[gmx-users] PMF on dihedral
Hi I would like to perform calculations of potential of mean force on a dihedral angle. But it seems that all the options are parametrized for a PMF calculation on a distance. This question has been already posted 4 years ago (http://www.mail-archive.com/gmx-users@gromacs.org/msg00384.html) without any answer. I hope that somebody will be able to help me. Thanks, Landry -- 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] ffyw3f library not found..
Dear users I am trying to install Gromacs-4.5 with fftw-3.2.2 in Fedora version 9, when I am trying to install the Groamcs after installing fftw it is giving me an error that ftwf library not found. Please hep me. -- Regards Kamalesh Roy -- 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] ffyw3f library not found..
Kamalesh Roy wrote: Dear users I am trying to install Gromacs-4.5 with fftw-3.2.2 in Fedora version 9, when I am trying to install the Groamcs after installing fftw it is giving me an error that ftwf library not found. Please hep me. At the very least you need to provide us with the command you gave. Detailed installation instructions are available on the Gromacs site: http://www.gromacs.org/index.php?title=Download_%26_Installation/Installation_Instructions -Justin -- Regards Kamalesh Roy -- 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
Re: [gmx-users] ffyw3f library not found..
On 09/23/2010 12:27 PM, Kamalesh Roy wrote: > Dear users > > I am trying to install Gromacs-4.5 with fftw-3.2.2 in Fedora version 9, > when I am trying to install the Groamcs > after installing fftw it is giving me an error that ftwf library not found. > > Please hep me. > > -- > Regards > Kamalesh Roy > Same problem here. Using: ./configure --prefix=/bgp/userinternal/cin0644a/gromacs \ --enable-ppc-sqrt \ --disable-ppc-altivec \ --with-fft=fftw3 \ --without-x \ CFLAGS="-O3 -qarch=auto -qtune=auto" \ CC="xlc_r -q64" \ CXX="xlC_r -q64" \ CXXFLAGS="-O3 -qarch=auto -qtune=auto" \ CPPFLAGS="-I/bgp/userinternal/cin0644a/fftwlibs/include" \ F77="xlf_r -q64" \ FFLAGS="-O3 -qnoprefetch -qarch=auto -qtune=auto" \ LDFLAGS="-L/bgp/userinternal/cin0644a/fftwlibs/lib" is fine with 4.0.7 but it generates checking for main in -lfftw3f... no configure: error: Cannot find fftw3f library in 4.5.1 I successfully installed 4.5.1 only using the --with-fft=fftpack Fabio -- * Fabio Affinito, PhD CINECA InterUniversity Computer Center Via Magnanelli, 6/3 Casalecchio di Reno (Bologna) ITALY +39/051/6171794 (Phone) e-mail: f.affin...@cineca.it -- 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] ffyw3f library not found..
Fabio Affinito wrote: On 09/23/2010 12:27 PM, Kamalesh Roy wrote: Dear users I am trying to install Gromacs-4.5 with fftw-3.2.2 in Fedora version 9, when I am trying to install the Groamcs after installing fftw it is giving me an error that ftwf library not found. Please hep me. -- Regards Kamalesh Roy Same problem here. Using: ./configure --prefix=/bgp/userinternal/cin0644a/gromacs \ --enable-ppc-sqrt \ --disable-ppc-altivec \ --with-fft=fftw3 \ --without-x \ CFLAGS="-O3 -qarch=auto -qtune=auto" \ CC="xlc_r -q64" \ CXX="xlC_r -q64" \ CXXFLAGS="-O3 -qarch=auto -qtune=auto" \ CPPFLAGS="-I/bgp/userinternal/cin0644a/fftwlibs/include" \ F77="xlf_r -q64" \ FFLAGS="-O3 -qnoprefetch -qarch=auto -qtune=auto" \ LDFLAGS="-L/bgp/userinternal/cin0644a/fftwlibs/lib" is fine with 4.0.7 but it generates checking for main in -lfftw3f... no configure: error: Cannot find fftw3f library in 4.5.1 Did you install floating-point or double-precision libraries? In this case, it appears that you've at least set LDFLAGS correctly, now the issue is whether or not you've got a precision mismatch. -Justin I successfully installed 4.5.1 only using the --with-fft=fftpack Fabio -- 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
Re: [gmx-users] ffyw3f library not found..
- Original Message - From: Fabio Affinito Date: Thursday, September 23, 2010 20:54 Subject: Re: [gmx-users] ffyw3f library not found.. To: Discussion list for GROMACS users > On 09/23/2010 12:27 PM, Kamalesh Roy wrote: > > Dear users > > > > I am trying to install Gromacs-4.5 with fftw-3.2.2 in > Fedora version 9, > > when I am trying to install the Groamcs > > after installing fftw it is giving me an error that ftwf > library not found. > > > > Please hep me. > > > > -- > > Regards > > Kamalesh Roy > > > > Same problem here. > Using: > ./configure --prefix=/bgp/userinternal/cin0644a/gromacs \ > --enable-ppc-sqrt \ > --disable-ppc-altivec \ > --with-fft=fftw3 \ > --without-x \ > CFLAGS="-O3 -qarch=auto -qtune=auto" \ > CC="xlc_r -q64" \ > CXX="xlC_r -q64" \ > CXXFLAGS="-O3 -qarch=auto -qtune=auto" \ > CPPFLAGS="-I/bgp/userinternal/cin0644a/fftwlibs/include" \ > F77="xlf_r -q64" \ > FFLAGS="-O3 -qnoprefetch -qarch=auto -qtune=auto" \ > LDFLAGS="-L/bgp/userinternal/cin0644a/fftwlibs/lib" > is fine with 4.0.7 but it generates > checking for main in -lfftw3f... no > configure: error: Cannot find fftw3f library > in 4.5.1 > > I successfully installed 4.5.1 only using the --with-fft=fftpack Don't use that, it will be diabolically slow for PME simulations! Unfortunately, the BlueGene-specific GROMACS installation instructions didn't have the clue that the precision of GROMACS and FFTW has to match. It does now. Presumably both you and the original poster need to install a single-precision copy of FFTW, or configure a double-precision version of GROMACS (if you know you need double precision, or don't mind your simulation being much slower). Mark -- 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] Getting started - Peptide
Dear Gromacs Users, I'm a freshman and would like to lear how to use GROMACS in my research starting from tutorial. I've just installed the newest version and try to repeat all of the steps from the chapter that describes the preparation of Ribonuclease A to MD simulation. In my case it is not possible, unfortunatelly. The grompp program crashes such a way: --- Program grompp, VERSION 4.5.1 Source code file: toppush.c, line: 1987 Fatal error: No such moleculetype SOL For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I tried to install GROMACS on other machine with different Linux distribution but the error in grompp was the same. What is important, I installed version 4.0.7 and it works well! I don't have any idea what is going on. Does anyone have a similar problem? Regards, Artur -- 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] GROMACS 4.5.1 and MPI
Hi, I have some questions about installation of GROMACS with MPI. Our system administrator has installed the 4.5.1 version in our system. When I tested the software with "openmpi/openmpi-1.3.3-gcc/bin/mpirun" with mdrun_mpi, I got all sorts of error message such as "opt/apps/gromacs/gromacs-4.5.1-mpi/bin/mdrun_mpi: Symbol `ompi_mpi_byte' has different size in shared object, consider re-linking", and many others. My questions: 1. When I prepare my system for simulations, do I have to consistently use *_mpi functions in gromacs_4.5.1_mpi directory? 2. Are there any details that I need to pay attention when I configure the software with openmpi? Thanks for your help in advance. Best, Simon -- 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 Pirzadeh
> >>> 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] GROMACS 4.5.1 and MPI
simon sham wrote: Hi, I have some questions about installation of GROMACS with MPI. Our system administrator has installed the 4.5.1 version in our system. When I tested the software with "openmpi/openmpi-1.3.3-gcc/bin/mpirun" with mdrun_mpi, I got all sorts of error message such as "opt/apps/gromacs/gromacs-4.5.1-mpi/bin/mdrun_mpi: Symbol `ompi_mpi_byte' has different size in shared object, consider re-linking", and many others. The error message suggests that perhaps a different version of the MPI implementation was used to compile the code. Find out from your admin how Gromacs was built. My questions: 1. When I prepare my system for simulations, do I have to consistently use *_mpi functions in gromacs_4.5.1_mpi directory? No, as a matter of fact, none of the other Gromacs utilities are MPI-aware. -Justin 2. Are there any details that I need to pay attention when I configure the software with openmpi? Thanks for your help in advance. Best, Simon -- 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
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 Pirzadeh
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 Pirzadeh
> > 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
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 Pirzadeh
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] Getting started - Peptide
On September 23, 2010 at 3:02 PM Artur Panczakiewicz wrote: > Dear Gromacs Users, > > I'm a freshman and would like to lear how to use GROMACS in my > research starting from tutorial. I've just installed the newest > version and try to repeat all of the steps from the chapter that > describes the preparation of Ribonuclease A to MD simulation. In my > case it is not possible, unfortunatelly. The grompp program crashes > such a way: > > --- > Program grompp, VERSION 4.5.1 > Source code file: toppush.c, line: 1987 > > Fatal error: > No such moleculetype SOL > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > --- This usually means you have "SOL" coupled to a temperature, and if you don't have SOL in your system/.top/.gro you will get this error. This coupling is in the .mdp file. If you are running the system in a vacuum you must remove the SOL from the mdp file. If you want some kind of SOL (SPC, TIP3P, etc), you must add this in by making a box with solvent in it. The tutorial will most likely have this in it. > > I tried to install GROMACS on other machine with different Linux > distribution but the error in grompp was the same. > What is important, I installed version 4.0.7 and it works well! I > don't have any idea what is going on. > Does anyone have a similar problem? > > Regards, > Artur > -- > gmx-users mailing list gmx-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 > TJ Mustard Email: musta...@onid.orst.edu -- 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
