Re: [gmx-users] Essential dynamics - concepts
Hi Kavya, On Sat, Jun 4, 2011 at 8:18 AM, Kavyashree M hmkv...@gmail.com wrote: Dear Gromacs users, I am new to essential dynamics, I have gone through some fundamentals in PCS, the mailing list related to ED and few publications by - Amadei (Proteins, 17, 412-425, 1993), a. Amadei (journal of biomolecular structure and dynamics, 13, 615, 1996) b. Berk Hess (Physical reviews E, 62, 8428-8448, 2000) c. Berk Hess (Physical reviews E, 63, 031910, 2002) d. Caterina (Biophysical chemistry, 92, 183-199, 2001) I have made a short note of what I understand. Please correct. the mistakes. 1. ED is principally used to study the anharmonic motions, ie those which are not equilibrated unlike equlibrated motions like bond vibrations, bending etc.. (Equilibrated in the time scale of study) No, ED does not make any assumptions on the nature of motions. It does not distinguish anharmonic from harmonic motions. It also does not distinguish between equilibrated and non-equilibrated motions. It will give insight in correlated (global) and non-correlated (local) motions. Note that it will only give linearly correlated motions, and neglects non-linear correlations. Also note that it will not give the motions that are most strongly correlated, btu those which have the largest extent of motion, collectivelye. (There is a modification on the gromacs contribution page to give the motions of highest correlation. 2. So one has to run a simulation long enough so that it is more than or equal to the time scale required for the specific motion (for eg. closing of loop takes place in few ps, one has to run MD for atleast a ns to investigate it) PCA/ED only allows one to make statements about the time scales simulated, so to describe a certain motion, the simulation has to be long enough to encompass the motion. 3. After MD for long enough time, when covariance matrix would indicate whether two atoms move in same direction, or opposite over the time of simulation based on positive or negative value. Extracting Eigenvalues and Eigenvectors from the matix gives the directions in which the highly correlated motions occur. The eigenvectors give the direction of the motion in conformational space, and the the eigenvalues the associated extents of the motions. An eigenvalue is an RMSF of the collective motion. 4. Analysing all the data values projected over the first few eigen vectors is the priciple component analysis. No, 'Principal component analysis' is rewriting the original data with many variables as a set of new variables that are linear combinations of the original ones but describe the underlying structure better. These new variables, the principal components or latent variables, presumably reflect the true degrees of freedom better. 5. if this experiment is done on same structure more than once (say 3), and the first few priciple components of all 3 simulations coincide, then it could be the most possible direction of motion in the protein otherwise the patern of PC's is most likely due to random motion. No, if they do not agree, then probably your system is ill-converged. But that is not the same as being random. My questions - 1. While chosing the period for covariance analysis, what is the criteria? in the paper b, author mention that a certain peroid was chosen because the peptide free enegry minimum. Not clear about this, because when the protein resides in an energy minimum how can there be transition to another configuration (eg a loop movement) without crossing the barrier. should we not consider the time which spans a native conformation to say an active conformation during the simulation? It depends on the time required for equilibration and the time scale of the process you're interested in. There's no golden standard there. 2. If we have done a long enough simulation of say 100ns for 4 proteins with similar structure but with sequence id of 40-60% (different chain lengths 230-260aa), Can we do a covar analysis of these 4 simulations? You can always do covariance analysis. Whether it makes sense is the real question ;) But it may certainly make sense to do covariance analysis on related systems. 3. How much should be the socine content to tell that it is not a random diffusion? All cows are animals, but not all animals are cows. Likewise, the principal components of random diffusion are characterised by their fit to a cosine series, but if you're projections yield a perfect fit to a cosine series... In most cases such a fit is obtained when the system is still equilibrating. 4. Is ED analysis itself is not enough to establish a important movement in the protein.. further ED sampling is required to prove it? Whether it's important is up to the researcher :) 5. Concept doubt - When all the structures at least square fitted before building a covariance matrix, where is the
[gmx-users] energy conservation
Hi all I have run a very long NVT simulation 500ns of one molecule (220 atoms) to try to assess the fluctuations in a particular event. When I analyse the energies it seems that the conserved quantity drifts significantly. Why would this be? Has it got to do with the thermostat I am using? Please find below the mdp file. title = Pull test cpp = include = define = integrator = md nsteps = 3 dt = 0.001 nstxout = 15 nstvout = 15 nstlog = 15 nstenergy = 15000 nstfout = 15 pbc = no nstlist = 0 ns_type = simple vdwtype = cut-off rlist = 0 rvdw_switch = 0 rvdw= 0 coulombtype = cut-off rcoulomb= 0 tcoupl = nose-hoover tc_grps = system tau_t = 0.1 ref_t = 400 gen_vel = no gen_temp= constraints = none comm_mode = angular Cheers Gavin -- 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] Essential dynamics - concepts
Dear Sir, Thanks for giving a clearer picture about essential dynamics. I was very eagerly awaiting for a reply. Thanks you very much :). No, ED does not make any assumptions on the nature of motions. It does not distinguish anharmonic from harmonic motions. It also does not distinguish between equilibrated and non-equilibrated motions. It will give insight in correlated (global) and non-correlated (local) motions. Note that it will only give linearly correlated motions, and neglects non-linear correlations. Also note that it will not give the motions that are most strongly correlated, btu those which have the largest extent of motion, collectivelye. (There is a modification on the gromacs contribution page to give the motions of highest correlation. Its g_covar contributed by Dr. Rossen apostolov if I am right. Here it states that those which are having correlation coefficient better than 0.5 will be reported, so covariance gives those which have correlation coefficient less than 0.5? PCA/ED only allows one to make statements about the time scales simulated, so to describe a certain motion, the simulation has to be long enough to encompass the motion. The eigenvectors give the direction of the motion in conformational space, and the the eigenvalues the associated extents of the motions. An eigenvalue is an RMSF of the collective motion. No, 'Principal component analysis' is rewriting the original data with many variables as a set of new variables that are linear combinations of the original ones but describe the underlying structure better. These new variables, the principal components or latent variables, presumably reflect the true degrees of freedom better. No, if they do not agree, then probably your system is ill-converged. But that is not the same as being random. So here the criteria for ill-convergence is the disagreement in the principle components of the 3 simulations, while random diffusion is the inherent property of PCA and its only the extent to which it can be fitted to a cosine that distinguishes if from a true random motion and any meaningful correlations. My questions - 1. While chosing the period for covariance analysis, what is the criteria? in the paper b, author mention that a certain peroid was chosen because the peptide free enegry minimum. Not clear about this, because when the protein resides in an energy minimum how can there be transition to another configuration (eg a loop movement) without crossing the barrier. should we not consider the time which spans a native conformation to say an active conformation during the simulation? It depends on the time required for equilibration and the time scale of the process you're interested in. There's no golden standard there. I understand here that time depends on the system under consideration. But my doubt was - for example if we consider a situation where time required for a conformational change of a protein from native to an active state is 100ps, then we run a simulation for some 5ns, so theoretically this change of conformations should have taken place 50 times in that 5ns time span. So if we take any 100ps (or to be on the safer side 500ps) time for the covariance analysis, after the system has equilibrated ie., leaving first few hundred ps, then we will be able to capture this feature of correlated movement in the covariance analysis, is that right? 2. If we have done a long enough simulation of say 100ns for 4 proteins with similar structure but with sequence id of 40-60% (different chain lengths 230-260aa), Can we do a covar analysis of these 4 simulations? You can always do covariance analysis. Whether it makes sense is the real question ;) But it may certainly make sense to do covariance analysis on related systems. In this case should we merge all the .xtc files and superpose all the conformations with a single pdb file. and then do a covar analysis? Will the difference in the amino acid and the length of the sequences matter during covariance analysis when we deal with structures with different sequence but with high degree of structural similarity? 3. How much should be the socine content to tell that it is not a random diffusion? All cows are animals, but not all animals are cows. Likewise, the principal components of random diffusion are characterised by their fit to a cosine series, but if you're projections yield a perfect fit to a cosine series... In most cases such a fit is obtained when the system is still equilibrating. Any numerical measure of the value of cosine content beyond which the analysis is said to be more of a random nature than being meaningful? 4. Is ED analysis itself is not enough to establish a important movement in the protein.. further ED sampling is required to prove it? Whether it's important is up to the researcher :) 5. Concept doubt -
[gmx-users] pull_vec
Hi all In umbrella sampling simulations: If pull_geometry = direction, and pull_vec is obviously a specified vector, does the distance between the two groups only vary along that vector? i.e Is the umbrella potential only defined along that vector? Many Thanks Gavin -- 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] writing trajectory with water molecules within a distance from protein
An update on this. I got the following to work: 1. use a vmd script closest.tcl (available on the vmd pages) to select closest N waters, and write a pdb file for each frame. 2. however, the above pdb files have different residue numbers for the water molecules for each frame because it is not the same N waters each frame. So use editconf to convert the pdbs to gros with the -resnr 1 option 3. concatenate the frames using trjcat ( -cat option) 4. make the correct time spacing using trjconv. (-timestep) The method is kinda tedious, but the final result is a trajectory of the protein with closest N-waters updated every step. Good enough for my analysis. On Tue, May 10, 2011 at 12:38 PM, Thomas Evangelidis teva...@gmail.comwrote: A work around will be available in the future as a plugin for VMD. For your reference read these threads: http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/14140.html http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/13217.html On 10 May 2011 03:12, Roland Schulz rol...@utk.edu wrote: On Mon, May 9, 2011 at 6:28 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 10/05/2011 12:50 AM, maria goranovic wrote: Dear experts I have a protein simulation in a water box. I now want to write a trajectory containing only the protein, and water molecules within 5 Angstroms of the protein, with the water list being updated each time step. How can one do this? Appreciate the help g_select is useful for dynamic selections of this type. g_select -select help can give examples and such. I'd hope it's been designed so that then using trjconv to extract such selections works, but I can't think how, having not ever tried. g_select writes out one index group per time frame. But trjconv can't use a different index group for each frame. Thus it can't be used to write out a trajectory with those atoms for each frame. Part of the problem is that the trajectory format doesn't support different number of atoms for different frames. What is possible is writing a small script around trjconv to produce one gro/trr file per frame with only those atoms. Roland 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 -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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 -- == Thomas Evangelidis PhD student Biomedical Research Foundation, Academy of Athens 4 Soranou Ephessiou , 115 27 Athens, Greece email: tev...@bioacademy.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- 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 -- Maria G. Technical University of Denmark Copenhagen -- 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] Essential dynamics - concepts
Hi Kavya, Its g_covar contributed by Dr. Rossen apostolov if I am right. Here it states that those which are having correlation coefficient better than 0.5 will be reported, so covariance gives those which have correlation coefficient less than 0.5? I don't know the modified version. But I presume that the components with eigenvalues higher than 0.5 are written out, which is not quite the same as having a correlation coefficient of 0.5. So here the criteria for ill-convergence is the disagreement in the principle components of the 3 simulations, while random diffusion is the inherent property of PCA and its only the extent to which it can be fitted to a cosine that distinguishes if from a true random motion and any meaningful correlations. Please get the random diffusion out of your head! :p Also, do some more background reading on PCA as a mathematical/statistical technique, not in relation to molecular simulations. It helps to form a better view on the matter. I understand here that time depends on the system under consideration. But my doubt was - for example if we consider a situation where time required for a conformational change of a protein from native to an active state is 100ps, then we run a simulation for some 5ns, so theoretically this change of conformations should have taken place 50 times in that 5ns time span. So if we take any 100ps (or to be on the safer side 500ps) time for the covariance analysis, after the system has equilibrated ie., leaving first few hundred ps, then we will be able to capture this feature of correlated movement in the covariance analysis, is that right? Most proteins will take quite a bit longer than 100ps to go from one to the other state. But besides that, if on average a process takes a certain time, it is not said that an interval of that length (or twice that length) will also contain the transition. You should have additional measures for the state of the protein and can then use PCA to understand which collective motions are related to the transition. In this case should we merge all the .xtc files and superpose all the conformations with a single pdb file. and then do a covar analysis? Will the difference in the amino acid and the length of the sequences matter during covariance analysis when we deal with structures with different sequence but with high degree of structural similarity? You can merge them. It's not the only way though, but I think it goes to far to try and explain the ins and outs here :p Do mind that any systems you want to compare have to have the same conformational space! In casu, that means that you have to extract trajectories of those parts of the system that are common to all variants. Any numerical measure of the value of cosine content beyond which the analysis is said to be more of a random nature than being meaningful? It's not about randomness! So in the paper, Berk Hess (Physical reviews E, 62, 8428-8448, 2000), an experiment conducted on Ompf porin, why is there a cosine nature in first four PC's, indicative of randomness, even when they have least-square fitted the structures before covariance analysis? Its quite unclear for me Sir as to what physically it means to say that there is random diffusion even after least-square fitting? If the scores (the projection of the trajectory) on the first principal component fit a cosine, it is indicative of a unidirectional process. Random diffusion of an atomic system is a unidirectional process. Note I'm not going to reply on covariance analysis more today :) Just be sure to take some time to think things over. Read a bit more from alternative sources, and let it all diffuse randomly into your head... :p Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials 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/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] Essential dynamics - concepts
Dear Sir, Thanks sir. I will go through them. However I have referred - A Tutorial on Principle component Analysis by Lindsay I Smith. Which gave a good understanding about the concepts. Still I have some doubts regarding eigen values, as you have told I will think over them again. But one statement I was not clear from your previous mail that - An eigenvalue is an RMSF of the collective motion. These eigenvalues are the solutions for an Nth order equation arising from N X N covar (sorry for using this term again) matrix (considering only x component). If we consider this covar matrix as a transformation matrix, eigen value would give the magnitude and direction by which the eigenvector is transformed linearly. Is it correct? I will try to think over it again. But I would be glad if you can clarify the doubt. (may be tomorrow). Or if you can provide some reference? Thank you Sir, With Regards M. Kavyashree On Mon, Jun 6, 2011 at 7:16 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Kavya, Its g_covar contributed by Dr. Rossen apostolov if I am right. Here it states that those which are having correlation coefficient better than 0.5 will be reported, so covariance gives those which have correlation coefficient less than 0.5? I don't know the modified version. But I presume that the components with eigenvalues higher than 0.5 are written out, which is not quite the same as having a correlation coefficient of 0.5. So here the criteria for ill-convergence is the disagreement in the principle components of the 3 simulations, while random diffusion is the inherent property of PCA and its only the extent to which it can be fitted to a cosine that distinguishes if from a true random motion and any meaningful correlations. Please get the random diffusion out of your head! :p Also, do some more background reading on PCA as a mathematical/statistical technique, not in relation to molecular simulations. It helps to form a better view on the matter. I understand here that time depends on the system under consideration. But my doubt was - for example if we consider a situation where time required for a conformational change of a protein from native to an active state is 100ps, then we run a simulation for some 5ns, so theoretically this change of conformations should have taken place 50 times in that 5ns time span. So if we take any 100ps (or to be on the safer side 500ps) time for the covariance analysis, after the system has equilibrated ie., leaving first few hundred ps, then we will be able to capture this feature of correlated movement in the covariance analysis, is that right? Most proteins will take quite a bit longer than 100ps to go from one to the other state. But besides that, if on average a process takes a certain time, it is not said that an interval of that length (or twice that length) will also contain the transition. You should have additional measures for the state of the protein and can then use PCA to understand which collective motions are related to the transition. In this case should we merge all the .xtc files and superpose all the conformations with a single pdb file. and then do a covar analysis? Will the difference in the amino acid and the length of the sequences matter during covariance analysis when we deal with structures with different sequence but with high degree of structural similarity? You can merge them. It's not the only way though, but I think it goes to far to try and explain the ins and outs here :p Do mind that any systems you want to compare have to have the same conformational space! In casu, that means that you have to extract trajectories of those parts of the system that are common to all variants. Any numerical measure of the value of cosine content beyond which the analysis is said to be more of a random nature than being meaningful? It's not about randomness! So in the paper, Berk Hess (Physical reviews E, 62, 8428-8448, 2000), an experiment conducted on Ompf porin, why is there a cosine nature in first four PC's, indicative of randomness, even when they have least-square fitted the structures before covariance analysis? Its quite unclear for me Sir as to what physically it means to say that there is random diffusion even after least-square fitting? If the scores (the projection of the trajectory) on the first principal component fit a cosine, it is indicative of a unidirectional process. Random diffusion of an atomic system is a unidirectional process. Note I'm not going to reply on covariance analysis more today :) Just be sure to take some time to think things over. Read a bit more from alternative sources, and let it all diffuse randomly into your head... :p Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and
[gmx-users] Fatal Error: The largest charge group contains 140 atoms. The maximum is 32
Hi All,
At this time, I am very much interested in using gromacs utilities for
analysis with {.dcd, .psf} files. Especially, eg., for g_density.
Primarily, I use NAMD/VMD for my work.
I am following this link from NAMD mailing list:
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/14046.html
As suggest, by Axel, I was able to get the {.top} file.
However, when I used gromacs's grompp command:
$ grompp -f minim1.mdp -c BL1_only.pdb -p BL1_only.top -o BL1_only.tpr
I was returned with an error like this:
* * *
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.4#
Generated 231 of the 231 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 231 of the 231 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'molecule0'
Excluding 3 bonded neighbours molecule type 'molecule1'
NOTE 1 [file BL1_only.top, line 1880]:
System has non-zero total charge: -5.99e+01
---
Program grompp, VERSION 4.5.4
Source code file:
/home/mandrake/rpm/BUILD/gromacs-4.5.4/src/kernel/grompp.c, line: 175
Fatal error:
The largest charge group contains 140 atoms. The maximum is 32.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---
My system is a mixed bilayer with negative 60 charge on it.
I am searching gromacs mailing list and still looking for an answer.
Is there a way to use g_density with my set of files - {.psf, .pdb, .dcd} ?
Please suggest and help.
Thanks a lot,
--- Lalit
p.s.: All relevant files: BL1_only.pdb; BL1_only.psf; BL1_only.top
minim1.mdp can be downloaded from:
http://lalitpkc.phy.uic.edu/~lalit/GROMACS_files
--
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] Fatal Error: The largest charge group contains 140 atoms. The maximum is 32
Lalit wrote:
Hi All,
At this time, I am very much interested in using gromacs utilities for
analysis with {.dcd, .psf} files. Especially, eg., for g_density.
Primarily, I use NAMD/VMD for my work.
I am following this link from NAMD mailing list:
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/14046.html
As suggest, by Axel, I was able to get the {.top} file.
However, when I used gromacs's grompp command:
$ grompp -f minim1.mdp -c BL1_only.pdb -p BL1_only.top -o BL1_only.tpr
I was returned with an error like this:
* * *
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.4#
Generated 231 of the 231 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 231 of the 231 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'molecule0'
Excluding 3 bonded neighbours molecule type 'molecule1'
NOTE 1 [file BL1_only.top, line 1880]:
System has non-zero total charge: -5.99e+01
---
Program grompp, VERSION 4.5.4
Source code file:
/home/mandrake/rpm/BUILD/gromacs-4.5.4/src/kernel/grompp.c, line: 175
Fatal error:
The largest charge group contains 140 atoms. The maximum is 32.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---
My system is a mixed bilayer with negative 60 charge on it.
I am searching gromacs mailing list and still looking for an answer.
Is there a way to use g_density with my set of files - {.psf, .pdb, .dcd} ?
The problem is the .top - as the error states, you have far too many atoms in a
charge group for grompp to actually let it pass. For simply doing analysis and
not an actual simulation, there is nothing wrong per se, but you will not be
able to create the necessary .tpr file. Charge groups should contain between 1
and 4 atoms, based on functional groups. The only way to make grompp work would
be to re-number your charge groups. See .rtp files for examples.
-Justin
Please suggest and help.
Thanks a lot,
--- Lalit
p.s.: All relevant files: BL1_only.pdb; BL1_only.psf; BL1_only.top
minim1.mdp can be downloaded from:
http://lalitpkc.phy.uic.edu/~lalit/GROMACS_files
http://lalitpkc.phy.uic.edu/%7Elalit/GROMACS_files
--
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
[gmx-users] proper tau_t value with SD
Hi, Gromacs manual says that when SD used as a thermostat, an appropriate value for tau_t is 2 ps, since this results in a friction that is lower than the internal friction of water, while it is high enough to remove excess heat (unless cut-off or reaction-field electrostatics is used). However, the free energy tutorial uses the smaller tau_t value, so I wonder whether I have to use 2 ps. Thanks. Hyunjin. -- 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] carbon nano tubes pdb file
Dear all, I need to create a starting pdb file for doble walled Carbon nano tube of desired radius with two graphene sheets.I already have one but when i use pdb2gmx gromacs The pdb file looks something like this.. RYST10.0000.0000.000 90.00 90.00 90.00 P 1 1 ATOM 1 C1 C04 X 1 -14.016 -14.520 -5.439 0.00 0.00 Q1 ATOM 2 C2 C04 X 1 -15.177 -15.176 -5.439 0.00 0.00 Q1 ATOM 3 C3 C04 X 1 -15.172 -16.503 -5.439 0.00 0.00 Q1 ATOM 4 C4 C04 X 1 -14.064 -17.290 -5.439 0.00 0.00 Q1 ATOM 5 C1 C04 X 1 -11.705 -14.546 -5.439 0.00 0.00 Q2 ATOM 6 C2 C04 X 1 -12.862 -15.229 -5.439 0.00 0.00 Q2 ATOM 7 C3 C04 X 1 -12.884 -16.614 -5.439 0.00 0.00 Q2 ATOM 8 C4 C04 X 1 -11.728 -17.307 -5.439 0.00 0.00 Q2 ATOM 9 C1 C04 X 1 -9.390 -14.555 -5.439 0.00 0.00 Q3 *pdb2gmx -f carbon.pdb -o out.pdb -p topol.top * its just a part of pdb i had attached the complete pdb file.i am able to view this in vmd.it fine.but when i do pdb2gmx it gives me the following error with charmm force field or any other force fields.. Processing chain 1 'X' (4765 atoms, 225 residues) There are 0 donors and 0 acceptors There are 0 hydrogen bonds Warning: Starting residue C041 in chain not identified as Protein/RNA/DNA. Warning: Starting residue C66B1 in chain not identified as Protein/RNA/DNA. Warning: Starting residue C66B2 in chain not identified as Protein/RNA/DNA. Warning: Starting residue C66B3 in chain not identified as Protein/RNA/DNA. Warning: Starting residue C66B4 in chain not identified as Protein/RNA/DNA. More than 5 unidentified residues at start of chain - disabling further warnings. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 8 out of 8 lines of specbond.dat converted successfully --- Program pdb2gmx, VERSION 4.5.3 Source code file: resall.c, line: 581 Fatal error: Residue 'C04' not found in residue topology database For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors any help please.. regards, sree. -- 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] proper tau_t value with SD
Hyunjin Kim wrote: Hi, Gromacs manual says that when SD used as a thermostat, an appropriate value for tau_t is 2 ps, since this results in a friction that is lower than the internal friction of water, while it is high enough to remove excess heat (unless cut-off or reaction-field electrostatics is used). However, the free energy tutorial uses the smaller tau_t value, so I wonder whether I have to use 2 ps. Some reference discussions: http://lists.gromacs.org/pipermail/gmx-users/2009-February/039508.html http://lists.gromacs.org/pipermail/gmx-users/2008-February/032341.html http://lists.gromacs.org/pipermail/gmx-users/2008-October/037339.html -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/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] carbon nano tubes pdb file
sreelakshmi ramesh wrote: Dear all, I need to create a starting pdb file for doble walled Carbon nano tube of desired radius with two graphene sheets.I already have one but when i use pdb2gmx gromacs The pdb file looks something like this.. RYST10.0000.0000.000 90.00 90.00 90.00 P 1 1 ATOM 1 C1 C04 X 1 -14.016 -14.520 -5.439 0.00 0.00 Q1 ATOM 2 C2 C04 X 1 -15.177 -15.176 -5.439 0.00 0.00 Q1 ATOM 3 C3 C04 X 1 -15.172 -16.503 -5.439 0.00 0.00 Q1 ATOM 4 C4 C04 X 1 -14.064 -17.290 -5.439 0.00 0.00 Q1 ATOM 5 C1 C04 X 1 -11.705 -14.546 -5.439 0.00 0.00 Q2 ATOM 6 C2 C04 X 1 -12.862 -15.229 -5.439 0.00 0.00 Q2 ATOM 7 C3 C04 X 1 -12.884 -16.614 -5.439 0.00 0.00 Q2 ATOM 8 C4 C04 X 1 -11.728 -17.307 -5.439 0.00 0.00 Q2 ATOM 9 C1 C04 X 1 -9.390 -14.555 -5.439 0.00 0.00 Q3 *pdb2gmx -f carbon.pdb -o out.pdb -p topol.top * its just a part of pdb i had attached the complete pdb file.i am able to view this in vmd.it http://vmd.it fine.but when i do pdb2gmx it gives me the following error with charmm force field or any other force fields.. Processing chain 1 'X' (4765 atoms, 225 residues) There are 0 donors and 0 acceptors There are 0 hydrogen bonds Warning: Starting residue C041 in chain not identified as Protein/RNA/DNA. Warning: Starting residue C66B1 in chain not identified as Protein/RNA/DNA. Warning: Starting residue C66B2 in chain not identified as Protein/RNA/DNA. Warning: Starting residue C66B3 in chain not identified as Protein/RNA/DNA. Warning: Starting residue C66B4 in chain not identified as Protein/RNA/DNA. More than 5 unidentified residues at start of chain - disabling further warnings. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 8 out of 8 lines of specbond.dat converted successfully --- Program pdb2gmx, VERSION 4.5.3 Source code file: resall.c, line: 581 Fatal error: Residue 'C04' not found in residue topology database For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors any help please.. The best place to start for all problems is to search the mailing list archive. This error comes up almost every week, and at least several times a year regarding CNT. I'll save you a few minutes and have you look here: http://www.gromacs.org/Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database For specifics about CNT and how to deal with them, refer to: http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube Some of the information is out of date, but there are posts in the archive that walk through almost all of the necessary information (again I say: search the archive). Don't use pdb2gmx; it doesn't handle non-linear molecules well. g_x2top is a much better option. -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/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] reg hydrophobicx interaction
Dear justin Thank u for your reply Is there is any tool to monitor the hydrophobic interactions between protein and any other ligand, or even within protein protein complexes? Also i want identify the residue which are responsible for hydrophobic interaction of my protein I sht ere is any tool? Thanks in advance -- 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] RE: Essential dynamics - concepts (Kavyashree M)
From: Tsjerk Wassenaar tsje...@gmail.com Subject: Re: [gmx-users] Essential dynamics - concepts To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: BANLkTim7wkRbvJZiJJbuHg=mkp5dgfu...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Hi Kavya, Its g_covar contributed by Dr. Rossen apostolov if I am right.? Here it states that those which are having correlation coefficient better than 0.5 will be reported, so covariance gives those which have correlation coefficient less than 0.5? I don't know the modified version. But I presume that the components with eigenvalues higher than 0.5 are written out, which is not quite the same as having a correlation coefficient of 0.5. It's the correlation coefficient indeed. the version is available from the Gromacs user contributions site. Ran -- 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
