Re: [gmx-users] snapshot

[Rama Krishna Koppisetti]

Thank you very much *Justin*.

--
Rama



On Mon, Jul 15, 2013 at 8:06 AM, Justin Lemkul  wrote:

>
>
> On 7/15/13 9:02 AM, Rama Krishna Koppisetti wrote:
>
>> Hi,
>>
>> The following command I used for the snapshots but I'm getting one frame
>> time 0 time 500. what are the changes I need to do in the command to get
>> snapshots in equal intervals of time for ex: 250ps. My production MD
>> trajectory was 15ns.
>> g_trjconv -s md.tpr -f md.trr -o beta.gro -skip 1 -dt 0 -dump 0 -sep
>>
>>
> The interval depends on how often you saved snapshots.  You do not need
> -dt and -dump options.  You will get separate coordinate files with -sep
> and the correct value of -skip will give you what you want.  If you saved a
> frame every 50 ps, then trjconv -skip 5 -sep will give you a frame every
> 250 ps.
>
>
> -Justin
>
> --
> ==**
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Associate
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul@outerbanks.umaryland.**edu  | 
> (410)
> 706-7441
>
> ==**
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Re: [gmx-users] snapshot

[Justin Lemkul]

On 7/15/13 9:02 AM, Rama Krishna Koppisetti wrote:

Hi,

The following command I used for the snapshots but I'm getting one frame
time 0 time 500. what are the changes I need to do in the command to get
snapshots in equal intervals of time for ex: 250ps. My production MD
trajectory was 15ns.
g_trjconv -s md.tpr -f md.trr -o beta.gro -skip 1 -dt 0 -dump 0 -sep



The interval depends on how often you saved snapshots.  You do not need -dt and 
-dump options.  You will get separate coordinate files with -sep and the correct 
value of -skip will give you what you want.  If you saved a frame every 50 ps, 
then trjconv -skip 5 -sep will give you a frame every 250 ps.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Associate

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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Re: [gmx-users] snapshot

[Rama Krishna Koppisetti]

Hi,

The following command I used for the snapshots but I'm getting one frame
time 0 time 500. what are the changes I need to do in the command to get
snapshots in equal intervals of time for ex: 250ps. My production MD
trajectory was 15ns.
g_trjconv -s md.tpr -f md.trr -o beta.gro -skip 1 -dt 0 -dump 0 -sep


Thanks in Advance.

Rama


On Mon, Jul 15, 2013 at 2:02 AM, Dr. Vitaly Chaban wrote:

> look for either "-dt" or "-skip".
>
>
>
>
> Dr. Vitaly V. Chaban
>
>
> On Mon, Jul 15, 2013 at 2:03 AM, Rama  wrote:
>
> > Hi,
> >
> > How to get a snapshots in equal intervals of time (250ps) from production
> > MD
> > trajectory. I'm using -sep , -t0, -timestep but output came only one .gro
> > file.
> >
> >
> >
> > --
> > View this message in context:
> > http://gromacs.5086.x6.nabble.com/snapshot-tp5009837.html
> > Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> > --
> > gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] snapshot

[Dr. Vitaly Chaban]

look for either "-dt" or "-skip".




Dr. Vitaly V. Chaban


On Mon, Jul 15, 2013 at 2:03 AM, Rama  wrote:

> Hi,
>
> How to get a snapshots in equal intervals of time (250ps) from production
> MD
> trajectory. I'm using -sep , -t0, -timestep but output came only one .gro
> file.
>
>
>
> --
> View this message in context:
> http://gromacs.5086.x6.nabble.com/snapshot-tp5009837.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] snapshot

[Justin Lemkul]

On 7/14/13 9:03 PM, Rama wrote:

Hi,

How to get a snapshots in equal intervals of time (250ps) from production MD
trajectory. I'm using -sep , -t0, -timestep but output came only one .gro
file.



trjconv -skip -sep should work, but without exact command lines and the output 
you received (as well as the output of gmxcheck on the trajectory), it's hard to 
be more specific.  The -t0 and -timestep options will have no effect except to 
modify the trajectory - read the information in -h carefully!


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Associate

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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[gmx-users] snapshot

[Rama]

Hi, 

How to get a snapshots in equal intervals of time (250ps) from production MD
trajectory. I'm using -sep , -t0, -timestep but output came only one .gro
file. 



--
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http://gromacs.5086.x6.nabble.com/snapshot-tp5009837.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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Re: [gmx-users] Snapshot and co-ordinate query

[Ankita naithani]

Hi Justin,

Thank you so much for the clarification.


Kind regards,

Ankita


On Wed, Jun 5, 2013 at 11:28 PM, Justin Lemkul  wrote:

>
>
> On 6/5/13 3:03 PM, Ankita naithani wrote:
>
>> Hi,
>>
>> I have two questions.
>>
>> I have performed a simulation on my protein structure and after the
>> simulation, I used trjconv to obtain snapshots after every 10 ns with the
>> following command:
>>
>> trjconv -f md.xtc -s md.tpr -b 1 -e 10001 -o md_10.pdb
>>
>>
> This command will produce one snapshot.  If you're looking to get multiple
> snapshots, it is easier to combine -skip -sep to write out multiple
> snapshots in one command.
>
>
>  and chose 0 (system) for the group.
>> However, when I see the same structure in PyMol as cartoon representation,
>> I see the protein structure and few of the residues scattered elsewhere of
>> a particular chain, say chain A. I am concerned whether my residues of
>> that
>> particular chain fragmented during simulation or is my way of obtaining
>> snapshots wrong?
>>
>>
> The molecule isn't fragmented, it's just split across periodic boundaries.
> trjconv can take care of that too (see trjconv -h).
>
>  Also, there was another question, I wanted to know how the geometry is
>> preserved in the average structure as computed by gromacs?The average
>>
>> structure calculated during analysis would be the average of all the
>> atomic
>> positions/co-ordinates during the length of simulation. But, I wanted to
>> know how are the bond angles treated for computation of the average
>> structure? Since, we use the structure for further analysis too. Are the
>> bond lengths distorted or they are retained while average is being
>> computed? Also, what are the co-ordinates used for this computation?
>>
>>
> http://www.gromacs.org/**Documentation/Terminology/**Average_Structure
>
> -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
>
> ==**==
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-- 
Ankita Naithani
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Re: [gmx-users] Snapshot and co-ordinate query

[Justin Lemkul]

On 6/5/13 3:03 PM, Ankita naithani wrote:

Hi,

I have two questions.

I have performed a simulation on my protein structure and after the
simulation, I used trjconv to obtain snapshots after every 10 ns with the
following command:

trjconv -f md.xtc -s md.tpr -b 1 -e 10001 -o md_10.pdb



This command will produce one snapshot.  If you're looking to get multiple 
snapshots, it is easier to combine -skip -sep to write out multiple snapshots in 
one command.



and chose 0 (system) for the group.
However, when I see the same structure in PyMol as cartoon representation,
I see the protein structure and few of the residues scattered elsewhere of
a particular chain, say chain A. I am concerned whether my residues of that
particular chain fragmented during simulation or is my way of obtaining
snapshots wrong?



The molecule isn't fragmented, it's just split across periodic boundaries. 
trjconv can take care of that too (see trjconv -h).



Also, there was another question, I wanted to know how the geometry is
preserved in the average structure as computed by gromacs?The average
structure calculated during analysis would be the average of all the atomic
positions/co-ordinates during the length of simulation. But, I wanted to
know how are the bond angles treated for computation of the average
structure? Since, we use the structure for further analysis too. Are the
bond lengths distorted or they are retained while average is being
computed? Also, what are the co-ordinates used for this computation?



http://www.gromacs.org/Documentation/Terminology/Average_Structure

-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


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[gmx-users] Snapshot and co-ordinate query

[Ankita naithani]

Hi,

I have two questions.

I have performed a simulation on my protein structure and after the
simulation, I used trjconv to obtain snapshots after every 10 ns with the
following command:

trjconv -f md.xtc -s md.tpr -b 1 -e 10001 -o md_10.pdb

and chose 0 (system) for the group.
However, when I see the same structure in PyMol as cartoon representation,
I see the protein structure and few of the residues scattered elsewhere of
a particular chain, say chain A. I am concerned whether my residues of that
particular chain fragmented during simulation or is my way of obtaining
snapshots wrong?

Also, there was another question, I wanted to know how the geometry is
preserved in the average structure as computed by gromacs?The average
structure calculated during analysis would be the average of all the atomic
positions/co-ordinates during the length of simulation. But, I wanted to
know how are the bond angles treated for computation of the average
structure? Since, we use the structure for further analysis too. Are the
bond lengths distorted or they are retained while average is being
computed? Also, what are the co-ordinates used for this computation?

I would be really grateful if you could kindly guide me towards these
queries.

Kind regards

-- 
Ankita Naithani
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Re: [gmx-users] Snapshot taken under certain condition

[Arik Cohen]

Thanks allot for all your help

Arik

Mark Abraham wrote:

Arik Cohen wrote:

Dear users,

Is there a way(in the mdp file) to take a snapshot of only the 
C-alpha atoms along a trajectory if certain condition are met(tested 
every time a snapshot needs to be taken) ?


If you know in advance you'll only ever want the C-alpha atoms for 
analysis (dangerous) then you can use xtc-groups to write only that 
set. Better is to savee all the data you might want, and then filter 
for the C-alpha atoms with trjconv at a suitable point.


You cannot apply your condition during the simulation, but must apply 
it after the fact. For example, use a suitable analysis tool, and then 
perhaps post-process that output to provide input to trjconv to 
extract the frames of interest. The detail of the necessary procedure 
will depend on the nature of the condition you want to apply.


Mark
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Re: [gmx-users] Snapshot taken under certain condition

[Mark Abraham]

Arik Cohen wrote:

Dear users,

Is there a way(in the mdp file) to take a snapshot of only the C-alpha 
atoms along a trajectory if certain condition are met(tested every time 
a snapshot needs to be taken) ?


If you know in advance you'll only ever want the C-alpha atoms for 
analysis (dangerous) then you can use xtc-groups to write only that set. 
Better is to savee all the data you might want, and then filter for the 
C-alpha atoms with trjconv at a suitable point.


You cannot apply your condition during the simulation, but must apply it 
after the fact. For example, use a suitable analysis tool, and then 
perhaps post-process that output to provide input to trjconv to extract 
the frames of interest. The detail of the necessary procedure will 
depend on the nature of the condition you want to apply.


Mark
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Re: [gmx-users] Snapshot taken under certain condition

[Arik Cohen]

Thanks for all your help and rapid response.

Arik

Justin A. Lemkul wrote:



Arik Cohen wrote:

Dear users,

Is there a way(in the mdp file) to take a snapshot of only the 
C-alpha atoms along a trajectory if certain condition are met(tested 
every time a snapshot needs to be taken) ?




No, but you could probably script it after the trajectory is run, 
using whatever analysis tool is appropriate to evaluate your 
condition, then trjconv to dump out the appropriate frame.


-Justin


Thanks

Arik
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Version: 8.5.420 / Virus Database: 270.14.5/2418 - Release Date: 10/06/09 18:34:00


  
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Re: [gmx-users] Snapshot taken under certain condition

[Justin A. Lemkul]

Arik Cohen wrote:

Dear users,

Is there a way(in the mdp file) to take a snapshot of only the C-alpha 
atoms along a trajectory if certain condition are met(tested every time 
a snapshot needs to be taken) ?




No, but you could probably script it after the trajectory is run, using whatever 
analysis tool is appropriate to evaluate your condition, then trjconv to dump 
out the appropriate frame.


-Justin


Thanks

Arik
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--


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


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[gmx-users] Snapshot taken under certain condition

[Arik Cohen]

Dear users,

Is there a way(in the mdp file) to take a snapshot of only the C-alpha 
atoms along a trajectory if certain condition are met(tested every time 
a snapshot needs to be taken) ?


Thanks

Arik
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