Re: [gmx-users] Re: rotational correlation function
OK, To summurize:
1. I calculate the Ctot(t) with g_rotacf using N-H index files.
2. Use trjconv to get a trajectory of internal motions.
= How I get the Cint(t)???
3. Crot = Ctot/Cint
But, is there any way to calculate the Crot(t) directly? Is trjconv the
solution again?
regards,
Paymon
On Thu, 2010-09-23 at 20:40 +0200, David van der Spoel wrote:
On 2010-09-23 20.38, Paymon Pirzadeh wrote:
Great tips and advices. I appreciate your attention.
But, what would the g_rms -fit rot+trans do?
compute the rmsd. something different. I said trjconv.
Paymon
On Thu, 2010-09-23 at 20:07 +0200, David van der Spoel wrote:
On 2010-09-23 18.14, Paymon Pirzadeh wrote:
Dear Dr. van der Spoel,
Thanks a lot for your clarification. But some questions yet:
1. If I do not provide the -aver option, will the program calculate
the C(t) for individual N-H bond?
Yes.
2. In a paper that I just read, JCP vol. 131 155103 (2009), they claim
they have calculated the Ctot(t) which could be factorized into
rotational and internal components, Ctot(t)=Crot(t)*Cint(t). I assume
g_rotacf gives the rotational part. How one can calculate the Ctot(t)
(they claim they calculatetd the Ctot and Crot with GROMACS utilities)?
How can we generate the rotation matrix (omega(t)) and use it? What's
the use of -fitfn? Is it sth that could be done in other data
processing softwares?
If your sim is long enough (10-20 times the rotation time, which for a
small protein is on the order of a couple of ns) you can fit all the
individual NH -acfs to two exponentials, 1 for the NH relaxation and one
for the overall.
3. How can we generate a trajectory with no internal motions? Does it
have anything to do with g_rms?
You can do the reverse by fitting trjconv -fit rot+trans this will give
you a protein with no overall rotation+translation from which you can
derive the order parameters and relaxation times of individual NH vectors.
Check this ref too:
@Article{Villa2006a,
author = {A. Villa and G. Stock},
title = {What NMR relaxation can tell us about the internal motion
of an RNA
hairpin: A molecular dynamics simulation study},
journal = {J. Chem. Theory Comput.},
volume = {2},
year= {2006},
pages = {1228-1236},
}
Sorry for mass of questions.
Regards,
Paymon
On Thu, 2010-09-23 at 08:20 +0200, David van der Spoel wrote:
On 2010-09-23 01.27, Paymon Pirzadeh wrote:
Dear Dr. Chaban,
I meant the N-H bond vectors of protein backbone for calculation of
rotational time correlation function to calculate the rotational
diffusion constant of my protein. I need a protocol which walks me step
by step through the procedure.
Thanks for your Attention.
define all NH bonds in an index file as
[ NH ]
5 6
10 11
23 24
etc.
Then run g_rotacf -P 2 [ more flags ] -aver
Analyze the ACF to extract the order parameters.
You will need to read Lipari Szabo papers:
@Article{ Lipari82a,
author = G. Lipari and A. Szabo and R. M. Levy,
title =Protein Dynamics and {NMR} relaxation: comparison of
simulations with experiment,
journal = BTnature,
year = 1982,
volume = 300,
pages =197-198
}
@Article{ Lipari82b,
author = G. Lipari and A. Szabo,
title =Model-Free Approach to the Interpretation of Nuclear
Magnetic Resonance Relaxation in
Macromolecules. 1. Theory and Range of Validity,
journal = BTjacs,
year = 1982,
volume = 104,
pages =4546-4559
}
Paymon
On Wed, 2010-09-22 at 19:03 -0400, Vitaly Chaban wrote:
Message: 2
Date: Wed, 22 Sep 2010 12:07:27 -0600
From: Paymon Pirzadehppirz...@ucalgary.ca
Subject: [gmx-users] rotational correlation function
To: gmx-users@gromacs.org
Message-ID:1285178847.11669.66.ca...@paymon-desktop
Content-Type: text/plain
Hello,
Imagine if the total correlation function of a protein could be
factorized into rotational and internal portions:
Ctot(t)=Crot(t)*Cint(t). With which commands I can calculate the
Ctot(t)
and with which I can get the Crot(t)? Does g_rotacf produce the
Crot(t)?
What does the g_rms -fit do? I am confused on how I can use gromacs
commands on my output files. Sorry for mass of e-mails.
Paymon
Hey, Paymon -
Do you mean the correlation function of the velocity (VACF)? Why not
to use g_velacc and g_rotacf for translational and rotational VACFs? I
suppose, your molecule is rigid (enough) for rotational velocoty to
make sense.
--
Dr. Vitaly V. Chaban
Department of Chemistry
University of Rochester
Rochester, NY 14627-0216
United States of America
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell
Re: [gmx-users] Re: rotational correlation function
On 2010-09-23 21.10, Paymon Pirzadeh wrote:
OK, To summurize:
1. I calculate the Ctot(t) with g_rotacf using N-H index files.
2. Use trjconv to get a trajectory of internal motions.
= How I get the Cint(t)???
3. Crot = Ctot/Cint
But, is there any way to calculate the Crot(t) directly? Is trjconv the
solution again?
No and no.
Maybe when you use the -debug option to trjconv it spits out the
rotation matrix but I'm not sure.
Anyway you need to start trying things out from here.
regards,
Paymon
On Thu, 2010-09-23 at 20:40 +0200, David van der Spoel wrote:
On 2010-09-23 20.38, Paymon Pirzadeh wrote:
Great tips and advices. I appreciate your attention.
But, what would the g_rms -fit rot+trans do?
compute the rmsd. something different. I said trjconv.
Paymon
On Thu, 2010-09-23 at 20:07 +0200, David van der Spoel wrote:
On 2010-09-23 18.14, Paymon Pirzadeh wrote:
Dear Dr. van der Spoel,
Thanks a lot for your clarification. But some questions yet:
1. If I do not provide the -aver option, will the program calculate
the C(t) for individual N-H bond?
Yes.
2. In a paper that I just read, JCP vol. 131 155103 (2009), they claim
they have calculated the Ctot(t) which could be factorized into
rotational and internal components, Ctot(t)=Crot(t)*Cint(t). I assume
g_rotacf gives the rotational part. How one can calculate the Ctot(t)
(they claim they calculatetd the Ctot and Crot with GROMACS utilities)?
How can we generate the rotation matrix (omega(t)) and use it? What's
the use of -fitfn? Is it sth that could be done in other data
processing softwares?
If your sim is long enough (10-20 times the rotation time, which for a
small protein is on the order of a couple of ns) you can fit all the
individual NH -acfs to two exponentials, 1 for the NH relaxation and one
for the overall.
3. How can we generate a trajectory with no internal motions? Does it
have anything to do with g_rms?
You can do the reverse by fitting trjconv -fit rot+trans this will give
you a protein with no overall rotation+translation from which you can
derive the order parameters and relaxation times of individual NH vectors.
Check this ref too:
@Article{Villa2006a,
author = {A. Villa and G. Stock},
title = {What NMR relaxation can tell us about the internal motion
of an RNA
hairpin: A molecular dynamics simulation study},
journal = {J. Chem. Theory Comput.},
volume = {2},
year= {2006},
pages = {1228-1236},
}
Sorry for mass of questions.
Regards,
Paymon
On Thu, 2010-09-23 at 08:20 +0200, David van der Spoel wrote:
On 2010-09-23 01.27, Paymon Pirzadeh wrote:
Dear Dr. Chaban,
I meant the N-H bond vectors of protein backbone for calculation of
rotational time correlation function to calculate the rotational
diffusion constant of my protein. I need a protocol which walks me step
by step through the procedure.
Thanks for your Attention.
define all NH bonds in an index file as
[ NH ]
5 6
10 11
23 24
etc.
Then run g_rotacf -P 2 [ more flags ] -aver
Analyze the ACF to extract the order parameters.
You will need to read LipariSzabo papers:
@Article{ Lipari82a,
author = G. Lipari and A. Szabo and R. M. Levy,
title =Protein Dynamics and {NMR} relaxation: comparison of
simulations with experiment,
journal = BTnature,
year = 1982,
volume = 300,
pages =197-198
}
@Article{ Lipari82b,
author = G. Lipari and A. Szabo,
title =Model-Free Approach to the Interpretation of Nuclear
Magnetic Resonance Relaxation in
Macromolecules. 1. Theory and Range of Validity,
journal = BTjacs,
year = 1982,
volume = 104,
pages =4546-4559
}
Paymon
On Wed, 2010-09-22 at 19:03 -0400, Vitaly Chaban wrote:
Message: 2
Date: Wed, 22 Sep 2010 12:07:27 -0600
From: Paymon Pirzadehppirz...@ucalgary.ca
Subject: [gmx-users] rotational correlation function
To: gmx-users@gromacs.org
Message-ID:1285178847.11669.66.ca...@paymon-desktop
Content-Type: text/plain
Hello,
Imagine if the total correlation function of a protein could be
factorized into rotational and internal portions:
Ctot(t)=Crot(t)*Cint(t). With which commands I can calculate the Ctot(t)
and with which I can get the Crot(t)? Does g_rotacf produce the Crot(t)?
What does the g_rms -fit do? I am confused on how I can use gromacs
commands on my output files. Sorry for mass of e-mails.
Paymon
Hey, Paymon -
Do you mean the correlation function of the velocity (VACF)? Why not
to use g_velacc and g_rotacf for translational and rotational VACFs? I
suppose, your molecule is rigid (enough) for rotational velocoty to
make sense.
--
Dr. Vitaly V. Chaban
Department of Chemistry
University of Rochester
Rochester, NY 14627-0216
United States of America
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell
Re: [gmx-users] Re: rotational correlation function
On 2010-09-23 01.27, Paymon Pirzadeh wrote:
Dear Dr. Chaban,
I meant the N-H bond vectors of protein backbone for calculation of
rotational time correlation function to calculate the rotational
diffusion constant of my protein. I need a protocol which walks me step
by step through the procedure.
Thanks for your Attention.
define all NH bonds in an index file as
[ NH ]
5 6
10 11
23 24
etc.
Then run g_rotacf -P 2 [ more flags ] -aver
Analyze the ACF to extract the order parameters.
You will need to read Lipari Szabo papers:
@Article{ Lipari82a,
author = G. Lipari and A. Szabo and R. M. Levy,
title =Protein Dynamics and {NMR} relaxation: comparison of
simulations with experiment,
journal = BTnature,
year = 1982,
volume = 300,
pages =197-198
}
@Article{ Lipari82b,
author = G. Lipari and A. Szabo,
title =Model-Free Approach to the Interpretation of Nuclear
Magnetic Resonance Relaxation in
Macromolecules. 1. Theory and Range of Validity,
journal = BTjacs,
year = 1982,
volume = 104,
pages =4546-4559
}
Paymon
On Wed, 2010-09-22 at 19:03 -0400, Vitaly Chaban wrote:
Message: 2
Date: Wed, 22 Sep 2010 12:07:27 -0600
From: Paymon Pirzadehppirz...@ucalgary.ca
Subject: [gmx-users] rotational correlation function
To: gmx-users@gromacs.org
Message-ID:1285178847.11669.66.ca...@paymon-desktop
Content-Type: text/plain
Hello,
Imagine if the total correlation function of a protein could be
factorized into rotational and internal portions:
Ctot(t)=Crot(t)*Cint(t). With which commands I can calculate the Ctot(t)
and with which I can get the Crot(t)? Does g_rotacf produce the Crot(t)?
What does the g_rms -fit do? I am confused on how I can use gromacs
commands on my output files. Sorry for mass of e-mails.
Paymon
Hey, Paymon -
Do you mean the correlation function of the velocity (VACF)? Why not
to use g_velacc and g_rotacf for translational and rotational VACFs? I
suppose, your molecule is rigid (enough) for rotational velocoty to
make sense.
--
Dr. Vitaly V. Chaban
Department of Chemistry
University of Rochester
Rochester, NY 14627-0216
United States of America
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
--
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] Re: rotational correlation function
Dear Dr. van der Spoel,
Thanks a lot for your clarification. But some questions yet:
1. If I do not provide the -aver option, will the program calculate
the C(t) for individual N-H bond?
2. In a paper that I just read, JCP vol. 131 155103 (2009), they claim
they have calculated the Ctot(t) which could be factorized into
rotational and internal components, Ctot(t)=Crot(t)*Cint(t). I assume
g_rotacf gives the rotational part. How one can calculate the Ctot(t)
(they claim they calculatetd the Ctot and Crot with GROMACS utilities)?
How can we generate the rotation matrix (omega(t)) and use it? What's
the use of -fitfn? Is it sth that could be done in other data
processing softwares?
3. How can we generate a trajectory with no internal motions? Does it
have anything to do with g_rms?
Sorry for mass of questions.
Regards,
Paymon
On Thu, 2010-09-23 at 08:20 +0200, David van der Spoel wrote:
On 2010-09-23 01.27, Paymon Pirzadeh wrote:
Dear Dr. Chaban,
I meant the N-H bond vectors of protein backbone for calculation of
rotational time correlation function to calculate the rotational
diffusion constant of my protein. I need a protocol which walks me step
by step through the procedure.
Thanks for your Attention.
define all NH bonds in an index file as
[ NH ]
5 6
10 11
23 24
etc.
Then run g_rotacf -P 2 [ more flags ] -aver
Analyze the ACF to extract the order parameters.
You will need to read Lipari Szabo papers:
@Article{ Lipari82a,
author = G. Lipari and A. Szabo and R. M. Levy,
title =Protein Dynamics and {NMR} relaxation: comparison of
simulations with experiment,
journal = BTnature,
year = 1982,
volume = 300,
pages =197-198
}
@Article{ Lipari82b,
author = G. Lipari and A. Szabo,
title =Model-Free Approach to the Interpretation of Nuclear
Magnetic Resonance Relaxation in
Macromolecules. 1. Theory and Range of Validity,
journal = BTjacs,
year = 1982,
volume = 104,
pages =4546-4559
}
Paymon
On Wed, 2010-09-22 at 19:03 -0400, Vitaly Chaban wrote:
Message: 2
Date: Wed, 22 Sep 2010 12:07:27 -0600
From: Paymon Pirzadehppirz...@ucalgary.ca
Subject: [gmx-users] rotational correlation function
To: gmx-users@gromacs.org
Message-ID:1285178847.11669.66.ca...@paymon-desktop
Content-Type: text/plain
Hello,
Imagine if the total correlation function of a protein could be
factorized into rotational and internal portions:
Ctot(t)=Crot(t)*Cint(t). With which commands I can calculate the Ctot(t)
and with which I can get the Crot(t)? Does g_rotacf produce the Crot(t)?
What does the g_rms -fit do? I am confused on how I can use gromacs
commands on my output files. Sorry for mass of e-mails.
Paymon
Hey, Paymon -
Do you mean the correlation function of the velocity (VACF)? Why not
to use g_velacc and g_rotacf for translational and rotational VACFs? I
suppose, your molecule is rigid (enough) for rotational velocoty to
make sense.
--
Dr. Vitaly V. Chaban
Department of Chemistry
University of Rochester
Rochester, NY 14627-0216
United States of America
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:+46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
--
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] Re: rotational correlation function
On 2010-09-23 18.14, Paymon Pirzadeh wrote:
Dear Dr. van der Spoel,
Thanks a lot for your clarification. But some questions yet:
1. If I do not provide the -aver option, will the program calculate
the C(t) for individual N-H bond?
Yes.
2. In a paper that I just read, JCP vol. 131 155103 (2009), they claim
they have calculated the Ctot(t) which could be factorized into
rotational and internal components, Ctot(t)=Crot(t)*Cint(t). I assume
g_rotacf gives the rotational part. How one can calculate the Ctot(t)
(they claim they calculatetd the Ctot and Crot with GROMACS utilities)?
How can we generate the rotation matrix (omega(t)) and use it? What's
the use of -fitfn? Is it sth that could be done in other data
processing softwares?
If your sim is long enough (10-20 times the rotation time, which for a
small protein is on the order of a couple of ns) you can fit all the
individual NH -acfs to two exponentials, 1 for the NH relaxation and one
for the overall.
3. How can we generate a trajectory with no internal motions? Does it
have anything to do with g_rms?
You can do the reverse by fitting trjconv -fit rot+trans this will give
you a protein with no overall rotation+translation from which you can
derive the order parameters and relaxation times of individual NH vectors.
Check this ref too:
@Article{Villa2006a,
author = {A. Villa and G. Stock},
title = {What NMR relaxation can tell us about the internal motion
of an RNA
hairpin: A molecular dynamics simulation study},
journal = {J. Chem. Theory Comput.},
volume = {2},
year= {2006},
pages = {1228-1236},
}
Sorry for mass of questions.
Regards,
Paymon
On Thu, 2010-09-23 at 08:20 +0200, David van der Spoel wrote:
On 2010-09-23 01.27, Paymon Pirzadeh wrote:
Dear Dr. Chaban,
I meant the N-H bond vectors of protein backbone for calculation of
rotational time correlation function to calculate the rotational
diffusion constant of my protein. I need a protocol which walks me step
by step through the procedure.
Thanks for your Attention.
define all NH bonds in an index file as
[ NH ]
5 6
10 11
23 24
etc.
Then run g_rotacf -P 2 [ more flags ] -aver
Analyze the ACF to extract the order parameters.
You will need to read Lipari Szabo papers:
@Article{ Lipari82a,
author = G. Lipari and A. Szabo and R. M. Levy,
title =Protein Dynamics and {NMR} relaxation: comparison of
simulations with experiment,
journal = BTnature,
year = 1982,
volume = 300,
pages =197-198
}
@Article{ Lipari82b,
author = G. Lipari and A. Szabo,
title =Model-Free Approach to the Interpretation of Nuclear
Magnetic Resonance Relaxation in
Macromolecules. 1. Theory and Range of Validity,
journal = BTjacs,
year = 1982,
volume = 104,
pages =4546-4559
}
Paymon
On Wed, 2010-09-22 at 19:03 -0400, Vitaly Chaban wrote:
Message: 2
Date: Wed, 22 Sep 2010 12:07:27 -0600
From: Paymon Pirzadehppirz...@ucalgary.ca
Subject: [gmx-users] rotational correlation function
To: gmx-users@gromacs.org
Message-ID:1285178847.11669.66.ca...@paymon-desktop
Content-Type: text/plain
Hello,
Imagine if the total correlation function of a protein could be
factorized into rotational and internal portions:
Ctot(t)=Crot(t)*Cint(t). With which commands I can calculate the Ctot(t)
and with which I can get the Crot(t)? Does g_rotacf produce the Crot(t)?
What does the g_rms -fit do? I am confused on how I can use gromacs
commands on my output files. Sorry for mass of e-mails.
Paymon
Hey, Paymon -
Do you mean the correlation function of the velocity (VACF)? Why not
to use g_velacc and g_rotacf for translational and rotational VACFs? I
suppose, your molecule is rigid (enough) for rotational velocoty to
make sense.
--
Dr. Vitaly V. Chaban
Department of Chemistry
University of Rochester
Rochester, NY 14627-0216
United States of America
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
--
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] Re: rotational correlation function
Great tips and advices. I appreciate your attention.
But, what would the g_rms -fit rot+trans do?
Paymon
On Thu, 2010-09-23 at 20:07 +0200, David van der Spoel wrote:
On 2010-09-23 18.14, Paymon Pirzadeh wrote:
Dear Dr. van der Spoel,
Thanks a lot for your clarification. But some questions yet:
1. If I do not provide the -aver option, will the program calculate
the C(t) for individual N-H bond?
Yes.
2. In a paper that I just read, JCP vol. 131 155103 (2009), they claim
they have calculated the Ctot(t) which could be factorized into
rotational and internal components, Ctot(t)=Crot(t)*Cint(t). I assume
g_rotacf gives the rotational part. How one can calculate the Ctot(t)
(they claim they calculatetd the Ctot and Crot with GROMACS utilities)?
How can we generate the rotation matrix (omega(t)) and use it? What's
the use of -fitfn? Is it sth that could be done in other data
processing softwares?
If your sim is long enough (10-20 times the rotation time, which for a
small protein is on the order of a couple of ns) you can fit all the
individual NH -acfs to two exponentials, 1 for the NH relaxation and one
for the overall.
3. How can we generate a trajectory with no internal motions? Does it
have anything to do with g_rms?
You can do the reverse by fitting trjconv -fit rot+trans this will give
you a protein with no overall rotation+translation from which you can
derive the order parameters and relaxation times of individual NH vectors.
Check this ref too:
@Article{Villa2006a,
author = {A. Villa and G. Stock},
title = {What NMR relaxation can tell us about the internal motion
of an RNA
hairpin: A molecular dynamics simulation study},
journal = {J. Chem. Theory Comput.},
volume = {2},
year= {2006},
pages = {1228-1236},
}
Sorry for mass of questions.
Regards,
Paymon
On Thu, 2010-09-23 at 08:20 +0200, David van der Spoel wrote:
On 2010-09-23 01.27, Paymon Pirzadeh wrote:
Dear Dr. Chaban,
I meant the N-H bond vectors of protein backbone for calculation of
rotational time correlation function to calculate the rotational
diffusion constant of my protein. I need a protocol which walks me step
by step through the procedure.
Thanks for your Attention.
define all NH bonds in an index file as
[ NH ]
5 6
10 11
23 24
etc.
Then run g_rotacf -P 2 [ more flags ] -aver
Analyze the ACF to extract the order parameters.
You will need to read Lipari Szabo papers:
@Article{ Lipari82a,
author = G. Lipari and A. Szabo and R. M. Levy,
title =Protein Dynamics and {NMR} relaxation: comparison of
simulations with experiment,
journal = BTnature,
year = 1982,
volume = 300,
pages =197-198
}
@Article{ Lipari82b,
author = G. Lipari and A. Szabo,
title =Model-Free Approach to the Interpretation of Nuclear
Magnetic Resonance Relaxation in
Macromolecules. 1. Theory and Range of Validity,
journal = BTjacs,
year = 1982,
volume = 104,
pages =4546-4559
}
Paymon
On Wed, 2010-09-22 at 19:03 -0400, Vitaly Chaban wrote:
Message: 2
Date: Wed, 22 Sep 2010 12:07:27 -0600
From: Paymon Pirzadehppirz...@ucalgary.ca
Subject: [gmx-users] rotational correlation function
To: gmx-users@gromacs.org
Message-ID:1285178847.11669.66.ca...@paymon-desktop
Content-Type: text/plain
Hello,
Imagine if the total correlation function of a protein could be
factorized into rotational and internal portions:
Ctot(t)=Crot(t)*Cint(t). With which commands I can calculate the Ctot(t)
and with which I can get the Crot(t)? Does g_rotacf produce the Crot(t)?
What does the g_rms -fit do? I am confused on how I can use gromacs
commands on my output files. Sorry for mass of e-mails.
Paymon
Hey, Paymon -
Do you mean the correlation function of the velocity (VACF)? Why not
to use g_velacc and g_rotacf for translational and rotational VACFs? I
suppose, your molecule is rigid (enough) for rotational velocoty to
make sense.
--
Dr. Vitaly V. Chaban
Department of Chemistry
University of Rochester
Rochester, NY 14627-0216
United States of America
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:+46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
--
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Re: [gmx-users] Re: rotational correlation function
On 2010-09-23 20.38, Paymon Pirzadeh wrote:
Great tips and advices. I appreciate your attention.
But, what would the g_rms -fit rot+trans do?
compute the rmsd. something different. I said trjconv.
Paymon
On Thu, 2010-09-23 at 20:07 +0200, David van der Spoel wrote:
On 2010-09-23 18.14, Paymon Pirzadeh wrote:
Dear Dr. van der Spoel,
Thanks a lot for your clarification. But some questions yet:
1. If I do not provide the -aver option, will the program calculate
the C(t) for individual N-H bond?
Yes.
2. In a paper that I just read, JCP vol. 131 155103 (2009), they claim
they have calculated the Ctot(t) which could be factorized into
rotational and internal components, Ctot(t)=Crot(t)*Cint(t). I assume
g_rotacf gives the rotational part. How one can calculate the Ctot(t)
(they claim they calculatetd the Ctot and Crot with GROMACS utilities)?
How can we generate the rotation matrix (omega(t)) and use it? What's
the use of -fitfn? Is it sth that could be done in other data
processing softwares?
If your sim is long enough (10-20 times the rotation time, which for a
small protein is on the order of a couple of ns) you can fit all the
individual NH -acfs to two exponentials, 1 for the NH relaxation and one
for the overall.
3. How can we generate a trajectory with no internal motions? Does it
have anything to do with g_rms?
You can do the reverse by fitting trjconv -fit rot+trans this will give
you a protein with no overall rotation+translation from which you can
derive the order parameters and relaxation times of individual NH vectors.
Check this ref too:
@Article{Villa2006a,
author = {A. Villa and G. Stock},
title = {What NMR relaxation can tell us about the internal motion
of an RNA
hairpin: A molecular dynamics simulation study},
journal = {J. Chem. Theory Comput.},
volume = {2},
year= {2006},
pages = {1228-1236},
}
Sorry for mass of questions.
Regards,
Paymon
On Thu, 2010-09-23 at 08:20 +0200, David van der Spoel wrote:
On 2010-09-23 01.27, Paymon Pirzadeh wrote:
Dear Dr. Chaban,
I meant the N-H bond vectors of protein backbone for calculation of
rotational time correlation function to calculate the rotational
diffusion constant of my protein. I need a protocol which walks me step
by step through the procedure.
Thanks for your Attention.
define all NH bonds in an index file as
[ NH ]
5 6
10 11
23 24
etc.
Then run g_rotacf -P 2 [ more flags ] -aver
Analyze the ACF to extract the order parameters.
You will need to read Lipari Szabo papers:
@Article{ Lipari82a,
author = G. Lipari and A. Szabo and R. M. Levy,
title =Protein Dynamics and {NMR} relaxation: comparison of
simulations with experiment,
journal = BTnature,
year = 1982,
volume = 300,
pages =197-198
}
@Article{ Lipari82b,
author = G. Lipari and A. Szabo,
title =Model-Free Approach to the Interpretation of Nuclear
Magnetic Resonance Relaxation in
Macromolecules. 1. Theory and Range of Validity,
journal = BTjacs,
year = 1982,
volume = 104,
pages =4546-4559
}
Paymon
On Wed, 2010-09-22 at 19:03 -0400, Vitaly Chaban wrote:
Message: 2
Date: Wed, 22 Sep 2010 12:07:27 -0600
From: Paymon Pirzadehppirz...@ucalgary.ca
Subject: [gmx-users] rotational correlation function
To: gmx-users@gromacs.org
Message-ID:1285178847.11669.66.ca...@paymon-desktop
Content-Type: text/plain
Hello,
Imagine if the total correlation function of a protein could be
factorized into rotational and internal portions:
Ctot(t)=Crot(t)*Cint(t). With which commands I can calculate the Ctot(t)
and with which I can get the Crot(t)? Does g_rotacf produce the Crot(t)?
What does the g_rms -fit do? I am confused on how I can use gromacs
commands on my output files. Sorry for mass of e-mails.
Paymon
Hey, Paymon -
Do you mean the correlation function of the velocity (VACF)? Why not
to use g_velacc and g_rotacf for translational and rotational VACFs? I
suppose, your molecule is rigid (enough) for rotational velocoty to
make sense.
--
Dr. Vitaly V. Chaban
Department of Chemistry
University of Rochester
Rochester, NY 14627-0216
United States of America
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
--
gmx-users mailing listgmx-users@gromacs.org
Re: [gmx-users] Re: rotational correlation function
Dear Dr. Chaban, I meant the N-H bond vectors of protein backbone for calculation of rotational time correlation function to calculate the rotational diffusion constant of my protein. I need a protocol which walks me step by step through the procedure. Thanks for your Attention. Paymon On Wed, 2010-09-22 at 19:03 -0400, Vitaly Chaban wrote: Message: 2 Date: Wed, 22 Sep 2010 12:07:27 -0600 From: Paymon Pirzadeh ppirz...@ucalgary.ca Subject: [gmx-users] rotational correlation function To: gmx-users@gromacs.org Message-ID: 1285178847.11669.66.ca...@paymon-desktop Content-Type: text/plain Hello, Imagine if the total correlation function of a protein could be factorized into rotational and internal portions: Ctot(t)=Crot(t)*Cint(t). With which commands I can calculate the Ctot(t) and with which I can get the Crot(t)? Does g_rotacf produce the Crot(t)? What does the g_rms -fit do? I am confused on how I can use gromacs commands on my output files. Sorry for mass of e-mails. Paymon Hey, Paymon - Do you mean the correlation function of the velocity (VACF)? Why not to use g_velacc and g_rotacf for translational and rotational VACFs? I suppose, your molecule is rigid (enough) for rotational velocoty to make sense. -- Dr. Vitaly V. Chaban Department of Chemistry University of Rochester Rochester, NY 14627-0216 United States of America -- 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] Re: rotational correlation function
Hmm... Rotational time..? If you need diffusion constant, just use g_rotacf and then integrate the resulting VACF. If I recall correctly, you should make an index file with three numbers to define two vectors for the calculation. On Wed, Sep 22, 2010 at 7:27 PM, Paymon Pirzadeh ppirz...@ucalgary.ca wrote: Dear Dr. Chaban, I meant the N-H bond vectors of protein backbone for calculation of rotational time correlation function to calculate the rotational diffusion constant of my protein. I need a protocol which walks me step by step through the procedure. Thanks for your Attention. Paymon On Wed, 2010-09-22 at 19:03 -0400, Vitaly Chaban wrote: Message: 2 Date: Wed, 22 Sep 2010 12:07:27 -0600 From: Paymon Pirzadeh ppirz...@ucalgary.ca Subject: [gmx-users] rotational correlation function To: gmx-users@gromacs.org Message-ID: 1285178847.11669.66.ca...@paymon-desktop Content-Type: text/plain Hello, Imagine if the total correlation function of a protein could be factorized into rotational and internal portions: Ctot(t)=Crot(t)*Cint(t). With which commands I can calculate the Ctot(t) and with which I can get the Crot(t)? Does g_rotacf produce the Crot(t)? What does the g_rms -fit do? I am confused on how I can use gromacs commands on my output files. Sorry for mass of e-mails. Paymon Hey, Paymon - Do you mean the correlation function of the velocity (VACF)? Why not to use g_velacc and g_rotacf for translational and rotational VACFs? I suppose, your molecule is rigid (enough) for rotational velocoty to make sense. -- Dr. Vitaly V. Chaban Department of Chemistry University of Rochester Rochester, NY 14627-0216 United States of America -- 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
