[gmx-users] about g_sas analysis
Dear gromacs users, I have some doubts regarding the options to be selected in g_sas program. g_sas asks for two groups, first one for calculation and second one for output. As I have understood from the manual that first group should contain all non solvent groups and second one the whole or part of these groups. Now my doubt is that in a system of protein+ligand, when I am selecting both the protein and ligand in option 1 ( in the calculation group) it automatically is sending the second selected group to second option ( that is in the output group). Is the solvent accessible area given in terms of the output group in the xvg file? I want to calculate solvent accessibility of the ligand which is surrounded by the protein. Selecting what option can mimic that situation most closely? Regards Supti NIMHANS, BANGALORE -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] about g_sas analysis
supti mukherjee wrote: Dear gromacs users, I have some doubts regarding the options to be selected in g_sas program. g_sas asks for two groups, first one for calculation and second one for output. As I have understood from the manual that first group should contain all non solvent groups and second one the whole or part of these groups. Now my doubt is that in a system of protein+ligand, when I am selecting both the protein and ligand in option 1 ( in the calculation group) it automatically is sending the second selected group to second option ( that is in the output group). Is the solvent accessible area given in terms of the output group in the xvg file? I want to calculate solvent accessibility of the ligand which is surrounded by the protein. Selecting what option can mimic that situation most closely? Regards Supti NIMHANS, BANGALORE You need to create new group which contains atoms from both protein and ligand (make_ndx or by hand) and input number of this new group - the most of the programs reads only one group per input (the rest write something about selecting two groups...). Therefore the second number is read for the second input (as the group for output). About the rest of you question - I don't feel fully qualified to answer it and I hope, somebody will. Best. Milan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] about g_sas analysis
Hi, Recently there was a relatively extensive discussion on the list regarding g_sas. Check the archives. Cheers, Tsjerk On Thu, Mar 18, 2010 at 9:07 AM, Milan Melichercik wrote: > supti mukherjee wrote: >> >> Dear gromacs users, >> I have some doubts regarding the options to be selected in g_sas program. >> g_sas asks for two groups, first one for calculation and second one for >> output. As I have understood from the manual that first group should contain >> all non solvent groups and second one the whole or part of these groups. Now >> my doubt is that in a system of protein+ligand, when I am selecting both the >> protein and ligand in option 1 ( in the calculation group) it automatically >> is sending the second selected group to second option ( that is in the >> output group). Is the solvent accessible area given in terms of the output >> group in the xvg file? >> I want to calculate solvent accessibility of the ligand which is >> surrounded by the protein. Selecting what option can mimic that situation >> most closely? >> Regards >> Supti >> NIMHANS, BANGALORE >> >> >> > You need to create new group which contains atoms from both protein and > ligand (make_ndx or by hand) and input number of this new group - the most > of the programs reads only one group per input (the rest write something > about selecting two groups...). Therefore the second number is read for the > second input (as the group for output). > About the rest of you question - I don't feel fully qualified to answer it > and I hope, somebody will. > Best. > > Milan > -- > gmx-users mailing list gmx-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] query regarding normal mode analysis
hi, I am trying to do a normal mode analysis on a protein.I tried to energy minimize the structure, but was not being able to bring the Fmax less than that of the order 1.0e-03. Then I used the following ".mdp" file where I used the l-bfgs minimization method, using "cut-off" for electrostatics and Van der Waals interaction with rvdw and rcuolomb=0. define = -DFLEXIBLE constraints = none integrator = l-bfgs tinit= 0 nsteps = 15000 nbfgscorr= 50 emtol= .001 emstep = 0.1 gen_vel = yes gen-temp = 300 nstcomm = 1 ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 0 ; ns algorithm (simple or grid) ns-type = simple ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = no ; nblist cut-off rlist= 0 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = Cut-Off rcoulomb-switch = 0 rcoulomb = 0 ; Dielectric constant (DC) for cut-off or DC of reaction field epsilon-r= 1 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw-switch = 0 rvdw = 0 The Fmax went down to Maximum force = 9.67927896882578e-07 on atom 3271, after doing the energy minimization with the above parameters twice. Then I used the same parameters, (while only changing the "integrator=nm") and did the normal mode analysis. The maximum force as calculated before the NMA was Maximum force: 9.67928e-07. Thus the Fmax as calculated at the end of the energy minimization and at the start of the NMA was the same. But while going through the gromacs manual and the user mailing list archives, I have seen that the it is suggested that the van der Waals and Coulomb interactions should be calculated as switched Coulomb & van der Waals interactions; cutoffs e.g. at 1.0 nm, switched from 0.8 nm (or shifted from 0 nm). rlist at 1.2 to 1.3 Changing the parameters in nm.mdp file gives the following message:Maximum force: 2.50866e+02 Maximum force probably not small enough to ensure that you are in anenergy well. Be aware that negative eigenvalues may occur when theresulting matrix is diagonalized. If I use these parameters in the energy minimization step the Fmax does not go down. Have I done the process correctly, or should I try again to reduce the Fmax in energy minimization step using switched cuolomb and van der waals interactions and then do NMA. Any suggestion will be of great help. Thanking You, Sarbani Chattopadhyay -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] query regarding normal mode analysis
hi, I am trying to do a normal mode analysis on a protein.I tried to energy minimize the structure, but was not being able to bring the Fmax less than that of the order 1.0e-03. Then I used the following ".mdp" file where I used the l-bfgs minimization method, using "cut-off" for electrostatics and Van der Waals interaction with rvdw and rcuolomb=0. define = -DFLEXIBLE constraints = none integrator = l-bfgs tinit= 0 nsteps = 15000 nbfgscorr= 50 emtol= .001 emstep = 0.1 gen_vel = yes gen-temp = 300 nstcomm = 1 ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 0 ; ns algorithm (simple or grid) ns-type = simple ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = no ; nblist cut-off rlist= 0 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = Cut-Off rcoulomb-switch = 0 rcoulomb = 0 ; Dielectric constant (DC) for cut-off or DC of reaction field epsilon-r= 1 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw-switch = 0 rvdw = 0 The Fmax went down to Maximum force = 9.67927896882578e-07 on atom 3271, after doing the energy minimization with the above parameters twice. Then I used the same parameters, (while only changing the "integrator=nm") and did the normal mode analysis. The maximum force as calculated before the NMA was Maximum force: 9.67928e-07. Thus the Fmax as calculated at the end of the energy minimization and at the start of the NMA was the same. But while going through the gromacs manual and the user mailing list archives, I have seen that the it is suggested that the van der Waals and Coulomb interactions should be calculated as switched Coulomb & van der Waals interactions; cutoffs e.g. at 1.0 nm, switched from 0.8 nm (or shifted from 0 nm). rlist at 1.2 to 1.3 Changing the parameters in nm.mdp file gives the following message:Maximum force: 2.50866e+02 Maximum force probably not small enough to ensure that you are in anenergy well. Be aware that negative eigenvalues may occur when theresulting matrix is diagonalized. If I use these parameters in the energy minimization step the Fmax does not go down. Have I done the process correctly, or should I try again to reduce the Fmax in energy minimization step using switched cuolomb and van der waals interactions and then do NMA. Any suggestion will be of great help. Thanking You, Sarbani Chattopadhyay -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Re: script to constraint distance between ligand and protein
Hi, I don't have a version of this tool that I'm comfortable distributing at this point (for what it's worth, the message you're referring to is almost 4 years old!). You should be able to get help with your specific topology file problem on-list. Free energy calculations are one of the hardest things you can do with gromacs. I'd encourage you to start by doing some plain simulations in gromacs before trying to set up free energy calculations. The specific error you are seeing is undoubtedly because the protein in your system only contains 2591 atoms and you are trying to add restraints between some atom in the protein and atom 2606, which you think is in the ligand. For restraints to work, you need the protein and ligand to be part of the same [ atoms ] section in the topology file, so that the ligand will be numbered consecutively with the protein. (Technically, the protein and ligand must be part of the same gromacs "molecule", even though they are not connected). Again, this should go on-list. On Mar 18, 2010, at 7:48 AM, sunita gupta wrote: > Hi David > > I appologise for bothering on your personal mail id again as you have already > told me not to interrupt u personally. > > bt after going through the mailing archive > http://www.mail-archive.com/gmx-users@gromacs.org/msg03610.html, you have > suggested use of a script which can be asked off-list. > I am really new to gromacs and trying to calculate binding free energy of a > protein-ligand.. After referring through many research articles...I got to > know to add restraints on the bond, angle and dihedrals of protein and > ligand, as it is also involved in thermodynamics cycle. > > I tried to add distance restraints between a protein and ligand atom and > encountered with the following error > Fatal error: > [ file 3z.top, line 16103 ]: > Atom index (2606) in distance_restraints out of bounds (1-2591). > > Kindly send me that script which can merge the topologies for ligand and > protein, I have individual .top and .gro files for protein and ligand. > > Thanks in Advance > -- > Best Regards > SUNITA GUPTA > David Mobley dmob...@gmail.com 504-383-3662 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Re: g_desort
Dear Jennifer:
I have tried to download the package to reproduce your problem, but
have been unable.
http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Other_software
links to G_DESORT.tgz, but that link sends me to:
http://www.gromacs.org/@api/deki/files/54/=G_DESORT.tgz
with the text:
Internal Error (500)
Could not retrieve attachment fileid 109 rev 1
My memory is not perfect on g_desort because it has been a long time
since I wrote it or even used it. Gromacs version 4 uses domain
decomposition which essentially re-sorts at every neighbourlist update
and also sorts over a 3 dimensional grid (gromacs 3 with sort simply
grids on the x dimension). Therefore gromacs 4 is recommended.
If this assistance does not work, and if you still need g_desort, then
please describe how you downloaded it and I will take another look.
Regarding the error, I am not sure why the tarball contains a
Makefile, I would think that you need your own. Try this:
1. cat Makefile.i386-apple-darwin8.10.1 | sed "s/template/g_desort/g"
> Makefile.g_desort
2. Make -f Makefile.g_desort
If that doesn't work, then perhaps you have an old version of
g_desort. The first one that I uploaded was missing a semi-colon after
one of the lines in
static char *desc[] = {
at the top of main(). That was eventually fixed, but perhaps not in
the version that you obtained.
The allowance of deshuffling and not desorting was, I think,
unfortunate. I have no inside scoop on the why, but as best as I can
guess, sorting made sense and allowed a speed gain and was thus used
in benchmarking tests to evidence the fantastic speed of gromacs. The
fact that the trajectory was essentially unusable and un-resortable
was not immediately obvious to a new user. g_desort remedies this
problem, although I mention again that in gromacs 4 there is no need
for g_desort and I suggest that you migrate to gromacs 4.
Chris.
Quoting Jennifer Rendell :
Good morning, Chris.
I have just downloaded a copy of g_desort and am trying to compile it.
My C programming is way in the past. I am geting an error:
$ make -f Makefile.g_desort
cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused
-malign-double -funroll-all-loops -I/usr/local/gromacs/include/gromacs
-c -o g_desort.o g_desort.c
g_desort.c:1: error: unknown -malign-X option specified: 'double'
make: *** [g_desort.o] Error 1
I have put the tarball in
/usr/local/gromacs-3.3.2/share/gromacs/template which now contains the
files:
$ ls
Makefile.g_desort g_desort.c
Makefile.i386-apple-darwin8.10.1 template.c
README
If I edit the Makefile.g_desort and remove references to
-malign-double, then I get lots and lots of errors that start like this:
$ make -f Makefile.g_desort
cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused
-funroll-all-loops -I/usr/local/gromacs/include/gromacs -c -o
g_desort.o g_desort.c
g_desort.c:40:22: error: statutil.h: No such file or directory
g_desort.c:41:22: error: typedefs.h: No such file or directory
g_desort.c:42:21: error: smalloc.h: No such file or directory
g_desort.c:43:17: error: vec.h: No such file or directory
g_desort.c:44:22: error: copyrite.h: No such file or directory
g_desort.c:46:19: error: tpxio.h: No such file or directory
g_desort.c: In function ‘main’:
...
(271 lines in total)
So I think it needs something the -malign-double gives it. Now I'm out
of ideas... Are you able to help?
I understand the point of shuffling (distributing evenly the atoms over
N cpus) and sorting (makes more sense to distribute nearby molecules on
the same node). But why make it possible to deshuffle (with provided
index file) and not to desort (no index file, and no command)??? Must
be an historical reason...
In hope and advance appreciation, Jennifer
--
Jennifer Rendell
Dept. of Biochemistry
Memorial University of Newfoundland & Labrador
709-737-6733
--
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[gmx-users] charge group assignment with AMBER parameters
I am attempting a simulation of a drug molecule using the ffamber/gaff within gromacs. When it comes to assigning charge groups the manual says that one should group together nearby atoms and the groups should have a net integer charge. Since AMBER charge parameters are obtained from QM calculations of the specific molecule they do not form into integer charge groups like with OPLS whose charge parameters are dictated by atom type and stay the constant in different molecules. I was wondering if somebody who has worked with AMBER in GROMACS could give some guidance with regards to charge group assignment. Thanks Jake Spooner University of the Fraser Valley -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] g_covar -ref
Hi Has anyone studied the effect of using different reference structures, not the average structure, when carrying out PCA. Does it make sense to use a structure besides the average to calculate the covariance matrix? Thanks Vijaya _ Hotmail: Trusted email with powerful SPAM protection. http://clk.atdmt.com/GBL/go/210850553/direct/01/-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] g_covar -ref
Hi Does anyone studied the effect of using different reference structures, not the average structure, when carrying out PCA. Does it make sense to use a structure besides the average to calculate the covariance matrix? Thanks Vijaya _ Hotmail: Trusted email with powerful SPAM protection. http://clk.atdmt.com/GBL/go/210850553/direct/01/-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] charge group assignment with AMBER parameters
Jacob Spooner wrote: I am attempting a simulation of a drug molecule using the ffamber/gaff within gromacs. When it comes to assigning charge groups the manual says that one should group together nearby atoms and the groups should have a net integer charge. Since AMBER charge parameters are obtained from QM calculations of the specific molecule they do not form into integer charge groups like with OPLS whose charge parameters are dictated by atom type and stay the constant in different molecules. I was wondering if somebody who has worked with AMBER in GROMACS could give some guidance with regards to charge group assignment. A quick look through some of the .rtp files from the ffamber distributions indicates that, at least for amino acid and nucleic acid residues, each atom is its own charge group. That probably has something to do with the underlying theory of the force field (i.e., the derivation scheme did not use charge groups), but you can look into the literature there to be sure. -Justin Thanks Jake Spooner University of the Fraser Valley -- 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/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/mailing_lists/users.php
Re: [gmx-users] g_covar -ref
Hi Vijaya, Well, to start with that will be something as calculating the 'fluctuation' as sum((xi-ri)^2)/N, with xi and ri denoting the ith atom of the conformation x and the reference structure r and the sum is over time/observations. In the case of no variation in xi, the value you get will still be finite, in stead of zero, as would probably be most meaningful. Now for the covariances, there's a bit more to it. The covariance is the product moment of the deviations: sum((xi-ri)(xj-rj))/N. When there is no correlation, the deviations about the mean are random and average out to zero. But with the deviations against a reference, that is not the case. So the results should be regarded meaningless, unless you have a good reason for doing so, and come with a solid justification. Okay, there may be a purpose, but I'll leave that to your imagination :) Hope it helps, Tsjerk On Thu, Mar 18, 2010 at 5:33 PM, vijaya subramanian wrote: > Hi > Has anyone studied the effect of using different reference structures, > not the average structure, when carrying out PCA. Does it make sense to use > a structure besides the average to calculate the covariance matrix? > Thanks > Vijaya > > > > > Hotmail: Trusted email with powerful SPAM protection. Sign up now. > -- > gmx-users mailing list gmx-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
RE: [gmx-users] g_covar -ref
PCA refers to covariance analysis (though SVD gives the same results). Principal components are obtained by projecting the trajectory onto the eigenvectors of the covariance matrix. I just wanted to know why the option -ref was offered and if it had any significance. Thanks Vijaya > Date: Thu, 18 Mar 2010 17:51:04 +0100 > Subject: Re: [gmx-users] g_covar -ref > From: tsje...@gmail.com > To: gmx-users@gromacs.org > > Hi Vijaya, > > Well, to start with that will be something as calculating the > 'fluctuation' as sum((xi-ri)^2)/N, with xi and ri denoting the ith > atom of the conformation x and the reference structure r and the sum > is over time/observations. In the case of no variation in xi, the > value you get will still be finite, in stead of zero, as would > probably be most meaningful. > Now for the covariances, there's a bit more to it. The covariance is > the product moment of the deviations: sum((xi-ri)(xj-rj))/N. When > there is no correlation, the deviations about the mean are random and > average out to zero. But with the deviations against a reference, that > is not the case. So the results should be regarded meaningless, unless > you have a good reason for doing so, and come with a solid > justification. Okay, there may be a purpose, but I'll leave that to > your imagination :) > > Hope it helps, > > Tsjerk > > On Thu, Mar 18, 2010 at 5:33 PM, vijaya subramanian > wrote: > > Hi > > Has anyone studied the effect of using different reference structures, > > not the average structure, when carrying out PCA. Does it make sense to use > > a structure besides the average to calculate the covariance matrix? > > Thanks > > Vijaya > > > > > > > > > > Hotmail: Trusted email with powerful SPAM protection. Sign up now. > > -- > > gmx-users mailing listgmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > > post-doctoral researcher > Molecular Dynamics Group > Groningen Institute for Biomolecular Research and Biotechnology > University of Groningen > The Netherlands > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php _ Hotmail: Trusted email with Microsoft’s powerful SPAM protection. http://clk.atdmt.com/GBL/go/210850552/direct/01/-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] g_covar -ref
Hi Vijaya, I'm sorry if I didn't quite get that first sentence of yours. Did you meant to start it with "I thought that ..."? Or were you trying to explain me something you thought I missed? PCA stands for 'principal component analysis', not 'covariance analysis'. For instance, PCA can be applied to correlations, and then is 'correlation analysis'. SVD is a particular flavour of PCA and here yields the same results as traditional PCA because the covariance matrix is symmetric, but otherwise they're not strictly the same. That is to say, the SVD is obtained by extracting the eigenvectors from the matrices transpose(S) x S and S x transpose(S). Which are quite obviously identical if S is a symmetric matrix. By the way, was your question regarding the -ref option answered, or did the answer elude you? If the latter is the case, maybe if now you feel sufficiently confident that I know a bit about PCA, you can go through the answer again. Cheers, Tsjerk On Thu, Mar 18, 2010 at 7:01 PM, vijaya subramanian wrote: > PCA refers to covariance analysis (though SVD gives the same results). > Principal components are obtained by projecting the trajectory onto > the eigenvectors of the covariance matrix. > I just wanted to know why the option -ref was offered and if it had any > significance. > Thanks > Vijaya > >> Date: Thu, 18 Mar 2010 17:51:04 +0100 >> Subject: Re: [gmx-users] g_covar -ref >> From: tsje...@gmail.com >> To: gmx-users@gromacs.org >> >> Hi Vijaya, >> >> Well, to start with that will be something as calculating the >> 'fluctuation' as sum((xi-ri)^2)/N, with xi and ri denoting the ith >> atom of the conformation x and the reference structure r and the sum >> is over time/observations. In the case of no variation in xi, the >> value you get will still be finite, in stead of zero, as would >> probably be most meaningful. >> Now for the covariances, there's a bit more to it. The covariance is >> the product moment of the deviations: sum((xi-ri)(xj-rj))/N. When >> there is no correlation, the deviations about the mean are random and >> average out to zero. But with the deviations against a reference, that >> is not the case. So the results should be regarded meaningless, unless >> you have a good reason for doing so, and come with a solid >> justification. Okay, there may be a purpose, but I'll leave that to >> your imagination :) >> >> Hope it helps, >> >> Tsjerk >> >> On Thu, Mar 18, 2010 at 5:33 PM, vijaya subramanian >> wrote: >> > Hi >> > Has anyone studied the effect of using different reference structures, >> > not the average structure, when carrying out PCA. Does it make sense to >> > use >> > a structure besides the average to calculate the covariance matrix? >> > Thanks >> > Vijaya >> > >> > >> > >> > >> > Hotmail: Trusted email with powerful SPAM protection. Sign up now. >> > -- >> > gmx-users mailing list gmx-us...@gromacs.org >> > http://lists.gromacs.org/mailman/listinfo/gmx-users >> > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php >> > >> >> >> >> -- >> Tsjerk A. Wassenaar, Ph.D. >> >> post-doctoral researcher >> Molecular Dynamics Group >> Groningen Institute for Biomolecular Research and Biotechnology >> University of Groningen >> The Netherlands >> -- >> 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/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/mailing_lists/users.php > > > Hotmail: Trusted email with Microsoft’s powerful SPAM protection. Sign up > now. > -- > gmx-users mailing list gmx-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
RE: [gmx-users] g_covar -ref
Hi Your answer truly eludes me, unless -ref is an useless option. In any case it isn't particularly important. Vijaya > Date: Thu, 18 Mar 2010 19:37:40 +0100 > Subject: Re: [gmx-users] g_covar -ref > From: tsje...@gmail.com > To: gmx-users@gromacs.org > > Hi Vijaya, > > I'm sorry if I didn't quite get that first sentence of yours. Did you > meant to start it with "I thought that ..."? Or were you trying to > explain me something you thought I missed? > > PCA stands for 'principal component analysis', not 'covariance > analysis'. For instance, PCA can be applied to correlations, and then > is 'correlation analysis'. SVD is a particular flavour of PCA and here > yields the same results as traditional PCA because the covariance > matrix is symmetric, but otherwise they're not strictly the same. That > is to say, the SVD is obtained by extracting the eigenvectors from the > matrices transpose(S) x S and S x transpose(S). Which are quite > obviously identical if S is a symmetric matrix. > > By the way, was your question regarding the -ref option answered, or > did the answer elude you? If the latter is the case, maybe if now you > feel sufficiently confident that I know a bit about PCA, you can go > through the answer again. > > Cheers, > > Tsjerk > > On Thu, Mar 18, 2010 at 7:01 PM, vijaya subramanian > wrote: > > PCA refers to covariance analysis (though SVD gives the same results). > > Principal components are obtained by projecting the trajectory onto > > the eigenvectors of the covariance matrix. > > I just wanted to know why the option -ref was offered and if it had any > > significance. > > Thanks > > Vijaya > > > >> Date: Thu, 18 Mar 2010 17:51:04 +0100 > >> Subject: Re: [gmx-users] g_covar -ref > >> From: tsje...@gmail.com > >> To: gmx-users@gromacs.org > >> > >> Hi Vijaya, > >> > >> Well, to start with that will be something as calculating the > >> 'fluctuation' as sum((xi-ri)^2)/N, with xi and ri denoting the ith > >> atom of the conformation x and the reference structure r and the sum > >> is over time/observations. In the case of no variation in xi, the > >> value you get will still be finite, in stead of zero, as would > >> probably be most meaningful. > >> Now for the covariances, there's a bit more to it. The covariance is > >> the product moment of the deviations: sum((xi-ri)(xj-rj))/N. When > >> there is no correlation, the deviations about the mean are random and > >> average out to zero. But with the deviations against a reference, that > >> is not the case. So the results should be regarded meaningless, unless > >> you have a good reason for doing so, and come with a solid > >> justification. Okay, there may be a purpose, but I'll leave that to > >> your imagination :) > >> > >> Hope it helps, > >> > >> Tsjerk > >> > >> On Thu, Mar 18, 2010 at 5:33 PM, vijaya subramanian > >> wrote: > >> > Hi > >> > Has anyone studied the effect of using different reference structures, > >> > not the average structure, when carrying out PCA. Does it make sense to > >> > use > >> > a structure besides the average to calculate the covariance matrix? > >> > Thanks > >> > Vijaya > >> > > >> > > >> > > >> > > >> > Hotmail: Trusted email with powerful SPAM protection. Sign up now. > >> > -- > >> > gmx-users mailing listgmx-users@gromacs.org > >> > http://lists.gromacs.org/mailman/listinfo/gmx-users > >> > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > >> > > >> > >> > >> > >> -- > >> Tsjerk A. Wassenaar, Ph.D. > >> > >> post-doctoral researcher > >> Molecular Dynamics Group > >> Groningen Institute for Biomolecular Research and Biotechnology > >> University of Groningen > >> The Netherlands > >> -- > >> 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/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/mailing_lists/users.php > > > > > > Hotmail: Trusted email with Microsoft’s powerful SPAM protection. Sign up > > now. > > -- > > gmx-users mailing listgmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > > post-doctoral researcher > Molecular Dynamics Group > Groningen Institute for Biomolec
[gmx-users] What is Dmax, and are .tpr files transferrable between operating systems
Can someone tell me what the Dmax value is that is output to the terminal during energy minimization? Example output: Step= 2164, Dmax= 6.2e-03 nm, Epot= -1.17364e+06 Fmax= 8.49209e+02, atom= 56 Step= 2165, Dmax= 7.5e-03 nm, Epot= -1.17365e+06 Fmax= 1.05171e+04, atom= 56 Step= 2166, Dmax= 9.0e-03 nm, Epot= -1.17370e+06 Fmax= 3.16057e+03, atom= 56 Step= 2168, Dmax= 5.4e-03 nm, Epot= -1.17370e+06 Fmax= 5.04184e+03, atom= 56 Step= 2169, Dmax= 6.4e-03 nm, Epot= -1.17371e+06 Fmax= 4.79470e+03, atom= 56 Step= 2171, Dmax= 3.9e-03 nm, Epot= -1.17373e+06 Fmax= 1.10629e+03, atom= 56 And second, are .tpr files platform independent, i.e. if I create a .tpr file using MacOSX, can I simply copy it onto a system running Linux invoke mdrun to run the simulation? I'm using the same version (4.0.7) on both platforms. Thanks, Warren Gallin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] What is Dmax, and are .tpr files transferrable between operating systems
Warren Gallin wrote: Can someone tell me what the Dmax value is that is output to the terminal during energy minimization? Dmax is the largest step size taken. Example output: Step= 2164, Dmax= 6.2e-03 nm, Epot= -1.17364e+06 Fmax= 8.49209e+02, atom= 56 Step= 2165, Dmax= 7.5e-03 nm, Epot= -1.17365e+06 Fmax= 1.05171e+04, atom= 56 Step= 2166, Dmax= 9.0e-03 nm, Epot= -1.17370e+06 Fmax= 3.16057e+03, atom= 56 Step= 2168, Dmax= 5.4e-03 nm, Epot= -1.17370e+06 Fmax= 5.04184e+03, atom= 56 Step= 2169, Dmax= 6.4e-03 nm, Epot= -1.17371e+06 Fmax= 4.79470e+03, atom= 56 Step= 2171, Dmax= 3.9e-03 nm, Epot= -1.17373e+06 Fmax= 1.10629e+03, atom= 56 And second, are .tpr files platform independent, i.e. if I create a .tpr file using MacOSX, can I simply copy it onto a system running Linux invoke mdrun to run the simulation? I'm using the same version (4.0.7) on both platforms. Yes. -Justin Thanks, Warren Gallin -- 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/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/mailing_lists/users.php
Re: [gmx-users] g_covar -ref
Hi Vijaya, > Your answer truly eludes me, unless -ref is an useless option. Well, that's pretty close to the conclusion. The use is limited to a few very specific cases and it might be better to hide the option from the view of casual users. But apparently you didn't catch the why yet. If you imagine a pendulum going back and forth, the principal components will be commonly determined by taking the deviations from the mean position. Then you get two components, one for the direction of the motion and one for the deflection from linearity, right? But now, you calculate the deviations not with respect to the average position, but you take the deviations with respect to a position that is away from the mean, say halfway to the left. Now you can follow the same procedure, calculating a matrix of cross products for these deviations, and diagonalizing it. But what do these results then mean? This is a neat example to run with pen and paper... You should even be able to solve it analytically :) Have fun, Tsjerk > In any case it isn't particularly important. > Vijaya > > > >> Date: Thu, 18 Mar 2010 19:37:40 +0100 >> Subject: Re: [gmx-users] g_covar -ref >> From: tsje...@gmail.com >> To: gmx-users@gromacs.org >> >> Hi Vijaya, >> >> I'm sorry if I didn't quite get that first sentence of yours. Did you >> meant to start it with "I thought that ..."? Or were you trying to >> explain me something you thought I missed? >> >> PCA stands for 'principal component analysis', not 'covariance >> analysis'. For instance, PCA can be applied to correlations, and then >> is 'correlation analysis'. SVD is a particular flavour of PCA and here >> yields the same results as traditional PCA because the covariance >> matrix is symmetric, but otherwise they're not strictly the same. That >> is to say, the SVD is obtained by extracting the eigenvectors from the >> matrices transpose(S) x S and S x transpose(S). Which are quite >> obviously identical if S is a symmetric matrix. >> >> By the way, was your question regarding the -ref option answered, or >> did the answer elude you? If the latter is the case, maybe if now you >> feel sufficiently confident that I know a bit about PCA, you can go >> through the answer again. >> >> Cheers, >> >> Tsjerk >> >> On Thu, Mar 18, 2010 at 7:01 PM, vijaya subramanian >> wrote: >> > PCA refers to covariance analysis (though SVD gives the same results). >> > Principal components are obtained by projecting the trajectory onto >> > the eigenvectors of the covariance matrix. >> > I just wanted to know why the option -ref was offered and if it had any >> > significance. >> > Thanks >> > Vijaya >> > >> >> Date: Thu, 18 Mar 2010 17:51:04 +0100 >> >> Subject: Re: [gmx-users] g_covar -ref >> >> From: tsje...@gmail.com >> >> To: gmx-users@gromacs.org >> >> >> >> Hi Vijaya, >> >> >> >> Well, to start with that will be something as calculating the >> >> 'fluctuation' as sum((xi-ri)^2)/N, with xi and ri denoting the ith >> >> atom of the conformation x and the reference structure r and the sum >> >> is over time/observations. In the case of no variation in xi, the >> >> value you get will still be finite, in stead of zero, as would >> >> probably be most meaningful. >> >> Now for the covariances, there's a bit more to it. The covariance is >> >> the product moment of the deviations: sum((xi-ri)(xj-rj))/N. When >> >> there is no correlation, the deviations about the mean are random and >> >> average out to zero. But with the deviations against a reference, that >> >> is not the case. So the results should be regarded meaningless, unless >> >> you have a good reason for doing so, and come with a solid >> >> justification. Okay, there may be a purpose, but I'll leave that to >> >> your imagination :) >> >> >> >> Hope it helps, >> >> >> >> Tsjerk >> >> >> >> On Thu, Mar 18, 2010 at 5:33 PM, vijaya subramanian >> >> wrote: >> >> > Hi >> >> > Has anyone studied the effect of using different reference >> >> > structures, >> >> > not the average structure, when carrying out PCA. Does it make sense >> >> > to >> >> > use >> >> > a structure besides the average to calculate the covariance matrix? >> >> > Thanks >> >> > Vijaya >> >> > >> >> > >> >> > >> >> > >> >> > Hotmail: Trusted email with powerful SPAM protection. Sign up now. >> >> > -- >> >> > gmx-users mailing list gmx-us...@gromacs.org >> >> > http://lists.gromacs.org/mailman/listinfo/gmx-users >> >> > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php >> >> > >> >> >> >> >> >> >> >> -- >> >> Tsjerk A. Wassenaar, Ph.D. >> >> >> >> post-doctoral researcher >> >> Molecular Dynamics Group >> >> Groningen Institute for Biomolecular Research and Biotechnology >> >> University of Groningen
RE: [gmx-users] g_covar -ref
Hi Thanks for your input, what are the few specific cases where a reference structure might be used? Vijaya > Date: Thu, 18 Mar 2010 20:42:36 +0100 > Subject: Re: [gmx-users] g_covar -ref > From: tsje...@gmail.com > To: gmx-users@gromacs.org > > Hi Vijaya, > > > Your answer truly eludes me, unless -ref is an useless option. > > Well, that's pretty close to the conclusion. The use is limited to a > few very specific cases and it might be better to hide the option from > the view of casual users. > > But apparently you didn't catch the why yet. If you imagine a pendulum > going back and forth, the principal components will be commonly > determined by taking the deviations from the mean position. Then you > get two components, one for the direction of the motion and one for > the deflection from linearity, right? But now, you calculate the > deviations not with respect to the average position, but you take the > deviations with respect to a position that is away from the mean, say > halfway to the left. Now you can follow the same procedure, > calculating a matrix of cross products for these deviations, and > diagonalizing it. But what do these results then mean? This is a neat > example to run with pen and paper... You should even be able to solve > it analytically :) > > Have fun, > > Tsjerk > > > > In any case it isn't particularly important. > > Vijaya > > > > > > > >> Date: Thu, 18 Mar 2010 19:37:40 +0100 > >> Subject: Re: [gmx-users] g_covar -ref > >> From: tsje...@gmail.com > >> To: gmx-users@gromacs.org > >> > >> Hi Vijaya, > >> > >> I'm sorry if I didn't quite get that first sentence of yours. Did you > >> meant to start it with "I thought that ..."? Or were you trying to > >> explain me something you thought I missed? > >> > >> PCA stands for 'principal component analysis', not 'covariance > >> analysis'. For instance, PCA can be applied to correlations, and then > >> is 'correlation analysis'. SVD is a particular flavour of PCA and here > >> yields the same results as traditional PCA because the covariance > >> matrix is symmetric, but otherwise they're not strictly the same. That > >> is to say, the SVD is obtained by extracting the eigenvectors from the > >> matrices transpose(S) x S and S x transpose(S). Which are quite > >> obviously identical if S is a symmetric matrix. > >> > >> By the way, was your question regarding the -ref option answered, or > >> did the answer elude you? If the latter is the case, maybe if now you > >> feel sufficiently confident that I know a bit about PCA, you can go > >> through the answer again. > >> > >> Cheers, > >> > >> Tsjerk > >> > >> On Thu, Mar 18, 2010 at 7:01 PM, vijaya subramanian > >> wrote: > >> > PCA refers to covariance analysis (though SVD gives the same results). > >> > Principal components are obtained by projecting the trajectory onto > >> > the eigenvectors of the covariance matrix. > >> > I just wanted to know why the option -ref was offered and if it had any > >> > significance. > >> > Thanks > >> > Vijaya > >> > > >> >> Date: Thu, 18 Mar 2010 17:51:04 +0100 > >> >> Subject: Re: [gmx-users] g_covar -ref > >> >> From: tsje...@gmail.com > >> >> To: gmx-users@gromacs.org > >> >> > >> >> Hi Vijaya, > >> >> > >> >> Well, to start with that will be something as calculating the > >> >> 'fluctuation' as sum((xi-ri)^2)/N, with xi and ri denoting the ith > >> >> atom of the conformation x and the reference structure r and the sum > >> >> is over time/observations. In the case of no variation in xi, the > >> >> value you get will still be finite, in stead of zero, as would > >> >> probably be most meaningful. > >> >> Now for the covariances, there's a bit more to it. The covariance is > >> >> the product moment of the deviations: sum((xi-ri)(xj-rj))/N. When > >> >> there is no correlation, the deviations about the mean are random and > >> >> average out to zero. But with the deviations against a reference, that > >> >> is not the case. So the results should be regarded meaningless, unless > >> >> you have a good reason for doing so, and come with a solid > >> >> justification. Okay, there may be a purpose, but I'll leave that to > >> >> your imagination :) > >> >> > >> >> Hope it helps, > >> >> > >> >> Tsjerk > >> >> > >> >> On Thu, Mar 18, 2010 at 5:33 PM, vijaya subramanian > >> >> wrote: > >> >> > Hi > >> >> > Has anyone studied the effect of using different reference > >> >> > structures, > >> >> > not the average structure, when carrying out PCA. Does it make sense > >> >> > to > >> >> > use > >> >> > a structure besides the average to calculate the covariance matrix? > >> >> > Thanks > >> >> > Vijaya > >> >> > > >> >> > > >> >> > > >> >> > > >> >> > Hotmail: Trusted email with powerful SPAM protection. Sign up now. > >> >> > -- > >> >> > gmx-users mailing listgmx-users@gromacs.org > >> >> > http://lists.gromacs.org/mailman/listinfo/gmx-users > >> >> > Please search the archive at http://www.gromacs
Re: [gmx-users] g_covar -ref
Hi Vijaya, Hmmm. Well, it may make some sense to take a defined extreme point to take deviations from. Like for motion on an arc, it may make sense to take the center of the circle to determine the deviations. But what that will yield; how that translates to wiggling proteins... :S Cheers, Tsjerk On Thu, Mar 18, 2010 at 9:11 PM, vijaya subramanian wrote: > Hi > Thanks for your input, what are the few specific cases where > a reference structure might be used? > Vijaya > >> Date: Thu, 18 Mar 2010 20:42:36 +0100 >> Subject: Re: [gmx-users] g_covar -ref >> From: tsje...@gmail.com >> To: gmx-users@gromacs.org >> >> Hi Vijaya, >> >> > Your answer truly eludes me, unless -ref is an useless option. >> >> Well, that's pretty close to the conclusion. The use is limited to a >> few very specific cases and it might be better to hide the option from >> the view of casual users. >> >> But apparently you didn't catch the why yet. If you imagine a pendulum >> going back and forth, the principal components will be commonly >> determined by taking the deviations from the mean position. Then you >> get two components, one for the direction of the motion and one for >> the deflection from linearity, right? But now, you calculate the >> deviations not with respect to the average position, but you take the >> deviations with respect to a position that is away from the mean, say >> halfway to the left. Now you can follow the same procedure, >> calculating a matrix of cross products for these deviations, and >> diagonalizing it. But what do these results then mean? This is a neat >> example to run with pen and paper... You should even be able to solve >> it analytically :) >> >> Have fun, >> >> Tsjerk >> >> >> > In any case it isn't particularly important. >> > Vijaya >> > >> > >> > >> >> Date: Thu, 18 Mar 2010 19:37:40 +0100 >> >> Subject: Re: [gmx-users] g_covar -ref >> >> From: tsje...@gmail.com >> >> To: gmx-users@gromacs.org >> >> >> >> Hi Vijaya, >> >> >> >> I'm sorry if I didn't quite get that first sentence of yours. Did you >> >> meant to start it with "I thought that ..."? Or were you trying to >> >> explain me something you thought I missed? >> >> >> >> PCA stands for 'principal component analysis', not 'covariance >> >> analysis'. For instance, PCA can be applied to correlations, and then >> >> is 'correlation analysis'. SVD is a particular flavour of PCA and here >> >> yields the same results as traditional PCA because the covariance >> >> matrix is symmetric, but otherwise they're not strictly the same. That >> >> is to say, the SVD is obtained by extracting the eigenvectors from the >> >> matrices transpose(S) x S and S x transpose(S). Which are quite >> >> obviously identical if S is a symmetric matrix. >> >> >> >> By the way, was your question regarding the -ref option answered, or >> >> did the answer elude you? If the latter is the case, maybe if now you >> >> feel sufficiently confident that I know a bit about PCA, you can go >> >> through the answer again. >> >> >> >> Cheers, >> >> >> >> Tsjerk >> >> >> >> On Thu, Mar 18, 2010 at 7:01 PM, vijaya subramanian >> >> wrote: >> >> > PCA refers to covariance analysis (though SVD gives the same >> >> > results). >> >> > Principal components are obtained by projecting the trajectory onto >> >> > the eigenvectors of the covariance matrix. >> >> > I just wanted to know why the option -ref was offered and if it had >> >> > any >> >> > significance. >> >> > Thanks >> >> > Vijaya >> >> > >> >> >> Date: Thu, 18 Mar 2010 17:51:04 +0100 >> >> >> Subject: Re: [gmx-users] g_covar -ref >> >> >> From: tsje...@gmail.com >> >> >> To: gmx-users@gromacs.org >> >> >> >> >> >> Hi Vijaya, >> >> >> >> >> >> Well, to start with that will be something as calculating the >> >> >> 'fluctuation' as sum((xi-ri)^2)/N, with xi and ri denoting the ith >> >> >> atom of the conformation x and the reference structure r and the sum >> >> >> is over time/observations. In the case of no variation in xi, the >> >> >> value you get will still be finite, in stead of zero, as would >> >> >> probably be most meaningful. >> >> >> Now for the covariances, there's a bit more to it. The covariance is >> >> >> the product moment of the deviations: sum((xi-ri)(xj-rj))/N. When >> >> >> there is no correlation, the deviations about the mean are random >> >> >> and >> >> >> average out to zero. But with the deviations against a reference, >> >> >> that >> >> >> is not the case. So the results should be regarded meaningless, >> >> >> unless >> >> >> you have a good reason for doing so, and come with a solid >> >> >> justification. Okay, there may be a purpose, but I'll leave that to >> >> >> your imagination :) >> >> >> >> >> >> Hope it helps, >> >> >> >> >> >> Tsjerk >> >> >> >> >> >> On Thu, Mar 18, 2010 at 5:33 PM, vijaya subramanian >> >> >> wrote: >> >> >> > Hi >> >> >> > Has anyone studied the effect of using different reference >> >> >> > structures, >> >> >> > not the average structure, when carryin
[gmx-users] T-coupling groups
Dear GROMACS users, I have checked the mails in archive which deal with the problem I am facing but did not find the answer what I do wrong. I want to compile a PEO chain centered in box of 2900 water molecules. In my md.mdp the relevant section is as follows Tcoupl = nose-hoover tc-grps = PEO SOL tau_t = 0.1 0.1 ref_t = 50 50 gen_vel = yes gen_temp = 50 50 I have generated an index file where I have defined the PEO group. The [ SOL ] group contains 129-8828 atoms and the [ PEO ] contains 1-128atoms. This matches with the gro file. I tried to prepare a tpr file using grompp -f md.mdp -c PEO18_2900TIP3P_opt.gro -n PEO18_2900TIP3P.ndx -p topol.top -o PEO18_2900TIP3P_50K and got message Program grompp, VERSION 4.0.3 Source code file: readir.c, line: 1050 Fatal error: 16 atoms are not part of any of the T-Coupling groups I tried the compilations with 4.0.3 and 4.0.5 versions but the message was the same. I would be really thankful for an advice which can move me further. Thank you in advance. Zuzana -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] T-coupling groups
Zuzana Benkova wrote: Dear GROMACS users, I have checked the mails in archive which deal with the problem I am facing but did not find the answer what I do wrong. I want to compile a PEO chain centered in box of 2900 water molecules. In my md.mdp the relevant section is as follows Tcoupl = nose-hoover tc-grps = PEO SOL tau_t = 0.1 0.1 ref_t = 50 50 gen_vel = yes gen_temp= 50 50 I have generated an index file where I have defined the PEO group. The [ SOL ] group contains 129-8828 atoms and the [ PEO ] contains 1-128atoms. This matches with the gro file. I tried to prepare a tpr file using You shouldn't have to do this. By default, each moleculetype is given its own default index group: http://www.gromacs.org/Documentation/Terminology/Default_Index_Groups grompp -f md.mdp -c PEO18_2900TIP3P_opt.gro -n PEO18_2900TIP3P.ndx -p topol.top -o PEO18_2900TIP3P_50K and got message Program grompp, VERSION 4.0.3 Source code file: readir.c, line: 1050 Fatal error: 16 atoms are not part of any of the T-Coupling groups I tried the compilations with 4.0.3 and 4.0.5 versions but the message was the same. This is not a version-specific bug, so I'd imagine not. There's something in your system that is not coupled. Perhaps you've done something wrong in setting the index groups. Try without an index file (see above comment). If there's something else in the system, it needs to be accounted for. -Justin I would be really thankful for an advice which can move me further. Thank you in advance. Zuzana -- 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/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/mailing_lists/users.php
Re: [gmx-users] T-coupling groups
Dear Zuzana, Recently i have done similar selection, I have got this error only when i miss some atoms or when i have some atoms in both groups. I would suggest you to check your groups carefully or you can make indexes for these selections in VMD and check whether you are missing some atoms from both groups. Srinivs. On Thu, Mar 18, 2010 at 4:55 PM, Zuzana Benkova wrote: > Dear GROMACS users, > I have checked the mails in archive which deal with the problem I am facing > but did not find the answer what I do wrong. > > I want to compile a PEO chain centered in box of 2900 water molecules. > > In my md.mdp the relevant section is as follows > Tcoupl = nose-hoover > tc-grps = PEO SOL > tau_t = 0.1 0.1 > ref_t = 50 50 > gen_vel = yes > gen_temp= 50 50 > > I have generated an index file where I have defined the PEO group. The [ > SOL ] group contains 129-8828 atoms and the [ PEO ] contains 1-128atoms. > This matches with the gro file. I tried to prepare a tpr file using > > grompp -f md.mdp -c PEO18_2900TIP3P_opt.gro -n PEO18_2900TIP3P.ndx -p > topol.top -o PEO18_2900TIP3P_50K > > and got message > > Program grompp, VERSION 4.0.3 > Source code file: readir.c, line: 1050 > > Fatal error: > 16 atoms are not part of any of the T-Coupling groups > > I tried the compilations with 4.0.3 and 4.0.5 versions but the message was > the same. > > > I would be really thankful for an advice which can move me further. Thank > you in advance. > > Zuzana > > > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > -- * J. Srinivasa Rao Ph.D. Post-doctoral Research Associate C/o Prof. Luis R Cruz Cruz Computational Biophysics Group Department of Physics Drexel University 3141 Chestnut St Philadelphia, PA 19104, USA. Ph: Off: 215-895-1989 Mob: 704-706-4191 Web:http://jsrao.web.officelive.com/default.aspx ** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] g_bundle problem
I have tried using g_bundle in order to analyse helix axes in my transmembran helices. I created two groups in my ndx file that included the alpha carbons of the first half of my helix and a second group for the alpha carbons for the second half. When I try using g_bundle the following error comes up: "Fatal error: The size of one of your index groups is not a multiple of n" What am I doing wrong? Thank you -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] g_bundle problem
Stefan Hoorman wrote: I have tried using g_bundle in order to analyse helix axes in my transmembran helices. I created two groups in my ndx file that included the alpha carbons of the first half of my helix and a second group for the alpha carbons for the second half. When I try using g_bundle the following error comes up: "Fatal error: The size of one of your index groups is not a multiple of n" What am I doing wrong? Not a clue - What is your exact command line? How many atoms are in each index group? The value of n is the number of parts into which the axes are divided and there are several criteria in the code that must be met, else you get this error. So without this information, the best guess is: some criterion is not being met. -Justin Thank you -- 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/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/mailing_lists/users.php
Re: [gmx-users] g_bundle problem
Justin A. Lemkul wrote: Stefan Hoorman wrote: I have tried using g_bundle in order to analyse helix axes in my transmembran helices. I created two groups in my ndx file that included the alpha carbons of the first half of my helix and a second group for the alpha carbons for the second half. When I try using g_bundle the following error comes up: "Fatal error: The size of one of your index groups is not a multiple of n" What am I doing wrong? Not a clue - What is your exact command line? How many atoms are in each index group? The value of n is the number of parts into which the axes are divided and there are several criteria in the code that must be *Edit* The value of n is the number of parts into which the *groups* are divided, not the axes...been one of those days, sorry. -Justin -- 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/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/mailing_lists/users.php
Re: [gmx-users] g_bundle problem
On Friday 19 March 2010 02:36:49 Stefan Hoorman wrote: > I have tried using g_bundle in order to analyse helix axes in my > transmembran helices. I created two groups in my ndx file that included the > alpha carbons of the first half of my helix and a second group for the > alpha carbons for the second half. When I try using g_bundle the following > error comes up: > "Fatal error: > The size of one of your index groups is not a multiple of n" > What am I doing wrong? g_bundle analyzes bundles of axes - and therefore number of atoms each group have to be divisible by number of axes (entered by -na). And I suppose, you are interested in analyzing only one axis, don't you? Milan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] removal of center of mass motion needed for accelerated water molecules?
Hi all, I have a periodical system comprised a nanotube and water solvent. Positive acceleration is applied to every water molecules and I am trying to count the water flux through the nanotube. I also specified force constraints (1000) on the nanotube to keep it in place. The question is whether removal of center of mass motion is needed for this kind system with accelerated water molecules. I performed the simulation with removal of center of mass motion for the nanotube and water as two groups (nstcomm=1, comm-mode=Linear, comm-grps=CNT SOL).The flux result is significantly smaller than the result from simulations w/o removal of center of mass motion. As I understand it, removal of center of mass motion is generally required for equilibrium MD runs in Gromacs. However, the simulations that I performed are non-equilibrium MD runs. Could anyone help me with some advices on this problem? I highly appreciate your help! Sincerely, Yang -- -- Life is elsewhere -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] compile problem on Centos X86_64 with gcc44 and fftw2
Title: compile problem on Centos X86_64 with gcc44 and fftw2 Dear all users, I compiled the program likes this: a, fftw3 ./configure --enable-float make make install. All sounds ok b, gromacs4.0.5 ./configure --with-fft=fftw3 make make install. All sound ok. However when I copy gmxtest to the direcotry amd typed: make tests, the output is as following: (if test -d "gmxtest"; then cd "gmxtest"; ./gmxtest.pl all; cd ..; \ else echo "No gmxtest directory found. Please download and unpack it here.";\ fi) All 16 simple tests PASSED FAILED. Check files in aminoacids FAILED. Check files in field FAILED. Check files in tip4p FAILED. Check files in tip4pflex FAILED. Check files in water 5 out of 14 complex tests FAILED FAILED. Check files in kernel020 FAILED. Check files in kernel120 FAILED. Check files in kernel121 FAILED. Check files in kernel122 FAILED. Check files in kernel123 FAILED. Check files in kernel124 FAILED. Check files in kernel220 FAILED. Check files in kernel221 FAILED. Check files in kernel222 FAILED. Check files in kernel223 FAILED. Check files in kernel224 FAILED. Check files in kernel320 FAILED. Check files in kernel321 FAILED. Check files in kernel322 FAILED. Check files in kernel323 FAILED. Check files in kernel324 16 out of 63 kernel tests FAILED All 45 pdb2gmx tests PASSED Seems that my compilation failed? Please give some suggestions. Also best configurations for my platform recommended from you are welcome Best regards R Q Wu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] compile problem on Centos X86_64 with gcc44 and fftw2
Wu Rongqin wrote: Dear all users, I compiled the program likes this: a, fftw3 ./configure --enable-float make make install. All sounds ok b, gromacs4.0.5 ./configure --with-fft=fftw3 make make install. All sound ok. Why not install the latest version (4.0.7)? You'll get the latest bug fixes and features, rather than using a distribution that is seven months old. However when I copy gmxtest to the direcotry amd typed: make tests, the output is as following: (if test -d "gmxtest"; then cd "gmxtest"; ./gmxtest.pl all; cd ..; \ else echo "No gmxtest directory found. Please download and unpack it here.";\ fi) As the message advises you, in order to do this you have to actually download the gmxtest package: http://www.gromacs.org/index.php?title=Download_%26_Installation/Test-Set But, be warned, that it is relatively useless. It does not rigorously test many feature combinations, and the failures it reports can often be spurious. -Justin All 16 simple tests PASSED FAILED. Check files in aminoacids FAILED. Check files in field FAILED. Check files in tip4p FAILED. Check files in tip4pflex FAILED. Check files in water 5 out of 14 complex tests FAILED FAILED. Check files in kernel020 FAILED. Check files in kernel120 FAILED. Check files in kernel121 FAILED. Check files in kernel122 FAILED. Check files in kernel123 FAILED. Check files in kernel124 FAILED. Check files in kernel220 FAILED. Check files in kernel221 FAILED. Check files in kernel222 FAILED. Check files in kernel223 FAILED. Check files in kernel224 FAILED. Check files in kernel320 FAILED. Check files in kernel321 FAILED. Check files in kernel322 FAILED. Check files in kernel323 FAILED. Check files in kernel324 16 out of 63 kernel tests FAILED All 45 pdb2gmx tests PASSED Seems that my compilation failed? Please give some suggestions. Also best configurations for my platform recommended from you are welcome Best regards R Q Wu -- 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/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/mailing_lists/users.php
答复: [gmx-users] compile problem on Cen tos X86_64 with gcc44 and fftw2
Title: ´ð¸´: [gmx-users] compile problem on Centos X86_64 with gcc44 and fftw2 Dear Dr. Justin, I also followed your tutorial "Lysozyme in Water" on website. However, on the energy miminization step, I cannot reproduce your results. The minimization stopped at 61 steps. However, Sometimes it might stop at 760 steps. I do not why gromacs cannot reproduce. A problem from compile? Regards Wu -Original Message- From: gmx-users-boun...@gromacs.org 代表 Justin A. Lemkul Sent: 2010-3-19 (星期五) 11:48 To: Discussion list for GROMACS users Subject: Re: [gmx-users] compile problem on Centos X86_64 with gcc44 and fftw2 Wu Rongqin wrote: > Dear all users, > > I compiled the program likes this: > > a, fftw3 > ./configure --enable-float make make install. All sounds ok > b, gromacs4.0.5 > ./configure --with-fft=fftw3 make make install. All sound ok. > Why not install the latest version (4.0.7)? You'll get the latest bug fixes and features, rather than using a distribution that is seven months old. > However when I copy gmxtest to the direcotry amd typed: > make tests, > the output is as following: > > (if test -d "gmxtest"; then cd "gmxtest"; ./gmxtest.pl all; cd ..; \ > else echo "No gmxtest directory found. Please download and > unpack it here.";\ > fi) As the message advises you, in order to do this you have to actually download the gmxtest package: http://www.gromacs.org/index.php?title=Download_%26_Installation/Test-Set But, be warned, that it is relatively useless. It does not rigorously test many feature combinations, and the failures it reports can often be spurious. -Justin > All 16 simple tests PASSED > FAILED. Check files in aminoacids > FAILED. Check files in field > FAILED. Check files in tip4p > FAILED. Check files in tip4pflex > FAILED. Check files in water > 5 out of 14 complex tests FAILED > FAILED. Check files in kernel020 > FAILED. Check files in kernel120 > FAILED. Check files in kernel121 > FAILED. Check files in kernel122 > FAILED. Check files in kernel123 > FAILED. Check files in kernel124 > FAILED. Check files in kernel220 > FAILED. Check files in kernel221 > FAILED. Check files in kernel222 > FAILED. Check files in kernel223 > FAILED. Check files in kernel224 > FAILED. Check files in kernel320 > FAILED. Check files in kernel321 > FAILED. Check files in kernel322 > FAILED. Check files in kernel323 > FAILED. Check files in kernel324 > 16 out of 63 kernel tests FAILED > All 45 pdb2gmx tests PASSED > > > Seems that my compilation failed? Please give some suggestions. > > Also best configurations for my platform recommended from you are welcome > > Best regards > > R Q Wu > -- 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 list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: 答复: [gmx-users] compile probl em on Centos X86_64 with gcc44 and fftw2
- Original Message - From: Wu Rongqin Date: Friday, March 19, 2010 16:10 Subject: 答复: [gmx-users] compile problem on Centos X86_64 with gcc44 and fftw2 To: jalem...@vt.edu, Discussion list for GROMACS users , Discussion list for GROMACS users > ´ð¸´: [gmx-users] compile problem on Centos X86_64 with gcc44 and fftw2 --- | > Dear Dr. Justin, > > I also followed your tutorial "Lysozyme in Water" on website. > However, on the energy miminization step, I cannot reproduce your results. > The minimization stopped at 61 steps. However, Sometimes it might stop at 760 steps. > I do not why gromacs cannot reproduce. A problem from compile? EM should be quite reproducible. You're probably not reproducing the same calculation. 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/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/mailing_lists/users.php
