Re: [gmx-users] How to concatenate tpr files?

2017-01-25 Thread Mark Abraham 
Hi,

Measuring a root mean square deviation requires knowing what conformation
you want to measure a deviation from, which doesn't have to come from any
tpr, either. Preferably you should know what you'll learn from that
measurement, too.

Mark

On Wed, 25 Jan 2017 09:41 leila karami  wrote:

> Dear Justin and Erik,
>
> Thanks for your answers.
>
> How to resolve my problem? How to obtain a reasonable RMSD curve from
> 10 consecutive MD runs? How to make an appropriate tpr for calculating
> RMSD?
>
> Best,
> --
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[gmx-users] How to concatenate tpr files?

2017-01-25 Thread leila karami 
Dear Justin and Erik,

Thanks for your answers.

How to resolve my problem? How to obtain a reasonable RMSD curve from
10 consecutive MD runs? How to make an appropriate tpr for calculating RMSD?

Best,
-- 
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http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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Re: [gmx-users] How to concatenate tpr files?

2017-01-24 Thread Erik Marklund 
Dear Leila,

The RMSD is, by default, calculated with respect to the coordinates in the tpr 
file, which is why you get different results with different tprs. Which one to 
choose depends on exactly what you want to measure.

Kind regards,
Erik

__
Erik Marklund, PhD
Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC
Uppsala Universtity
erik.markl...@kemi.uu.se

On 23 Jan 2017, at 17:10, leila karami 
> wrote:

Dear gromacs users,

About the concatenation trajectory files, I have a question.

I did 10 MD simulations (each section 10 ns). Now, I want to concatenate
all of the trajectories and determine RMSD on whole trajectory. To do this,
I used the following command:

gmx trjcat -f md1.trr md2.trr md3.trr md4.trr md5.trr md6.trr md7.trr
md8.trr md9.trr md10.trr -o all_md.xtc –settime

The whole trajectory file made correctly. To determined RMSD, I used the
following command.

gmx  rms  -f  all_md.xtc  -s  *.tpr  -n index.ndx  -o rmsd.xvg  -tu  ns

I want to know, which tpr file must be used? tpr1 or tpr2 or tpr3 or …?

I tried this command with md1.tpr and md10.tpr and in each time, RMSD had
the different values. So, should I concatenate the tpr files and use the
complete tpr file.

How can I concatenate the tpr files?

Best
--
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[gmx-users] How to concatenate tpr files?

2017-01-23 Thread leila karami 
Dear Justin,

Thanks for your answer.

> If you use gmx convert-tpr to simply change the number of steps

> (much easier and cleaner!)

Based on your suggestion, I used following command to extend first tpr
to all steps.

gmx convert-tpr -f final.xtc -s md1.tpr -n index.ndx -o new.tpr -extend 10

After that, RMSDs with md1.tpr and new.tpr are the same.

Please, check this link:

https://ln.sync.com/dl/d123d6b00#6nqcqdrf-cgebd3c7-htj4vydi-vfiihiy6

Note that there are no problem in the other analysis such as gmx
mindist, gmx angle anf gmx gyrate.

Best,
-- 
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Re: [gmx-users] How to concatenate tpr files?

2017-01-23 Thread Justin Lemkul 



On 1/23/17 11:10 AM, leila karami wrote:

Dear gromacs users,

About the concatenation trajectory files, I have a question.

I did 10 MD simulations (each section 10 ns). Now, I want to concatenate
all of the trajectories and determine RMSD on whole trajectory. To do this,
I used the following command:

gmx trjcat -f md1.trr md2.trr md3.trr md4.trr md5.trr md6.trr md7.trr
md8.trr md9.trr md10.trr -o all_md.xtc –settime

The whole trajectory file made correctly. To determined RMSD, I used the
following command.

gmx  rms  -f  all_md.xtc  -s  *.tpr  -n index.ndx  -o rmsd.xvg  -tu  ns

I want to know, which tpr file must be used? tpr1 or tpr2 or tpr3 or …?

I tried this command with md1.tpr and md10.tpr and in each time, RMSD had
the different values. So, should I concatenate the tpr files and use the
complete tpr file.

How can I concatenate the tpr files?



You don't.  A .tpr file has a configuration, velocities, state information, and 
a set of instructions.  The one you choose depends on how you created them.  If 
you re-invoked grompp to create them for each interval, they will each contain a 
different state, so naturally the result of an RMSD calculation will differ 
because there are different coordinates in each .tpr file.  If you use gmx 
convert-tpr to simply change the number of steps (much easier and cleaner!) then 
the coordinates are always the same, only the number of steps differs, so the 
.tpr files are not substantively different for the purposes of analysis.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] How to concatenate tpr files?

2017-01-23 Thread leila karami 
Dear gromacs users,

About the concatenation trajectory files, I have a question.

I did 10 MD simulations (each section 10 ns). Now, I want to concatenate
all of the trajectories and determine RMSD on whole trajectory. To do this,
I used the following command:

gmx trjcat -f md1.trr md2.trr md3.trr md4.trr md5.trr md6.trr md7.trr
md8.trr md9.trr md10.trr -o all_md.xtc –settime

The whole trajectory file made correctly. To determined RMSD, I used the
following command.

gmx  rms  -f  all_md.xtc  -s  *.tpr  -n index.ndx  -o rmsd.xvg  -tu  ns

I want to know, which tpr file must be used? tpr1 or tpr2 or tpr3 or …?

I tried this command with md1.tpr and md10.tpr and in each time, RMSD had
the different values. So, should I concatenate the tpr files and use the
complete tpr file.

How can I concatenate the tpr files?

Best
-- 
Gromacs Users mailing list

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http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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