the one that contains the structure you wish to serve as your reference.

-Justin



Thanks,

Anirban



--


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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