subject:"\[gmx\-users\] extracting a list of frames from a trajectory"

Re: [gmx-users] extracting a list of frames from a trajectory

2017-01-13 Thread Irem Altan

When I do that it still reads from the beginning, saying “skipping frame”. I’ll 
divide the file in a few pieces and save all configurations. I’ll then cat the 
configs that I want. This is the simplest thing I can think of.

> On Jan 13, 2017, at 3:17 PM, Justin Lemkul  wrote:
> 
> 
> 
> On 1/13/17 9:15 AM, Irem Altan wrote:
>> I need to sample with logarithmic time intervals.
>> 
> 
> Use -b to speed up moving through the trajectory before dumping the desired 
> time frame, or split the massive trajectory into smaller, more manageable 
> chunks that you can loop over simultaneously.
> 
> -Justin
> 
>> On Jan 13, 2017, at 3:12 PM, David van der Spoel 
>> > wrote:
>> 
>> On 13/01/17 14:41, Irem Altan wrote:
>> Hi,
>> 
>> So for some reason, the frame numbers I list won't match the timestamps when 
>> I use -fr. Is there a way to extract frames based on timestamps? The problem 
>> is, I want to be reading the file only once (or a few times), as it is huge 
>> (~500 GB), so I can’t use -dump by calling trjconv hundreds of times.
>> 
>> How about the -dt flag?
>> 
>> Best,
>> Irem
>> 
>> On Jan 13, 2017, at 2:31 PM, Mark Abraham 
>> > wrote:
>> 
>> Hi,
>> 
>> Sadly there's nothing to be done except ignore the field or do multiple
>> passes. The history of trjconv is a large number of people adding features
>> convenient for their use case, and not knowing how it interacts with the
>> huge surface area of the set of all other features. So the person who
>> wanted such automatic regularisation trips the implementation of -fr, etc.
>> 
>> Mark
>> 
>> On Fri, 13 Jan 2017 14:22 Irem Altan 
>> > wrote:
>> 
>> Hi,
>> 
>> I’m trying to extract a list of frames from a long trajectory:
>> 
>> gmx trjconv -f complete.trr -s nvt.tpr -novel -ndec 14 -fr frames.ndx -pbc
>> atom -o conf_test.gro -sep
>> 
>> where frames.ndx contains the following:
>> 
>> [ frames ]
>> 2 3 4 5 6 8 ...
>> 
>> Each frame is supposed to be separated by 10 ps, so that for frame 2, t=
>> 20.. Hence, conf_test1.gro starts with "Generated by trjconv : Protein
>> in water t=  20.0”, which is what we expect. However, the timestamps in
>> the subsequent files are:
>> 
>> Generated by trjconv : Protein in water t=  30.0
>> Generated by trjconv : Protein in water t=  40.0
>> Generated by trjconv : Protein in water t=  50.0
>> Generated by trjconv : Protein in water t=  70.0
>> Generated by trjconv : Protein in water t=  80.0
>> …
>> 
>> while it should have been 30, 40, 50, 60, 80,  This happens a lot of
>> times throughout the whole list of frames. Why does it happen? How can I
>> fix it?
>> 
>> Best,
>> Irem
>> --
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Re: [gmx-users] extracting a list of frames from a trajectory

2017-01-13 Thread Justin Lemkul

On 1/13/17 9:15 AM, Irem Altan wrote:

I need to sample with logarithmic time intervals.

Use -b to speed up moving through the trajectory before dumping the desired time 
frame, or split the massive trajectory into smaller, more manageable chunks that 
you can loop over simultaneously.

-Justin

On Jan 13, 2017, at 3:12 PM, David van der Spoel 
> wrote:

On 13/01/17 14:41, Irem Altan wrote:
Hi,

So for some reason, the frame numbers I list won't match the timestamps when I 
use -fr. Is there a way to extract frames based on timestamps? The problem is, 
I want to be reading the file only once (or a few times), as it is huge (~500 
GB), so I can’t use -dump by calling trjconv hundreds of times.

How about the -dt flag?

Best,
Irem

On Jan 13, 2017, at 2:31 PM, Mark Abraham 
> wrote:

Hi,

Sadly there's nothing to be done except ignore the field or do multiple
passes. The history of trjconv is a large number of people adding features
convenient for their use case, and not knowing how it interacts with the
huge surface area of the set of all other features. So the person who
wanted such automatic regularisation trips the implementation of -fr, etc.

Mark

On Fri, 13 Jan 2017 14:22 Irem Altan 
> wrote:

Hi,

I’m trying to extract a list of frames from a long trajectory:

gmx trjconv -f complete.trr -s nvt.tpr -novel -ndec 14 -fr frames.ndx -pbc
atom -o conf_test.gro -sep

where frames.ndx contains the following:

[ frames ]
2 3 4 5 6 8 ...

Each frame is supposed to be separated by 10 ps, so that for frame 2, t=
20.. Hence, conf_test1.gro starts with "Generated by trjconv : Protein
in water t=  20.0”, which is what we expect. However, the timestamps in
the subsequent files are:

Generated by trjconv : Protein in water t=  30.0
Generated by trjconv : Protein in water t=  40.0
Generated by trjconv : Protein in water t=  50.0
Generated by trjconv : Protein in water t=  70.0
Generated by trjconv : Protein in water t=  80.0
…

while it should have been 30, 40, 50, 60, 80,  This happens a lot of
times throughout the whole list of frames. Why does it happen? How can I
fix it?

Best,
Irem
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Re: [gmx-users] extracting a list of frames from a trajectory

2017-01-13 Thread Irem Altan

I need to sample with logarithmic time intervals.

On Jan 13, 2017, at 3:12 PM, David van der Spoel 
> wrote:

On 13/01/17 14:41, Irem Altan wrote:
Hi,

So for some reason, the frame numbers I list won't match the timestamps when I 
use -fr. Is there a way to extract frames based on timestamps? The problem is, 
I want to be reading the file only once (or a few times), as it is huge (~500 
GB), so I can’t use -dump by calling trjconv hundreds of times.

How about the -dt flag?

Best,
Irem

On Jan 13, 2017, at 2:31 PM, Mark Abraham 
> wrote:

Hi,

Sadly there's nothing to be done except ignore the field or do multiple
passes. The history of trjconv is a large number of people adding features
convenient for their use case, and not knowing how it interacts with the
huge surface area of the set of all other features. So the person who
wanted such automatic regularisation trips the implementation of -fr, etc.

Mark

On Fri, 13 Jan 2017 14:22 Irem Altan 
> wrote:

Hi,

I’m trying to extract a list of frames from a long trajectory:

gmx trjconv -f complete.trr -s nvt.tpr -novel -ndec 14 -fr frames.ndx -pbc
atom -o conf_test.gro -sep

where frames.ndx contains the following:

[ frames ]
2 3 4 5 6 8 ...

Each frame is supposed to be separated by 10 ps, so that for frame 2, t=
20.. Hence, conf_test1.gro starts with "Generated by trjconv : Protein
in water t=  20.0”, which is what we expect. However, the timestamps in
the subsequent files are:

Generated by trjconv : Protein in water t=  30.0
Generated by trjconv : Protein in water t=  40.0
Generated by trjconv : Protein in water t=  50.0
Generated by trjconv : Protein in water t=  70.0
Generated by trjconv : Protein in water t=  80.0
…

while it should have been 30, 40, 50, 60, 80,  This happens a lot of
times throughout the whole list of frames. Why does it happen? How can I
fix it?

Best,
Irem
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Re: [gmx-users] extracting a list of frames from a trajectory

2017-01-13 Thread David van der Spoel


On 13/01/17 14:41, Irem Altan wrote:

Hi,

So for some reason, the frame numbers I list won't match the timestamps when I 
use -fr. Is there a way to extract frames based on timestamps? The problem is, 
I want to be reading the file only once (or a few times), as it is huge (~500 
GB), so I can’t use -dump by calling trjconv hundreds of times.


How about the -dt flag?


Best,
Irem


On Jan 13, 2017, at 2:31 PM, Mark Abraham  wrote:

Hi,

Sadly there's nothing to be done except ignore the field or do multiple
passes. The history of trjconv is a large number of people adding features
convenient for their use case, and not knowing how it interacts with the
huge surface area of the set of all other features. So the person who
wanted such automatic regularisation trips the implementation of -fr, etc.

Mark

On Fri, 13 Jan 2017 14:22 Irem Altan  wrote:


Hi,

I’m trying to extract a list of frames from a long trajectory:

gmx trjconv -f complete.trr -s nvt.tpr -novel -ndec 14 -fr frames.ndx -pbc
atom -o conf_test.gro -sep

where frames.ndx contains the following:

[ frames ]
2 3 4 5 6 8 ...

Each frame is supposed to be separated by 10 ps, so that for frame 2, t=
20.. Hence, conf_test1.gro starts with "Generated by trjconv : Protein
in water t=  20.0”, which is what we expect. However, the timestamps in
the subsequent files are:

Generated by trjconv : Protein in water t=  30.0
Generated by trjconv : Protein in water t=  40.0
Generated by trjconv : Protein in water t=  50.0
Generated by trjconv : Protein in water t=  70.0
Generated by trjconv : Protein in water t=  80.0
…

while it should have been 30, 40, 50, 60, 80,  This happens a lot of
times throughout the whole list of frames. Why does it happen? How can I
fix it?

Best,
Irem
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Re: [gmx-users] extracting a list of frames from a trajectory

2017-01-13 Thread Irem Altan

Hi,

So for some reason, the frame numbers I list won't match the timestamps when I 
use -fr. Is there a way to extract frames based on timestamps? The problem is, 
I want to be reading the file only once (or a few times), as it is huge (~500 
GB), so I can’t use -dump by calling trjconv hundreds of times.

Best,
Irem

> On Jan 13, 2017, at 2:31 PM, Mark Abraham  wrote:
> 
> Hi,
> 
> Sadly there's nothing to be done except ignore the field or do multiple
> passes. The history of trjconv is a large number of people adding features
> convenient for their use case, and not knowing how it interacts with the
> huge surface area of the set of all other features. So the person who
> wanted such automatic regularisation trips the implementation of -fr, etc.
> 
> Mark
> 
> On Fri, 13 Jan 2017 14:22 Irem Altan  wrote:
> 
>> Hi,
>> 
>> I’m trying to extract a list of frames from a long trajectory:
>> 
>> gmx trjconv -f complete.trr -s nvt.tpr -novel -ndec 14 -fr frames.ndx -pbc
>> atom -o conf_test.gro -sep
>> 
>> where frames.ndx contains the following:
>> 
>> [ frames ]
>> 2 3 4 5 6 8 ...
>> 
>> Each frame is supposed to be separated by 10 ps, so that for frame 2, t=
>> 20.. Hence, conf_test1.gro starts with "Generated by trjconv : Protein
>> in water t=  20.0”, which is what we expect. However, the timestamps in
>> the subsequent files are:
>> 
>> Generated by trjconv : Protein in water t=  30.0
>> Generated by trjconv : Protein in water t=  40.0
>> Generated by trjconv : Protein in water t=  50.0
>> Generated by trjconv : Protein in water t=  70.0
>> Generated by trjconv : Protein in water t=  80.0
>> …
>> 
>> while it should have been 30, 40, 50, 60, 80,  This happens a lot of
>> times throughout the whole list of frames. Why does it happen? How can I
>> fix it?
>> 
>> Best,
>> Irem
>> --
>> Gromacs Users mailing list
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Re: [gmx-users] extracting a list of frames from a trajectory

2017-01-13 Thread Mark Abraham

Hi,

Sadly there's nothing to be done except ignore the field or do multiple
passes. The history of trjconv is a large number of people adding features
convenient for their use case, and not knowing how it interacts with the
huge surface area of the set of all other features. So the person who
wanted such automatic regularisation trips the implementation of -fr, etc.

Mark

On Fri, 13 Jan 2017 14:22 Irem Altan  wrote:

> Hi,
>
> I’m trying to extract a list of frames from a long trajectory:
>
> gmx trjconv -f complete.trr -s nvt.tpr -novel -ndec 14 -fr frames.ndx -pbc
> atom -o conf_test.gro -sep
>
> where frames.ndx contains the following:
>
> [ frames ]
> 2 3 4 5 6 8 ...
>
> Each frame is supposed to be separated by 10 ps, so that for frame 2, t=
> 20.. Hence, conf_test1.gro starts with "Generated by trjconv : Protein
> in water t=  20.0”, which is what we expect. However, the timestamps in
> the subsequent files are:
>
> Generated by trjconv : Protein in water t=  30.0
> Generated by trjconv : Protein in water t=  40.0
> Generated by trjconv : Protein in water t=  50.0
> Generated by trjconv : Protein in water t=  70.0
> Generated by trjconv : Protein in water t=  80.0
> …
>
> while it should have been 30, 40, 50, 60, 80,  This happens a lot of
> times throughout the whole list of frames. Why does it happen? How can I
> fix it?
>
> Best,
> Irem
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[gmx-users] extracting a list of frames from a trajectory

2017-01-13 Thread Irem Altan

Hi,

I’m trying to extract a list of frames from a long trajectory:

gmx trjconv -f complete.trr -s nvt.tpr -novel -ndec 14 -fr frames.ndx -pbc atom 
-o conf_test.gro -sep

where frames.ndx contains the following:

[ frames ]
2 3 4 5 6 8 ...

Each frame is supposed to be separated by 10 ps, so that for frame 2, t= 
20.. Hence, conf_test1.gro starts with "Generated by trjconv : Protein in 
water t=  20.0”, which is what we expect. However, the timestamps in the 
subsequent files are:

Generated by trjconv : Protein in water t=  30.0
Generated by trjconv : Protein in water t=  40.0
Generated by trjconv : Protein in water t=  50.0
Generated by trjconv : Protein in water t=  70.0
Generated by trjconv : Protein in water t=  80.0
…

while it should have been 30, 40, 50, 60, 80,  This happens a lot of times 
throughout the whole list of frames. Why does it happen? How can I fix it?

Best,
Irem
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Re: [gmx-users] extracting a list of frames from a trajectory

Re: [gmx-users] extracting a list of frames from a trajectory

Re: [gmx-users] extracting a list of frames from a trajectory

Re: [gmx-users] extracting a list of frames from a trajectory

Re: [gmx-users] extracting a list of frames from a trajectory

Re: [gmx-users] extracting a list of frames from a trajectory

[gmx-users] extracting a list of frames from a trajectory

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