Re: [gmx-users] Lateral Diffusion of Lipids
Am 8/12/13 5:26 AM, schrieb Kieu Thu Nguyen: Dear users, I want to use g_msd to measure diffusion coefficients of lipid bilayer. But i do not know how to choose the reference atom per lipid for an any type of lipid, such as POPC, DOPC,... Where i can get these references ? One suggestion: The two leaflets may move with respect to each other. Therefore, I recommend to compute D *within* each leaflet first - otherwise you may get a too large diffusion constant. Btw: g_select can be used to select the upper / lower phosphates into separate index groups. Jochen Thanks so much for any help ! ~Thu -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de/ --- -- 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] g_wham -sym
Hi, I think g_wham cannot symmetrize around a non-zero point. You'll have to write a little awk script or so and this yourself. Or edit the g_wham code. -zprof0 is not what you need. It sets the PMF to zero at a reference point, where the free energy is defined to zero. Best, Jochen Am 8/10/13 8:59 AM, schrieb Shima Arasteh: Thanks, I defined a new 0.0 position by -zprof0, and shifted the profile energy to a new 0.0. # g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kca -zprof0 -1.081898 -sym But -sym gets me an error: Fatal error: Cannot symmetrize profile around z=0 with min=-1.312664 and max=-1.081898 Why does the g_wham tries to still symmetrize the profile around z=0? Would you please give me any suggestion? Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Friday, August 9, 2013 2:40 PM Subject: Re: [gmx-users] g_wham -sym On 8/9/13 5:48 AM, Shima Arasteh wrote: Hi, I use the g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kca -sym I' d like to know if it is possible to symmetrize the profile around a non-zero point? forexample z=60? Use -zprof0. -Justin -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de/ --- -- 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] g_wham error analysis hangs
6100) Maximum change 1.345187e-05 6200) Maximum change 1.240432e-05 6300) Maximum change 1.143820e-05 6400) Maximum change 1.054720e-05 6500) Maximum change 9.725497e-06 6600) Maximum change 8.967716e-06 6700) Maximum change 8.268901e-06 6800) Maximum change 7.624473e-06 6900) Maximum change 7.030212e-06 7000) Maximum change 6.482219e-06 7100) Maximum change 5.976900e-06 7200) Maximum change 5.510938e-06 7300) Maximum change 5.081272e-06 7400) Maximum change 4.685081e-06 7500) Maximum change 4.319759e-06 7600) Maximum change 3.982905e-06 7700) Maximum change 3.672303e-06 7800) Maximum change 3.385910e-06 7900) Maximum change 3.121841e-06 8000) Maximum change 2.878356e-06 8100) Maximum change 2.653854e-06 8200) Maximum change 2.446856e-06 8300) Maximum change 2.255997e-06 8400) Maximum change 2.080021e-06 8500) Maximum change 1.917767e-06 8600) Maximum change 1.768166e-06 8700) Maximum change 1.630232e-06 8800) Maximum change 1.503056e-06 8900) Maximum change 1.385799e-06 9000) Maximum change 1.277687e-06 9100) Maximum change 1.178008e-06 9200) Maximum change 1.086104e-06 9300) Maximum change 1.001369e-06 Switched to exact iteration in iteration 9302 Converged in 9303 iterations. Final maximum change 9.98417e-07 Back Off! I just backed up profile.xvg to ./#profile.xvg.8# Wrote profile.xvg Any idea of what goes wrong? Best regards / Magnus -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de/ --- -- 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] Error bars - g_wham
Hi Stephen, computing errors from umbrella sampling is not trivial at al. Generally, there are two possibilities: - If each histogram overlaps only with one neighboring histogram, you *must* know the autocorrelation time of each window. This is often a problem in MD simulations, because there may be hidden slow transitions. In my experience, you always underestimate the autocorrelation time and as a consequence the statistical error. However, if you do know the autocorrelation time, then you can either (a) compute the PMF from blocks of the data (how you did), but this only works if the blocks are longer than the autocorrelation time or (b) use g_wham -bs-method traj to generate new synthentic histograms for bootstrapping (which incorporate the autocorrelation time). Important: You cannot do bootstrapping of complete histograms, because there is only one histogram at each window. - If you have many histograms overlapping each other, or if you did umbrella sampling at each window multiple times, you can assume that the different histograms represent all possible histograms at the respective position of the reaction coordinate. Then, you can do bootstrapping of histograms with g_wham -bs-method b-hist. It is not obvious how many histograms you need at each position, but maybe 10 is a reasonable number. Coming to your error from blocks of data (10-30, 30-50, 50-70, 70-100 ns). The small error you get could mean two things: a) you have a well-converged PMF (good) b) you have long autocorrelations. Therefore, the histograms from the blocks are similar. Therefore, you underestimate the error (bad). So you see, it is not trivial to estimate errors from umbrella sampling. My experience is that bootstrapping of histograms is more reliable, but it requires that you have multiple histograms at each position (and these histograms should be uncorrelated!!). But at least, this way you do not need to know the autocorrelation times, but instead only need to generate histograms which are independent. The latter is easier in practice, because independent simulations are more likely to be uncorrelated than frames *within* one simulation. I hope this helps a bit. Cheers, Jochen Am 2/19/13 3:22 PM, schrieb Steven Neumann: Dear Gmx Users, I run 10 US windows of 100 ns each - ion binding protein. I have a great convergence of profiles and good windows overlap.I tried to see PMF profiles from 10-30, 30-50, 50-70, 70-100 ns and they look very similar (Max. error would be 0.2 kcal/mol). The overal deltaG is about -5 kcal/mol. When I use g_wham with -nBootsrap 200 and -bins 200 I get error bars of -1.2 kcal/mol which is very significant. How can I impove my error bars? Why they are so large? Steven -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de/ --- -- 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] g_wham missing option
Hi Anthony, just one remark here: Make sure you have always a couple of histograms overlapping each other (maybe 5-10). If every histogram overlaps only with two neighbors, you will severely underestimate the error. Hence, to estimate the error, you need rather many histograms from many short umbrella simulations than few histograms from few long umbrella simulations. Cheers, Jochen Am 2/3/13 11:43 AM, schrieb Nash, Anthony: Hi Justin, Thanks for the reply. You were spot on about the version difference. Thanks again. Anthony From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: 02 February 2013 18:06 To: Discussion list for GROMACS users Subject: Re: [gmx-users] g_wham missing option On 2/2/13 12:58 PM, Nash, Anthony wrote: Hi All, I am using Gromacs 4.5.5 and running free energy calculations. According to the article g_wham - A Free Weighted Histogram.. (J. Chem. Theory. Comput. 2010, 6, 3713-3720), there is the option -bs-method. However, I am unable to find this option when running g_wham. I want to use bayesian bootstraps of complete histograms. I have a feeling I am missing something completely obvious. Any help would be appreciated. Take a closer look at g_wham -h. The option you're asking about is definitely there. Also be sure you're using the version you think you are; g_wham was overhauled between 4.0.7 and 4.5. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de/ --- -- 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] virtual site generation for backbone hydrogen
Sorry, I found the error. There was a bond -C N missing in the rtp file. Cheers, Jochen Am 12/17/12 5:28 PM, schrieb Jochen Hub: Hi all, I try to generate a topology using pdb2gmx of a protein that contains a non-native amino acid, that is lysine with some more atoms, which is treated a one amino acid RETK. Without vsites, everything works fine. With pdb2gmx -vsite hydrogen, a constraint is generated between the backbone CA and H (that gives an error later grompp since the constraint type CT-H is not defined). [ atoms ] ... 3603 H216 RETK H 3241 0.2747 1.008 3604 CT216 RETK CA 3242 -0.24 13.018 [ constraints ] 3603 3604 2 If the non-native aa is replaced by a LYS, pdb2gmx generates instead: [ virtual_sites3 ] 3603 3602 3600 3604 2 I now wonder how to tell pdb2gmx that RETK should be treated as any other amino acid, that is that the backbone-H should be turned into a virtual_site3. I have already added RETK into residuetypes.dat, and there are entries in the rtp and hdb. Many thanks in advance for any help, Jochen -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de/ --- -- 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] virtual site generation for backbone hydrogen
Hi all, I try to generate a topology using pdb2gmx of a protein that contains a non-native amino acid, that is lysine with some more atoms, which is treated a one amino acid RETK. Without vsites, everything works fine. With pdb2gmx -vsite hydrogen, a constraint is generated between the backbone CA and H (that gives an error later grompp since the constraint type CT-H is not defined). [ atoms ] ... 3603 H216 RETK H 3241 0.2747 1.008 3604 CT216 RETK CA 3242 -0.24 13.018 [ constraints ] 3603 3604 2 If the non-native aa is replaced by a LYS, pdb2gmx generates instead: [ virtual_sites3 ] 3603 3602 3600 3604 2 I now wonder how to tell pdb2gmx that RETK should be treated as any other amino acid, that is that the backbone-H should be turned into a virtual_site3. I have already added RETK into residuetypes.dat, and there are entries in the rtp and hdb. Many thanks in advance for any help, Jochen -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de/ --- -- 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] g_wham with pull_geometry=position
Hi, are you sure that you want to have pull_dim = Y Y Y (which is the default)? When you want to pull only in z direction, I would use pull_dim = N N Y. Otherwise, your z coordinate is not your reaction coordinate. If you want to pull in 3 dimensions you probably want to use pull_geomery=distance. Hope this helps, Jochen Am 11/4/12 7:17 PM, schrieb David Peeler: Hello all, My simulation involves the pulling of a protein in the negative direction of the z-axis into a stationary hydrophobic self-assembled monolayer surface model (MTHL) using the position pull geometry. My umbrella parameters in the md_umbrella.mdp file are as follows: pull= umbrella pull_geometry = position pull_vec1 = 0 0 1 pull_start = yes pull_ngroups= 1 pull_group0 = MTHL pull_group1 = Protein ;pull_init1 = 0 pull_rate1 = 0.0 pull_k1 = 500 My output pullf files have three dimensions in them because of the pull_vec definition, so I wrote a script to calculate the magnitude of the pull force and to return the files with a time column and a force column. I was told by g_wham to make my own pdo files, but am struggling to do so; it looks like I have to insert a header with all the umbrella information for each run in the beginning of each file. I believe the header for my files should look like this: # UMBRELLA 3.0 # Component selection: 0 0 1 # nSkip 1 # Ref. Group ’MTHL’ # Nr. of pull groups 1 # Group 1 'Protein’ Umb. Pos. Z Umb. Cons. 500 # I'm not sure what nSkip means and I'm not sure what I should put for Component selection. Can someone give me a quick tutorial or a script that helps create pdo files? I tried passing the files I created with the force magnitudes to g_wham as normal pullf files (since those don't have strange headers); however, using the -if option requires the -it option and those tpr files contain information about the pull_vec that generates this output: Fatal error: Found pull geometry 'position' and more than 1 pull dimension (3). Hence, the pull potential does not correspond to a one-dimensional umbrella potential. Is there a simpler way to do g_wham with position pull geometry? I believe my intuition to calculate the magnitude of the force is correct but would be interested to see if anyone thinks only the z-component of the umbrella force is of interest. Thanks, David Peeler Matysiak Biomolecular Modeling Laboratory Fischell Department of Bioengineering University of Maryland, College Park -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de/ --- -- 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: [gmx-developers] shell polarizable water model
= 32 fourier_nz = 32 pme_order= 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no gb_algorithm = Still nstgbradii = 0 rgbradii = 0 gb_saltconc = 0 implicit_solvent = No tcoupl = nose-hoover nsttcouple = -1 nh-chain-length = 10 tc-grps = system tau-t= 0.05 ref-t= 300 gen-vel = yes gen-temp = 300 gen-seed = 173529 constraints = all-bonds constraint-algorithm = shake continuation = no Shake-SOR= no shake-tol= 0.0001 lincs-order = 4 lincs-iter = 2 lincs-warnangle = 30 morse= no energygrp_excl = nwall= 0 wall_type= 9-3 wall_r_linpot= -1 wall_atomtype= wall_density = wall_ewald_zfac = 3 pull = no disre= No disre-weighting = Conservative disre-mixed = no disre-fc = 1000 disre-tau= 0 nstdisreout = 100 orire= no orire-fc = 0 orire-tau= 0 orire-fitgrp = nstorireout = 100 dihre= no dihre-fc = 1000 free-energy = no init-lambda = 0 delta-lambda = 0 foreign_lambda = sc-alpha = 0 sc-power = 0 sc-sigma = 0.3 nstdhdl = 10 separate-dhdl-file = yes dhdl-derivatives = yes dh_hist_size = 0 dh_hist_spacing = 0.1 couple-moltype = couple-lambda0 = vdw-q couple-lambda1 = vdw-q couple-intramol = no userreal4= 0 -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de/ --- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: genbox Not enough memory
Hi, this is due to the way genbox -ci is currently implemented. It calles add_conf() too often which leaks memory. So you'll have to edit the code. Jochen You'll have to edit the genbox code in order Am 10/10/12 7:14 PM, schrieb Dr. Vitaly Chaban: Thanks..You are right...The last line of gro file says 250 so it is in nm!... On 10 October 2012 12:30, Christopher Neale chris.ne...@mail.utoronto.ca wrote: Sounds like you ran out of memory. Many clusters have a few large-memory nodes. Can you use one of those? It's failing on a call for 1.3 Gb of memory, which by itself isn't really a lot... Also, can you confirm 250 A box length, not 250 nm box length? Gromacs defines length in units of nm. Chris. -- original message -- I am trying to build a polymer in solvent system by solvating my fully extended polymer chains in a box of size 250 250 250 A. I am adding 4500 solvent molecules as below genbox -cp Solute.gro -ci solvent.gro -o solvated.gro -nmol 4500 Adding solvents is a slow process and takes much time and at the end I get: Program genbox, VERSION 4.5.4 Source code file: smalloc.c, line: 214 Fatal error: Not enough memory. Failed to realloc 1338273212 bytes for grid-nra, grid-nra=0x0 (called from file nsgrid.c, line 483) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Is this happening because of the huge amount of free space to be filled with the solvent? Please help me. Genbox sometimes suffers from the out-of-memory error. Based on my own investigation, this is indeed what happens here, because the utility uses a kind of grid during its operation. The larger the cell, the more hungry it becomes, no matter how many molecules you want to insert. The standard advice therefore applies - add memory... Another question is why you need such a huge box? The only thing I could imaging is simulating a droplet-vapor/air interface... Another advice is to start with a smaller box and then extend its deminsions using editconf (which does not care about the box size). Dr. Vitaly V. Chaban MEMPHYS - Center for Biomembrane Physics Department of Physics, Chemistry and Pharmacy University of Southern Denmark Campusvej 55, 5230 Odense M, Denmark -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de/ --- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: genbox Not enough memory
ps: There is a fix for this issue in Gerrit code review: https://gerrit.gromacs.org/#/c/1175/ which introduces a fix genbox -allpair. This avoid the memory-leaky neighbor searching, which is the reason for your problem. Jochen Am 10/11/12 10:56 AM, schrieb Jochen Hub: Hi, this is due to the way genbox -ci is currently implemented. It calles add_conf() too often which leaks memory. So you'll have to edit the code. Jochen You'll have to edit the genbox code in order Am 10/10/12 7:14 PM, schrieb Dr. Vitaly Chaban: Thanks..You are right...The last line of gro file says 250 so it is in nm!... On 10 October 2012 12:30, Christopher Neale chris.ne...@mail.utoronto.ca wrote: Sounds like you ran out of memory. Many clusters have a few large-memory nodes. Can you use one of those? It's failing on a call for 1.3 Gb of memory, which by itself isn't really a lot... Also, can you confirm 250 A box length, not 250 nm box length? Gromacs defines length in units of nm. Chris. -- original message -- I am trying to build a polymer in solvent system by solvating my fully extended polymer chains in a box of size 250 250 250 A. I am adding 4500 solvent molecules as below genbox -cp Solute.gro -ci solvent.gro -o solvated.gro -nmol 4500 Adding solvents is a slow process and takes much time and at the end I get: Program genbox, VERSION 4.5.4 Source code file: smalloc.c, line: 214 Fatal error: Not enough memory. Failed to realloc 1338273212 bytes for grid-nra, grid-nra=0x0 (called from file nsgrid.c, line 483) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Is this happening because of the huge amount of free space to be filled with the solvent? Please help me. Genbox sometimes suffers from the out-of-memory error. Based on my own investigation, this is indeed what happens here, because the utility uses a kind of grid during its operation. The larger the cell, the more hungry it becomes, no matter how many molecules you want to insert. The standard advice therefore applies - add memory... Another question is why you need such a huge box? The only thing I could imaging is simulating a droplet-vapor/air interface... Another advice is to start with a smaller box and then extend its deminsions using editconf (which does not care about the box size). Dr. Vitaly V. Chaban MEMPHYS - Center for Biomembrane Physics Department of Physics, Chemistry and Pharmacy University of Southern Denmark Campusvej 55, 5230 Odense M, Denmark -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de/ --- -- 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] PhD position in Göttingen/Germany
Dear simulators, we have a PhD position available in the Computational Molecular Biophysics group in Göttingen (Germany). Please have a look here for more details: http://cmb.bio.uni-goettingen.de/jobs.html Thank you, Jochen -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de/ --- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Bootstrapping using g_wham
Hi, sorry for this late comment, I just stepped over this thread. Bootstrapping is indeed slow, because a complete WHAM analysis must be done for each bootstrap. I usually do much less bootstraps (around 50 to 100 gives a reasonable estimate), less bins, and I sometimes I reduce the tolerance for convergence. I would first play a bit with the tolerance and bins to see if they change your profile, probably they do not. Then you can use, e.g. -nBootstrap 100 -bins 200 -tol 1e-5 Cheers, Jochen Am 6/15/12 1:19 PM, schrieb Tsjerk Wassenaar: Hey, Most statistics texts on bootstrapping will advise taking in the order of a thousand bootstrap samples. Don't know about the number of bins, but in any case, the problem shouldn't be that hard computationally. Have you checked the process? Is it really still running, has it stalled? And how long does one bootstrap sample take to process? Always good to check one before running a thousand... Cheers, Tsjerk On Fri, Jun 15, 2012 at 12:35 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 6/14/12 5:51 PM, rainy908 wrote: Hi, I am currently using bootstrapping in g_wham to estimate the uncertainty in my PMF. I use a number of 1000 bootstraps. /software/gromacs/gromacs-4.0.7-plumed-1.2.0-x86_64/bin//g_wham \ -ip gwham.dat \ -bins 5000 \ -hist histo.xvg \ -bsres bsResult.xvg \ -nBootstrap 1000 This process has been running on 1 node for the past 4 days straight, and I am not sure when it will ever finish. Should I be concerned? I certainly would be. You're using a very large number of bins and bootstraps, far above the default value of 200 for each. Do you need that many? What happens if you run with values of 200 of -bins and -nBootstrap? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de/ --- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Force constant in g_wham
Hi, the umbrella potential is 0.5*k*(z-z0)^2 Jochen Am 6/14/12 11:41 PM, schrieb rainy908: Dear gmx-users, I am writing to clarify that the force constant kappa for g_wham corresponds to K_i itself, and not the quantity (1/2)*K_i in the umbrella potential W_i(ξ) = (K_i/2)*(ξ-ξ_i)^2. I recall reading somewhere that the force constant sometimes includes the (1/2) term in front of K_i, and sometimes not. Thank you, Lili -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de/ --- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] rare huge forces in constraint simulation with direction_periodic
Hi, I am running a constraint simulation, with 12 molecules restrained with respect to the center of mass of a lipid membrane. During 5ns of simulation, I get a few frames (e.g. 10 or so) with huge forces on all molecules, whereas the forces in all other frames are fine. When looking at the simulation, nothing looks spurious. There are no LINCS warnings or so. Here is an example. Note the large forces at t=385.32. In pullx.xvg, the molecules are not set to the correct constrained position in the problematic frame: pullf (12 pull groups, 4 pull shown here): 385.12 6.65942 325.524 -122.863 -156.645 ... 385.16 312.699 498.147 -282.365 66.9014 ... 385.2 271.748 581.749 42.3289 -48.3744 ... 385.24 256.169 481.929 -147.006 -163.566 ... 385.28 360.289 435.808 -128.435 126.654 ... 385.32 27214.7 27461.9 26817.9 27025.9 ... 385.36 140.386 129.482 359.494 -5.16442 ... 385.4 -0.0698604 -457.767-68.48173.24 ... 385.44 -323.406 -161.396 -187.093 396.581 ... 385.48 -427.383 19.5112 -144.655 -95.9228 ... 385.52 -102.406 61.0266 -758.817 35.7622 ... pullx (12 pull groups, reference group + 4 pull groups shown here). The four molecules shown here are restrained at z=-1.831 with respect to the lipid membrane: 385.123.5217-1.831-1.831-1.831-1.831 ... 385.163.5217-1.831-1.831-1.831-1.831 ... 385.23.5216-1.831-1.831-1.831-1.831 ... 385.24 3.52142-1.831-1.831-1.831-1.831 ... 385.28 3.52231-1.831-1.831-1.831-1.831 ... 385.323.5222 -1.83208 -1.83208 -1.83208 -1.83208 ... 385.36 3.52209-1.831-1.831-1.831-1.831 ... 385.4 3.52192-1.831-1.831-1.831-1.831 ... 385.44 3.52175-1.831-1.831-1.831-1.831 ... 385.48 3.52165-1.831-1.831-1.831-1.831 ... 385.52 3.52156-1.831-1.831-1.831-1.831 ... I used gmx 4.5.5-dev, the relevant mdp options are (pressure coupling in z is switched off): pull = constraint pull_geometry= direction_periodic pull_dim = N N Y pull_constr_tol = 1e-06 pull_ngroups = 12 pull_group0 = refgroup pull_weights0= pull_pbcatom0= 54 pull_group1 = Solute_Layer0_Channel0 pull_weights1= pull_pbcatom1= 0 pull_vec1= 0.0 0.0 1.0 pull_init1 = -1.8310 pull_rate1 = 0 ... Apart from this, I use the md integrator, LINCS for all bonds, V-rescale T-coupling (tau=5ps), pressure coupling in the xy plane only (compressibility = 4.5e-5 0 with Pcoupltype = semiisotropic), LJ cutoff at 1nm, PME, so normal settings. Did anyone see a similar behavior? Or any hints what one could try? Bug or feature of the constraint algorithm? Many thanks in advance, Jochen -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de/ --- -- 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] rare huge forces in constraint simulation with direction_periodic
Sorry, I forgot: I used gmx version 4.5.5-dev. Jochen Am 6/25/12 3:53 PM, schrieb Jochen Hub: Hi, I am running a constraint simulation, with 12 molecules restrained with respect to the center of mass of a lipid membrane. During 5ns of simulation, I get a few frames (e.g. 10 or so) with huge forces on all molecules, whereas the forces in all other frames are fine. When looking at the simulation, nothing looks spurious. There are no LINCS warnings or so. Here is an example. Note the large forces at t=385.32. In pullx.xvg, the molecules are not set to the correct constrained position in the problematic frame: pullf (12 pull groups, 4 pull shown here): 385.12 6.65942 325.524 -122.863 -156.645 ... 385.16 312.699 498.147 -282.365 66.9014 ... 385.2 271.748 581.749 42.3289 -48.3744 ... 385.24 256.169 481.929 -147.006 -163.566 ... 385.28 360.289 435.808 -128.435 126.654 ... 385.32 27214.7 27461.9 26817.9 27025.9 ... 385.36 140.386 129.482 359.494 -5.16442 ... 385.4 -0.0698604 -457.767-68.48173.24 ... 385.44 -323.406 -161.396 -187.093 396.581 ... 385.48 -427.383 19.5112 -144.655 -95.9228 ... 385.52 -102.406 61.0266 -758.817 35.7622 ... pullx (12 pull groups, reference group + 4 pull groups shown here). The four molecules shown here are restrained at z=-1.831 with respect to the lipid membrane: 385.123.5217-1.831-1.831-1.831-1.831 ... 385.163.5217-1.831-1.831-1.831-1.831 ... 385.23.5216-1.831-1.831-1.831-1.831 ... 385.24 3.52142-1.831-1.831-1.831-1.831 ... 385.28 3.52231-1.831-1.831-1.831-1.831 ... 385.323.5222 -1.83208 -1.83208 -1.83208 -1.83208 ... 385.36 3.52209-1.831-1.831-1.831-1.831 ... 385.4 3.52192-1.831-1.831-1.831-1.831 ... 385.44 3.52175-1.831-1.831-1.831-1.831 ... 385.48 3.52165-1.831-1.831-1.831-1.831 ... 385.52 3.52156-1.831-1.831-1.831-1.831 ... I used gmx 4.5.5-dev, the relevant mdp options are (pressure coupling in z is switched off): pull = constraint pull_geometry= direction_periodic pull_dim = N N Y pull_constr_tol = 1e-06 pull_ngroups = 12 pull_group0 = refgroup pull_weights0= pull_pbcatom0= 54 pull_group1 = Solute_Layer0_Channel0 pull_weights1= pull_pbcatom1= 0 pull_vec1= 0.0 0.0 1.0 pull_init1 = -1.8310 pull_rate1 = 0 ... Apart from this, I use the md integrator, LINCS for all bonds, V-rescale T-coupling (tau=5ps), pressure coupling in the xy plane only (compressibility = 4.5e-5 0 with Pcoupltype = semiisotropic), LJ cutoff at 1nm, PME, so normal settings. Did anyone see a similar behavior? Or any hints what one could try? Bug or feature of the constraint algorithm? Many thanks in advance, Jochen -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de/ --- -- 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] Umbrella sampling PMF, drug and membrane with pull_geometry=cylinder
Hi, we had similar trouble some time ago, and we could solve it by using a good PBC atom. Make sure that your pbc_atom is in the very center of your membrane. Btw, using distance to compare with cylinder is a bad test, since it does something very different (the distance is the same at z=com-1 and z=com+1. I would use direction or position for your test. You can also use position/direction for the umbrella simulations, you'll probably get similar results to the geometry cylinder, but you'll also have to make sure your pbc_atom is fine. Cheers, Jochen Am 4/29/12 9:20 PM, schrieb J B: Does the cylinder geometry work if you use pull_start = no and pull_init1 equal to your starting (restraint) distance? I'm just trying to go through all of the iterations of what might be failing. In theory, what you're doing is fine but I'd be interested to know if there was something failing in the input parsing such that pull_start is not being properly applied. The screen output of grompp will also tell you what it believes the restraint distance is. If it prints 0, then there's a problem with input processing. If the problem is reproducible in the latest Gromacs version (4.5.5), please file a bug report on redmine.gromacs.org so that it can be investigated. Please provide .tpr file of the system so that the developers can run what you are trying to do and see. -Justin It works if I set pull_start to the initial distance given by g_dist things work just fine. So this will be the way for now at least. Guess that there could be an error in the inout parsing then. Thanks a lot for your help, really appreciate it. -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de/ --- -- 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] Structures and topologies of cholesterol-containing membranes
Hi, we have recently put a website online with structures and topologies of a large set of 28 different cholesterol-containing membranes: http://cmb.bio.uni-goettingen.de/cholmembranes.html Structures of membranes containing - DMPC - DPPC - POPC - DOPC - POPE - POPE and POPC plus different amounts of cholesterol are available. Please feel free to use them if they are relevant for your research (we only ask to cite our papers). Happy simulating, Jochen -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de/ --- -- 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] g_wham position 0
Hi, the key Umb. Pos. 0.0 indicates the the umbrella center of this simulaiton is at 0.0, not that the profile should starts at zero. Beginning and end of profile are set with -min -max. cheers, Jochen Am 3/22/12 7:03 PM, schrieb rainy908: Hi all, I am experiencing a potential problem with my PMF curve not starting at position 0 of the reaction coordinate, which is defined by a path starting from 0.0 nm and ending at 0.5 nm. When I run the GROMACS g_wham analysis at Umb. Pos 0.0 (see below), to say, 0.02 nm, the PMF curve doesn't start out at 0.0 nm but gets offset to ~0.01 nm in the resulting figure. Its corresponding histogram also gets offset by the same amount. This is particularly peculiar to me because my frame1 *is* the structure at 0.0nm of the S path. I also double-checked my COLVAR file and there are no negative values in my COLVAR file: # UMBRELLA3.0 # Compnent selection: 0 0 1 # nSkip 1 # Ref. Group 'TestAtom' # Nr. of pull groups 1 # Group 1 'GR1' Umb. Pos. 0.0 Umb. Cons. 5 # 0.0300 0.47500 0.0400 0.000103337 0.0500 0.000163820 0.0600 0.000265547 0.0700 0.000408777 0.0800 0.000550200 0.0900 0.000653522 Has anyone else experienced this problem before? I'm hoping it's just some minor issue in g_wham. I even invoked the -zprof0 flag to - zprof 0 and it did not set my PMF curve to start at 0. Sincerely, Lili -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de/ --- -- 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] Statistical error of Umbrella Sampling
Hi, check http://pubs.acs.org/doi/abs/10.1021/ct100494z and g_wham -h Cheers, Jochen Am 3/20/12 10:10 AM, schrieb Steven Neumann: Dear Gmx Users, Could you please write me how to evaluate the statistical error of the binding free energy obtained by umbrella sampling? Thank you Steven -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de/ --- -- 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] g_wham with cylinder geometry
Hi MPID, I just stepped over your message quite late, so sorry for the late reply. You can simply generate a new set of tpr files with pull_dim= N N Y, and use that one in g_wham. g_wham only picks the force constants and umbrella centers from the tpr files, so you are fine with that. Jochen Am 2/11/12 1:22 AM, schrieb MPID: Hi everyone. I ran an umbrella sampling simulation of a protein in a membrane. I used pull_geometry=cylinder. I tried to analyze the results with g_wham. I got this error: Fatal error: With pull geometry 'cylinder', expected pulling in Z direction only. However, found dimensions [Y Y Y] The manual says that with this geometry the pulling is in the direction of pull_vec. I set pull_vec to 0 0 1. Do I have to redo these simulations with a line that says pull_dim = N N Y? Or does the data still mean what it is supposed to, but g_wham is just giving trouble and I can use a different wham program? Here is the pull part of my mdp file: pull = umbrella pull_geometry= cylinder pull_r0 = 2.0 pull_r1 = 1.5 pull_vec1= 0 0 1 pull_start = yes pull_group0 = DPPGB pull_group1 = PROT pull_k1 = 500 pull_nstxout = 1000 pull_nstfout = 1000 -- View this message in context: http://gromacs-users-forum.5086.n6.nabble.com/g-wham-with-cylinder-geometry-tp4385053p4385053.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de/ --- -- 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] Umbrella sampling and WHAM along a curved pathway?
Hi, since there is no pull type for curved pathways, you have to generate the gmx3-type pdo files from your simlation output and use these in g_wham (g_wham -ip). See g_wham -h for a example header of a pdo file. Cheers, Jochen Am 2/14/12 5:53 PM, schrieb HAO JIANG: Dear all, I would like to calculate the PMF along a curved reaction pathway using umbrella sampling. I just wonder if it is appropriate to use g_wham to extract the PMF along the curved pathway? Any help would be appreciated. Hao Jiang -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de/ --- -- 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] Spherical constraint (spherical force)
Hi Mikhail, we hard-coded the flat-bottom potential into bondfree.c which is in src/gmxlib. I send you the source file in a separate e-mail. The patch will replace all position restraints by a flatt-bottom spherical potential with a flat radius of 1.4nm. If you want a different radius you'll have to change the bondfree.c, look for the posre function. It's a quite dirty inflexible hack, but it was good enough for us. So you cannot have normal position restraints and the flat-bottom restraints at the same time. Note that you must define the reference position of all the position restraint potentials with the -r option of grompp. E.g., if your droplet is at the origin, you need a gro/pdb file with all coordinates set to 0,0,0 to be used with the -r option. The position restraints are defined as usual in the [ position_restraints ] sections in the topology. I hope this helps, please let us know if something is unclear. Jochen On 10/17/11 Oct 17,2:41 PM, Mikhail Stukan wrote: Dear gmx-user, I would like to simulate an isolated drop of water (without PBC). To prevent water molecules form evaporation I would like to create a spherical constraint around the system. In recent article in PNAS (Caleman, Hub, van Maaren, van der Spoel, v. 108, 6838 (2011)) where the authors considered similar system it is mentioned that: To avoid such evaporation, we applied a spherical flat-bottom quadratic potential acting on the water. That potential was implemented as an additional force F pointing toward the COM of the droplet... Could anybody give a hint how this approach can be realized in GROMACS? I looked through the manual, but did not find clear answer how to implement such a force. Thank you very much in advance. Mikhail = Dr Mikhail Stukan Schlumberger Dhahran Carbonate Research Center, Dhahran Techno Valley - KFUPM, P.O. Box 39011, Dammam / Doha Camp 31942, Kingdom of Saudi Arabia Tel: +966 3 331 6182 Fax:+966 3 330 0845 mstu...@slb.com mailto:mstu...@slb.com -- --- Dr. Jochen Hub Computational and Systems Biology Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4715056 Fax: +46-18-511755 http://xray.bmc.uu.se/~jochen/index.html --- -- 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] GPUs and umbrella sampling
On 7/18/11 Jul 18,5:37 PM, Guido Polles wrote: Hi everybody, I noticed that GPU version of gromacs do not support the pull code, hence i suppose g_wham cannot be used to extract a PMF. I would like to just ask if somebody could suggest or give any hint about the way to do umbrella sampling and extract a PMF without pull code, so that I will have an idea before I start diving deeper into the issue, make mistakes and potentially write useless code. Thanks in advance for any advice. Guido Polles You may also try to use position restraints, not sure if they are supported by the GPU version though. Then use g_traj to get the displacements with respect to the umbrella center and generate pdo files, which used to be the Gromacs 3 pull code output. g_wham can read pdo files. Please check g_wham -h for a typical pdo file header format. Cheers, Jochen -- --- Dr. Jochen Hub Computational and Systems Biology Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4715056 Fax: +46-18-511755 http://xray.bmc.uu.se/~jochen/index.html --- -- 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] error bars g_wham
On 6/20/11 Jun 20,1:01 PM, Gavin Melaugh wrote: Hi all I have read the manual and the recent JCTC paper on g_wham, and I was wondering how to actually get the error bars on the profile.xvg file outputted from g_wham. Many Thanks Gavin Hi Gavin, the error bars are at the moment only in bsResult.xvg (option -bsres), not in profile.xvg. Cheers, Jochen -- --- Dr. Jochen Hub Computational and Systems Biology Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4715056 Fax: +46-18-511755 http://xray.bmc.uu.se/~jochen/index.html --- -- 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] g_traj -ox -com slight inconsistency
Hi Chris, I noticed something similar some time ago. The issue is that the masses are read from atommass.dat according to the atom name, if you do not support a tpr file (that is with -s a.gro). In that case, sometimes the wrong mass is used. In my structure I had a hydrogens called HG (for H-gamma), and a mass of 200.59000 for mercury was used instaed of a mass of one. So I guess the only way to be really sure that the COM is computed correctly is to use a tpr file. Cheers, Jochen On 5/2/11 May 2,6:11 PM, Chris Neale wrote: Dear Users: I have noticed an inconsistency with g_traj -ox -com output when using -f a.gro and either -s a.gro or -s a.tpr where a.tpr was constructed from a.gro. There does not appear to be any difference when not using the -com flag. The difference is on the order of =0.008 nm so I suppose that it could be related to rounding and order of operations or precision. The same results exist for at least 4.0.5 and 4.5.3. Thanks, Chris. -- --- Dr. Jochen Hub Computational and Systems Biology Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4715056 Fax: +46-18-511755 http://xray.bmc.uu.se/~jochen/index.html --- -- 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] g_wham PMF profile
The reliability of the PMF curve depends on the reliability of sampling. If you're over-sampling in some regions along the reaction coordinate and under-sampling in others, then the weighting is probably wrong and the result inaccurate. I can't tell exactly from your description what's going on, but if you have largely overlapping histograms, then your window spacing and/or force constant settings are inappropriate. I don't really agree with the last point (with the first I fully agree). In my experience it helps a lot if you have multiple overlapping histograms. If each histograms overlaps only with the two neighbors, you typically get large uncertainties - even worse, since you usually don't know the autocorrelation time, you cannot even estimate your uncertainty. In addition, I don't see any reason why WHAM should have problems in case of largely overlapping histograms. My strong suggestion is to use as many histograms as possible, such that multiple histograms overlap. Make sure (if possible) that each histogram is independent by starting from independent initial frames (if these are available). Then you can use the boostrap of complete histograms (using the so-called Bayesian bootstrap) to compute the uncertainty: g_wham -nBootstrap 100 *-bs-method *b-hist ... As David just pointed out, please have a look into our recent paper: http://pubs.acs.org/doi/abs/10.1021/ct100494z Jochen S. Hub, Bert de Groot and David van der Spoel: g_wham - A free weighted histogram analysis implementation including robust error and autocorrelation estimates J. Chem. Theory Comput. 6 pp. 3713-3720 (2010) Cheers, Jochen -- --- Dr. Jochen Hub Computational and Systems Biology Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4715056 Fax: +46-18-511755 http://xray.bmc.uu.se/~jochen/index.html --- -- 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] Zero Potential of Mean Force with g_wham
Hi, please use g_wham 4.5.2 or later. We largely updated g_wham recently. If you get a flat PMF, check the warnings that g_wham gives you and --very important-- look at the histograms. That usually gives you a clue where the histograms to not overlap. In case you find a bug, please let me know. Otherwise, I have computed hundreds of PMFs with g_wham and it always worked fine. Cheers, Jochen On 3/9/11 Mar 9,11:08 PM, chris.ne...@utoronto.ca wrote: g_wham is not the only version of wham. Try using alan grossfield's version. Too often, I am afraid, gromacs accessory programs get broken in an update (not sure what the general solution is here beyond renewed calls for a proper test suite. Perhaps having 20+ programs is not ideal for a single software suite where the real focus is only on mdrun and grompp?) Chris. -- original message -- Hi, I ran g_wham 4.5.2 and did get a non-zero PMF curve. I assume that there is something going on with g_wham on version 4.5.1. Thank you for your help. Susana On Wed, Mar 9, 2011 at 3:00 PM, Mark Abraham Mark.Abraham at anu.edu.auwrote: -- --- Dr. Jochen Hub Computational and Systems Biology Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4715056 Fax: +46-18-511755 http://xray.bmc.uu.se/~jochen/index.html --- -- 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] WHAM with multiple force constants
On 2/10/11 Feb 10,6:08 AM, jk...@ifr88.cnrs-mrs.fr wrote: Hi, I'm running an Umbrella Sampling analysis, with 1A steps in the reaction coordinate (distance) to estimate a PMF. However, owing to (high?) energetic barriers between my two proteins, some coordinates are not sampled. I intend to run simulations with stronger force constants to prevent my protein from fleeing to the nearest energetic minima. So my question is : does using different force constants to restrain the distance between my two proteins influences the PMF estimated by g_wham ? No, it is perfectly fine (and sometimes necessary) to combine umbrella simulations with different force constants. The g_wham result should be fine (if not, tell me, thanks!). Cheers, Jochen From what I understood, it doesn't seems so, as long as the distributions are well overlapped. But since I intend to invest a considerable amount of CPU time, a confirmation would be really apreciated ! Thanks, Jonathan. -- Message envoyé via le Webmail de l'IFR88 (http://www.ifr88.cnrs-mrs.fr). -- --- Dr. Jochen Hub Computational and Systems Biology Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4715056 Fax: +46-18-511755 http://xray.bmc.uu.se/~jochen/index.html --- -- 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] harmonic restraint with OpenMM
Hi, I am trying to restrain an ion that is coordinated by a few protein atoms, to avoid that the ion might fly off. The simulation should be run on a GPU (with OpenMM) and implicit solvent. First I tried to restrain the ion using bonds of type 6, but harmonic potentials are not supported by OpenMM. Turning the restraint into a normal bond (type 1) would be fine since I only constrain bond lengths of hydrogens. However, that gives a grompp error, Cannot find length for atoms 386-2262 involved in angle meaning that the function find_gb_bondlength in topio.c does not find a bond length for the ion-protein atom bond, although the bond length is clearly defined in the topology. I am a bit stuck now. Does anyone know how one could introduce some kind of distance restraint with OpenMM and implicit solvent? I am using gmx 4.5.3 and OpenMM 2.0. Thanks a lot, Jochen -- --- Dr. Jochen Hub Computational and Systems Biology Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4715056 Fax: +46-18-511755 http://xray.bmc.uu.se/~jochen/index.html --- -- 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] g_wham: Pull geometry direction_periodic not supported
On 9/18/10 Sep 18,10:17 PM, Jochen Hub wrote: On 9/10/10 Sep 10,2:40 PM, Eudes Fileti wrote: Hi gmx-users I finished a series of pulling runs using the periodic_direction option and when I run the g_wham analysis I received the following message. --- Program g_wham, VERSION 4.5 Source code file: gmx_wham.c, line: 1369 Fatal error: Pull geometry direction_periodic not supported For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Is there any way to circumvent this or should I redo all my simulations with the option of direction instead direction_periodic? Hi Eudes, the g_wham has not been properly updated to gmx 4.5 yet. I'll do that as soon as possible. For now, I would recommend to use g_traj to write the coordinates of your pull group and your reference group and to write a script that writes pdo files. Check g_wham -h to see a typical pdo header. Then use g_wham -ip to compute your PMFs. Hi Eudes, the latest g_wham is now in (at least in the git version of) gromacs 4.5x. For your geometry, you'll have to write the pull forces (pullf.xvg files) and read those into g_wham with -if. g_wham cannot read the pullx files written by geometry direction_periodic or direction. Please let me know it if g_wham makes any more trouble. Cheers, Jochen -- --- Dr. Jochen Hub Computational and Systems Biology Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4715056 Fax: +46-18-511755 http://xray.bmc.uu.se/~jochen/index.html --- -- 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] OPLS-AA force field
Hi, see here for a start: http://www.gromacs.org/Documentation/How-tos/Parameterization Cheers, Jochen On 10/8/10 Oct 8,3:51 PM, lammps lammps wrote: Hi everybody, I want to use OPLS-AA force field to do simulation for dendrimer(see the attached files for figure and .pdb). If the pH4.0，the tertiary amines on the dendrimer will be protonated, i.e. (CH2)3-N will be changed to (CH2)3-NH+. Now, I have two questions as follows. 1. How can I use pdb2gmx to get the .gro and .itp? It seems there are not the /residue./ 2. I don't find the suitable force field for the N in (CH2)3-NH+, How can I deal with this? Any suggestion is appreciated. Thanks in advance. -- wende -- --- Dr. Jochen Hub Computational and Systems Biology Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4715056 Fax: +46-18-511755 http://xray.bmc.uu.se/~jochen/index.html --- -- 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] Split pmf
On 10/2/10 Oct 2,10:51 PM, Петр Попов wrote: Hello, dears gmx-users! I posted a message, but didn't get a response, it was my first one, so may be I did something wrong. Anyway, here it is: I've already run md and got pmf and it's correct. But I want to get not just a pmf of total force, but several profiles each of which corresponds to the different components. For example, one pmf - protein-protein interactions, another - protein-solvent interactions. Or another, one pmf corresponds to electrostatic, another to VdW etc. Should I change a program's code? If so, tell me please in what exactly program? Or may be gromacs have similar functions? Or is the another way to split pmf? Hi, what we did some years ago (Hub and de Groot, Does CO2 permeate through aquaporin-1, Biophys J 91, 842-848 (2006)), we used the energy file to decompose the potential (that is the enthalpic contribution to the PMF) into solute-water, solute-protein interactions, etc. You would have to make a tpr file with different energy groups and then do a rerun. Note that we do not decompose the mean force with that procedure though. I hope this helps. Cheers, Jochen Thank you for your attention! -- --- Dr. Jochen Hub Computational and Systems Biology Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4715056 Fax: +46-18-511755 http://xray.bmc.uu.se/~jochen/index.html --- -- 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] g_wham: Pull geometry direction_periodic not supported
On 9/10/10 Sep 10,2:40 PM, Eudes Fileti wrote: Hi gmx-users I finished a series of pulling runs using the periodic_direction option and when I run the g_wham analysis I received the following message. --- Program g_wham, VERSION 4.5 Source code file: gmx_wham.c, line: 1369 Fatal error: Pull geometry direction_periodic not supported For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Is there any way to circumvent this or should I redo all my simulations with the option of direction instead direction_periodic? Hi Eudes, the g_wham has not been properly updated to gmx 4.5 yet. I'll do that as soon as possible. For now, I would recommend to use g_traj to write the coordinates of your pull group and your reference group and to write a script that writes pdo files. Check g_wham -h to see a typical pdo header. Then use g_wham -ip to compute your PMFs. Cheers, Jochen Bests eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 http://fileti.ufabc.edu.br -- --- Dr. Jochen Hub Computational and Systems Biology Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4715056 Fax: +46-18-511755 http://xray.bmc.uu.se/~jochen/index.html --- -- 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] Can I make make_ndx interactive?
Jennifer Williams wrote: Hi, Is there some way of making the make_ndx file interactive so that I can include it in a script? I would usually type in a C_O and O_C to select my atoms I've tried altering the example on the webpage for making commands interactive: make_ndx -flags EOF a C_O OC q EOF -f nn_1.pdb try: cat EOF | make_ndx -f prot.pdb a C_O q EOF Jochen but -flags doesn't seem to be recognized. Does anyone know a work around? Thanks Jenny -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- -- 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] PMF profile using g_wham with pull_geometry = distance for ion channel
Thomas Piggot wrote: Hi again, Just before I reside myself to rerunning a large number of simulations I was wondering if it is possible to just rerun the simulations where the ion is above and below the reference using pull_geometry=position. Then could I combine these with the other simulations where pull_geometry=distance to get the complete PMF? Hm, that may get tricky but may be possible. g_wham can probably not deal with it when you use the -it and -ix input (with 2 different pulling geometries). But you could turn the pullx files into pdo files (check g_wham -h) to provide them with -ip to g_wham. That will certainly require a bit of scripting, but should not be too difficult. Make sure to get the direction (plus/minus z) right when turning the distance in the pullx into pdo files with z as reaction coordinate. Good luck, Jochen Tom Jochen Hub wrote: Thomas Piggot wrote: Jochen thanks for your help. That was what I was afraid of you saying. Oh well, at least this will hopefully provide a useful reference so somebody doesn't make this same mistake. On a side note I noticed a couple of small issues with g_wham. Firstly the -wcorr option says Input, opt. not Output, opt as I assume it should be. Ah thanks. I'll correct that soon. Also when using -min and -max with the -noauto option, the program quits with the error: Fatal error: With -auto, do not give -min or -max Ok, I guess I never checked that case. But as you point out, you don't have to use -noauto when providing min and max, the auto is switched off automatically. Thanks for the feedback, Jochen This is not a problem as with -min and -max (without specifying -noauto) g_wham switches automatically switches auto off, but I assumed that using -min and -max the -noauto option would have been the 'correct' way to do this. Cheers Tom Jochen Hub wrote: Thomas Piggot wrote: Hi, I am trying to construct a PMF profile for a phosphate ion passing through a membrane protein using umbrella sampling with GROMACS 4.0.5. I have performed the umbrella sampling simulations using the following mdp options and I am now attempting to construct the PMF using g_wham. ; Pull code pull= umbrella ; do umbrella sampling pull_geometry = distance ; can't get PMF with direction Hi Tom, if you want to distinguish between above and below, pull_geometry=position would have been your choice. What I would do now is to run g_wham twice with only the histograms from below and a second time only with the histograms from above your reference. YOu'll have to make appropriate tpr-files.dat and pullx-files.dat input files. Note however, that the PMF very close to your reference will be ill-defined since the pull code checked the distance to the reference and not the z-coordinate. Therefore I would remove simulations in which the ion was sometimes above and sometimes below the reference. To ge the full PMF along the z-axis (which is what you probably want) you'll have to do the simulation again (with pull_geometry=position) I'm afraid. I hope this helps, Jochen pull_dim= N N Y; just in the z pull_start = yes ; add com to pull_init1 pull_ngroups= 1; no. of groups to pull pull_group0 = Protein ; reference group pull_group1 = PO4 ; pull group pull_vec1 = 0 0 0; pull_init1 = 0; pull_rate1 = 0.0 ; no change in ref position pull_k1 = 1000 ; force constant for restraint pull_nstxout= 1000 ; every 2 ps pull_nstfout= 1000 ; every 2 ps The problem is that when running g_wham (using the following command) g_wham correctly reads all of the tpr and pullx files, however the data for the windows above and below the reference atom (the middle atom of the protein) are both included in the same part of the PMF profile. g_wham_4.0.5 -ix -it -cycl weighted -b 2000 I assume that this is occuring due to the pull_geometry = distance option, as the distance to the reference does not matter if the ion is above or below the reference? So my question is: Is there a way to construct the complete PMF profile with the simulations I have already run? I should also mention that I have tried using the -min and -max options with g_wham (rather than the auto determination of the boundaries) but this just produces outputs that have all the values as nan. I have also tried using g_wham 4.0.7 but with exactly the same issues ,as well as using the pullf.xvg files as input to g_wham. I apologise if I am missing something obvious (or doing something silly!) but any help would be greatly appreciated. Cheers Tom -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18
Re: [gmx-users] PMF of ligand transport
Aswathy wrote: Hi gromacs users, I am using Gromacs 4.0.4 package. I am doing SMD of a ligand transport through a channel. I performed SMD and did umbrella sampling (Thanks to Justin for his tutorial). Extracted frames with a window spacing interval of ~0.12nm. and did 1ns sampling. Histograms are with reasonabvle overlap. Then I used g_wham for plotting PMF considering first 300ps as equilibration. Isn't SMD usually referred to pulling at some finite pulling speed? That would not be umbrella sampling. Anyway, you'll have to provide a lot more data to enable us to help you. Jochen I am getting a plot , but potential is increasing constantly. ie, PMF is not converged as mentioned the tutorial? Do I need to extend the sampling ? or any other reason? Please help me. Thank you. -Aswathy -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- -- 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] PMF profile using g_wham with pull_geometry = distance for ion channel
Thomas Piggot wrote: Hi, I am trying to construct a PMF profile for a phosphate ion passing through a membrane protein using umbrella sampling with GROMACS 4.0.5. I have performed the umbrella sampling simulations using the following mdp options and I am now attempting to construct the PMF using g_wham. ; Pull code pull= umbrella ; do umbrella sampling pull_geometry = distance ; can't get PMF with direction Hi Tom, if you want to distinguish between above and below, pull_geometry=position would have been your choice. What I would do now is to run g_wham twice with only the histograms from below and a second time only with the histograms from above your reference. YOu'll have to make appropriate tpr-files.dat and pullx-files.dat input files. Note however, that the PMF very close to your reference will be ill-defined since the pull code checked the distance to the reference and not the z-coordinate. Therefore I would remove simulations in which the ion was sometimes above and sometimes below the reference. To ge the full PMF along the z-axis (which is what you probably want) you'll have to do the simulation again (with pull_geometry=position) I'm afraid. I hope this helps, Jochen pull_dim= N N Y; just in the z pull_start = yes ; add com to pull_init1 pull_ngroups= 1; no. of groups to pull pull_group0 = Protein ; reference group pull_group1 = PO4 ; pull group pull_vec1 = 0 0 0; pull_init1 = 0; pull_rate1 = 0.0 ; no change in ref position pull_k1 = 1000 ; force constant for restraint pull_nstxout= 1000 ; every 2 ps pull_nstfout= 1000 ; every 2 ps The problem is that when running g_wham (using the following command) g_wham correctly reads all of the tpr and pullx files, however the data for the windows above and below the reference atom (the middle atom of the protein) are both included in the same part of the PMF profile. g_wham_4.0.5 -ix -it -cycl weighted -b 2000 I assume that this is occuring due to the pull_geometry = distance option, as the distance to the reference does not matter if the ion is above or below the reference? So my question is: Is there a way to construct the complete PMF profile with the simulations I have already run? I should also mention that I have tried using the -min and -max options with g_wham (rather than the auto determination of the boundaries) but this just produces outputs that have all the values as nan. I have also tried using g_wham 4.0.7 but with exactly the same issues ,as well as using the pullf.xvg files as input to g_wham. I apologise if I am missing something obvious (or doing something silly!) but any help would be greatly appreciated. Cheers Tom -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- -- 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] PMF profile using g_wham with pull_geometry = distance for ion channel
Thomas Piggot wrote: Jochen thanks for your help. That was what I was afraid of you saying. Oh well, at least this will hopefully provide a useful reference so somebody doesn't make this same mistake. On a side note I noticed a couple of small issues with g_wham. Firstly the -wcorr option says Input, opt. not Output, opt as I assume it should be. Ah thanks. I'll correct that soon. Also when using -min and -max with the -noauto option, the program quits with the error: Fatal error: With -auto, do not give -min or -max Ok, I guess I never checked that case. But as you point out, you don't have to use -noauto when providing min and max, the auto is switched off automatically. Thanks for the feedback, Jochen This is not a problem as with -min and -max (without specifying -noauto) g_wham switches automatically switches auto off, but I assumed that using -min and -max the -noauto option would have been the 'correct' way to do this. Cheers Tom Jochen Hub wrote: Thomas Piggot wrote: Hi, I am trying to construct a PMF profile for a phosphate ion passing through a membrane protein using umbrella sampling with GROMACS 4.0.5. I have performed the umbrella sampling simulations using the following mdp options and I am now attempting to construct the PMF using g_wham. ; Pull code pull= umbrella ; do umbrella sampling pull_geometry = distance ; can't get PMF with direction Hi Tom, if you want to distinguish between above and below, pull_geometry=position would have been your choice. What I would do now is to run g_wham twice with only the histograms from below and a second time only with the histograms from above your reference. YOu'll have to make appropriate tpr-files.dat and pullx-files.dat input files. Note however, that the PMF very close to your reference will be ill-defined since the pull code checked the distance to the reference and not the z-coordinate. Therefore I would remove simulations in which the ion was sometimes above and sometimes below the reference. To ge the full PMF along the z-axis (which is what you probably want) you'll have to do the simulation again (with pull_geometry=position) I'm afraid. I hope this helps, Jochen pull_dim= N N Y; just in the z pull_start = yes ; add com to pull_init1 pull_ngroups= 1; no. of groups to pull pull_group0 = Protein ; reference group pull_group1 = PO4 ; pull group pull_vec1 = 0 0 0; pull_init1 = 0; pull_rate1 = 0.0 ; no change in ref position pull_k1 = 1000 ; force constant for restraint pull_nstxout= 1000 ; every 2 ps pull_nstfout= 1000 ; every 2 ps The problem is that when running g_wham (using the following command) g_wham correctly reads all of the tpr and pullx files, however the data for the windows above and below the reference atom (the middle atom of the protein) are both included in the same part of the PMF profile. g_wham_4.0.5 -ix -it -cycl weighted -b 2000 I assume that this is occuring due to the pull_geometry = distance option, as the distance to the reference does not matter if the ion is above or below the reference? So my question is: Is there a way to construct the complete PMF profile with the simulations I have already run? I should also mention that I have tried using the -min and -max options with g_wham (rather than the auto determination of the boundaries) but this just produces outputs that have all the values as nan. I have also tried using g_wham 4.0.7 but with exactly the same issues ,as well as using the pullf.xvg files as input to g_wham. I apologise if I am missing something obvious (or doing something silly!) but any help would be greatly appreciated. Cheers Tom -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- -- 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_wham gets stuck
Amir Marcovitz wrote: Thank you Jochem, In your last reply, did you mean that i can perform the WHAM on Various histograms that were collected with different force constants? i mean , will it know to do the correction for the biasing potential Yes, WHAM does not require identical force constants. Just make sure that the order of tpr and pullx files agree in the -it and -ix input agree. Jochen amir On Fri, Apr 30, 2010 at 4:00 PM, Jochen Hub joc...@xray.bmc.uu.se mailto:joc...@xray.bmc.uu.se wrote: Justin A. Lemkul wrote: Amir Marcovitz wrote: Thanks for your answers, I tried to struggle a bit more with that today. my input dat files listings (i.e., tpr-files.dat, pullf-files.dat and pullx-files.dat) are fine and consistent with other in terms of file numbering. i use gromacs 4.0.5 on Linux with gcc 4.1.2 compiler. Time and time again, we have to point out the bold warning on the Downloads page: WARNING: do not use the gcc 4.1.x set of compilers. They are broken. These compilers come with recent Linux distrubutions like Fedora 5/6 etc. Buggy behavior that is difficult to diagnose is often due to these faulty compilers. i run: *g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal -b 1000*(my data is 16ns long and i ignore the first ns) and it starts reporting that the file are read: Reading file topol742.tpr, VERSION 4.0.5 (single precision) File topol742.tpr, 1 groups, geometry distance, dimensions [N Y N], (1 dimensions) grp 0) k = 1000.000 inittial distance = 2.41331 Reading file topol748.tpr, VERSION 4.0.5 (single precision) Reading file topol761.tpr, VERSION 4.0.5 (single precision) Reading file topol792.tpr, VERSION 4.0.5 (single precision) and so on.. it reports that the boundaries are found and continue to read until it stucks.. However, when i do the WHAM with the pullx files (i.e., -ix pullx-files instead of -if pullf-files.dat) the wham converges within a reasonable time to a PMF profile which not so smooth. i therefore have some questions: 1) what is the difference in the profiles for using pullx or pullf files? In principle, there probably shouldn't be any, but if there is perhaps someone else has seen that. It should not make any difference at all. It it does, there is something wrong with the data or g_wham is buggy. With the pullf files, g_wham simply computes the pullx values from the force and the force constant. This is not really required since it is more natural to just work with the pullx, but I added to for the case that someone forgot to write the pullx and only has the pullf files. 2) suppose that my histograms overlap is poor for some locations along the pulling vector, how one can solve that? Better sampling (more time) within the sampling windows, or more closely-spaced windows. And maybe stronger force constants. g_wham can combine the runs with smaller and larger force constants, that is no problem. That is probably the reason for the weired PMF! Jochen 3) To generate the input configurations - what is the ideal pulling procedure? ( i used pull = constant_force, with a small value of K1) There isn't one best method, per se. The only criterion is that you have generated configurations from which you can derive reasonably-spaced windows in which you do sufficient sampling. -Justin Again, Thanks a lot for the quick reply Amir On Thu, Apr 29, 2010 at 10:33 AM, Jochen Hub joc...@xray.bmc.uu.se mailto:joc...@xray.bmc.uu.se mailto:joc...@xray.bmc.uu.se mailto:joc...@xray.bmc.uu.se wrote: Amir Marcovitz wrote: Hi All, I have some problems with g_wham, and i already gone through all the postings and didn't find a hint.. basically, I'm trying to calculate PMF between two charged plates. I've performed a pulling simulation between the 2 plates according to Justin's UMBRELLA tutorial in the website (all steps, i.e., minimization, equilibration etc. up to that point work fine) from the pulling i generated input configurations for the umbrella sampling runs (pull=umbrella , rate=0.0), which are 15
Re: [gmx-users] g_wham gets stuck
Justin A. Lemkul wrote: Amir Marcovitz wrote: Thanks for your answers, I tried to struggle a bit more with that today. my input dat files listings (i.e., tpr-files.dat, pullf-files.dat and pullx-files.dat) are fine and consistent with other in terms of file numbering. i use gromacs 4.0.5 on Linux with gcc 4.1.2 compiler. Time and time again, we have to point out the bold warning on the Downloads page: WARNING: do not use the gcc 4.1.x set of compilers. They are broken. These compilers come with recent Linux distrubutions like Fedora 5/6 etc. Buggy behavior that is difficult to diagnose is often due to these faulty compilers. i run: *g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal -b 1000*(my data is 16ns long and i ignore the first ns) and it starts reporting that the file are read: Reading file topol742.tpr, VERSION 4.0.5 (single precision) File topol742.tpr, 1 groups, geometry distance, dimensions [N Y N], (1 dimensions) grp 0) k = 1000.000 inittial distance = 2.41331 Reading file topol748.tpr, VERSION 4.0.5 (single precision) Reading file topol761.tpr, VERSION 4.0.5 (single precision) Reading file topol792.tpr, VERSION 4.0.5 (single precision) and so on.. it reports that the boundaries are found and continue to read until it stucks.. However, when i do the WHAM with the pullx files (i.e., -ix pullx-files instead of -if pullf-files.dat) the wham converges within a reasonable time to a PMF profile which not so smooth. i therefore have some questions: 1) what is the difference in the profiles for using pullx or pullf files? In principle, there probably shouldn't be any, but if there is perhaps someone else has seen that. It should not make any difference at all. It it does, there is something wrong with the data or g_wham is buggy. With the pullf files, g_wham simply computes the pullx values from the force and the force constant. This is not really required since it is more natural to just work with the pullx, but I added to for the case that someone forgot to write the pullx and only has the pullf files. 2) suppose that my histograms overlap is poor for some locations along the pulling vector, how one can solve that? Better sampling (more time) within the sampling windows, or more closely-spaced windows. And maybe stronger force constants. g_wham can combine the runs with smaller and larger force constants, that is no problem. That is probably the reason for the weired PMF! Jochen 3) To generate the input configurations - what is the ideal pulling procedure? ( i used pull = constant_force, with a small value of K1) There isn't one best method, per se. The only criterion is that you have generated configurations from which you can derive reasonably-spaced windows in which you do sufficient sampling. -Justin Again, Thanks a lot for the quick reply Amir On Thu, Apr 29, 2010 at 10:33 AM, Jochen Hub joc...@xray.bmc.uu.se mailto:joc...@xray.bmc.uu.se wrote: Amir Marcovitz wrote: Hi All, I have some problems with g_wham, and i already gone through all the postings and didn't find a hint.. basically, I'm trying to calculate PMF between two charged plates. I've performed a pulling simulation between the 2 plates according to Justin's UMBRELLA tutorial in the website (all steps, i.e., minimization, equilibration etc. up to that point work fine) from the pulling i generated input configurations for the umbrella sampling runs (pull=umbrella , rate=0.0), which are 15 ns long and collected all the output pullf.xvg and *.tpr files. You could also run g_wham -histonly to get the histogram file. Then check with xmgrace -nxy histo.xvg whether the histograms properly overlap. But if they do not overlap, I would rather expect g_wham to give a zero PMF or to iterate forever, so not sure what is wrong. Jochen i then run g_wham (with -it and -if) and it works fine at the beginning, but then the computer simply gets stuck (!?) and the calculation is killed - with no error massage. what is it that I'm doing wrong? it looks like my output data (pullf and tpr files) are fine, but is it possible that some of them causing the problem? this is really frustrating.. need your help, Amir -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting
Re: [gmx-users] g_wham gets stuck
Amir Marcovitz wrote: Hi All, I have some problems with g_wham, and i already gone through all the postings and didn't find a hint.. basically, I'm trying to calculate PMF between two charged plates. I've performed a pulling simulation between the 2 plates according to Justin's UMBRELLA tutorial in the website (all steps, i.e., minimization, equilibration etc. up to that point work fine) from the pulling i generated input configurations for the umbrella sampling runs (pull=umbrella , rate=0.0), which are 15 ns long and collected all the output pullf.xvg and *.tpr files. You could also run g_wham -histonly to get the histogram file. Then check with xmgrace -nxy histo.xvg whether the histograms properly overlap. But if they do not overlap, I would rather expect g_wham to give a zero PMF or to iterate forever, so not sure what is wrong. Jochen i then run g_wham (with -it and -if) and it works fine at the beginning, but then the computer simply gets stuck (!?) and the calculation is killed - with no error massage. what is it that I'm doing wrong? it looks like my output data (pullf and tpr files) are fine, but is it possible that some of them causing the problem? this is really frustrating.. need your help, Amir -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- -- 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_wham giving flat free energy
Michael McGovern wrote: Hi everyone. I'm having some trouble using g_wham to analyze some results. I have some simulations from gromacs 3.3 using the pull code. I'm using the latest version of g_wham to analyze the results, which the help file says is ok, using the -ip option. I've gotten almost everything to work, and it generates histograms that seem perfectly reasonable, but sometimes the free energy it outputs is completely flat, with each bin having a free energy value of 0. I've played around with the -b and -e options using only part of my data, and sometimes it gives non-flat free energies, other times not. I see no logic to when it works and when it doesn't. My data does have good overlap of the histograms, and it sometimes converges even when I use data that have no overlaps, so that doesn't seem to be the problem. I'm completely confused. Does anyone know what could cause this? Hi Micheal, how large is your data? Could you send me a tar.gz of your pdo files? I would like to make sure that there is no bug in g_wham. Jochen -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- -- 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] How can I maintain a distance of at least 0.5 nm from each other of solutes
rasoul nasiri wrote: Dear All, Hello I understand one can adjust distance of between solvent molecules by genbox command and -vdwd but I don't know, how do it between the solutes? If you want to place several identical solutes with genbox -ci, then you could copy the file vdwradii.dat to the present directory and largely increase the respective vdw radii in that file (e.g. the carbon radii) before running genbox. Best, Jochen Thanks for helping! Rasoul -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- -- 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] Concerns with g_wham
Jennifer Casey wrote: Hello, I have been using g_wham, but I have a few questions that I can't find answers to online. When using WHAM, one does not need the forces between the pull groups to calculate the PMF, yet g_wham won't run without it. Is there a reason for this? Hi Jennifer! As pointed out by Chris, you can use provide the pull positions (g_wham -ix) OR the pull forces with -if. When giving the pullf files, g_wham simply computes the pull positions from the forces and calculates the histograms etc... Also, when using the pull code, I am allowed to define the spring constant K for umbrella sampling, but I do not designate where the umbrella potential is centered. How does gromacs determine this? Umbrella positions and force constants (and pull geometry) are taken from the tpr files. That's why they must be provided to g_wham. I am interested as I would like to create a PMF using umbrella integration (from code I will write myself) rather than use WHAM. To do this and still use the umbrella sampling runs used with GROMACS, I need to know where my umbrella potentials are centered. If you want to integrate the mean forces, I would not use pull=umbrella but pull=constraint. You should get the same PMF compared to umbrella sampling and using g_wham. Please let me know if g_wham makes any trouble. Cheers, Jochen Thank you, Jennifer -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- -- 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] slow speed
nstlist = 50 ; ns algorithm (simple or grid) = ns_type = grid Oups, you are dong neighbor searching only every 50fs. Are you sure this is what you want? If you have a biological system this is probably not often enough. In biological systems people typically do neighbor searching every 10 to 20 fs. Jochen -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- -- 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] mean force.
lammps lammps wrote: Hi everyone, I use umbrella sample and g_wham to get potential of mean force. However, I also want to compute the mean force. How can I deal with this? Can I get it through calculating the average of data in pullf.xvg file? In principle, yes. But note that the position of the particle fluctuates within the umbrella window during your simulation. A more well-defined force would be computed by using pull = constraint and then by averaging the pullf.xvg output. In theory, you should then get the same PMF by either integrating the mean force or by using wham on the umbrella ouput. Best, Jochen Thanks in advance. Wende -- ;spring point is equal to ref_group0+pull_init+time*pull_rate*pull_vec， pull = Umbrella ;umbrella,constraint pull_geometry = Distance ;distance ,direction,cylinder,position pull_dim = Y Y Y pull_group0 = DEN1 pull_group1 = DEN2 pull_nstxout = 500 pull_nstfout = 50 pull_init1 = 5.7 pull_k1 = 1000 --- # This file was created Thu Feb 4 00:51:24 2010 # by the following command: # mdrun_mpi -rdd 1.4 -s npt.tpr -c npt.gro # # mdrun_mpi is part of G R O M A C S: # # Groningen Machine for Chemical Simulation # @ title Pull force @ xaxis label Time (ps) @ yaxis label Force (kJ/mol/nm) @TYPE xy 0. -28.8555 1.6000 -19.2897 3.2000 -18.59 4.8000 -20.7866 6.4000 -26.1605 8. -42.8572 9.6000 -50.7524 11.2000 -73.9647 12.8000 -74.2521 14.4000 -102.284 16. -96.5184 -- wende -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- -- 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] make ghost atom
Park, Jae Hyun nmn wrote: Dear all, I would like to change a specific atom into a ghost particle (no interaction with system) after some time (for example, 1ns). Is there any way to implement it in GROMACS? If I need change the code, what file do I have to look at? If you want to smoothly switch off the interaction you can use the free energy code for that (I would use sd-integrator in that case). Note sure if that is what you mean though. Cheers, Jochen I would deeply appreciate any comments. Jae H. Park Jae Hyun Park, Ph.D. Physics Division Oak Ridge National Laboratory P.O. Box 2008, MS-6372 Oak Ridge, TN 37831 Phone (865) 241-1482 E-mail pa...@ornl.gov -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- -- 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_wham error
g_wham -ix PREPxvg.dat -it PREPtpr.dat The -ix option expects the pull positions. If you want to provide the pull forces to g_wham, use the -if option. Cheers, Jochen PREPxvg.dat and PREPtpr.dat are lists of the respective xvg and tpr files. They are both in the same order, although they are ordered alphabetically instead of sequentially (i'm not sure if that matters or not). Here's PREPxvg.dat to illustrate the ordering: onePREP0.xvg onePREP16.xvg onePREP22.xvg onePREP29.xvg onePREP7.xvg onePREP10.xvg onePREP17.xvg onePREP23.xvg onePREP2.xvg onePREP8.xvg onePREP11.xvg onePREP18.xvg onePREP24.xvg onePREP30.xvg onePREP9.xvg onePREP12.xvg onePREP19.xvg onePREP25.xvg onePREP3.xvg onePREP13.xvg onePREP1.xvg onePREP26.xvg onePREP4.xvg onePREP14.xvg onePREP20.xvg onePREP27.xvg onePREP5.xvg onePREP15.xvg onePREP21.xvg onePREP28.xvg onePREP6.xvg Thanks for the help Gard -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- -- 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] PMF of large protein
According to tutorials, sampling at every 0.1nm is sufficient so 20 points*sampling time ~1 ns = 20ns which could be ok but then there is not time to allow for much protein rotation. Opinions about this? I think it is difficult to estimate how quickly such a PMF converges, but probably extremely slowly. You would have to sample over all rotations of the protein which would rather take microseconds (or longer) than nanoseconds. The question is, how exact should the PMF be. Plusminus 1kcal (no chance to get there, I guess), or plusminus 5 kcal (difficult?), or 10 kcal (possible?)? The only way to find out is to try. You can do the complete umbrella sampling twice with *really independent* starting frames (e.g. different protein orientations) and check the difference between the PMFs. Cheers, Jcohen My second question concerns the pull code. I understand how to use the umbrella sampling and g_wham to calculate PMF but how is constraint pulling used? Pros and cons? Thank you Matteus - Matteus Lindgren, graduate student Department of Chemistry, Umeå University SE-901 87 Umeå, Sweden Phone: +46 (0)90-7865368 -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- -- 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] Problems wtih g_wham
Jennifer Casey wrote: Hello, I am trying to create a PMF for the sodium cation and iodine anion in the presence of THF. I have been following the umbrella sampling tutorial on the gromacs website, and everything has been working out. I have finally created 14 different equilibriation simulations, whose starting configurations were obtained form a pull simulation with pull_rate = 0.06. To get the 14 different equilibriated runs, I left the pull code on, but I just made pull_rate = 0.00. I have created a list of the .tpr files and the pullf[].xvg files, and I tried to use g_wham. The error I got was as follows: This is not a tpr of an umbrella simulation. Found ir.ePul; = cylinder. Has anyone else found this error? I was not even using cylinder, I was using distance. Hi Jennifer, the error message is indeed wrong and should have been Found ir.ePull = constaint (epullg_names should have been epull_names, one g too much in gmx_wham.c). I have submitted a bugzilla for that. But the problem was, that you did not do umbrella sampling. For umbrella sampling, you restrain the system with a (normally harmonic) restraint along the reaction coordinate, using pull = umbrella. You have constrained the system at a fixed position along the reaction coordinate, which is not umbrella sampling. However, now comes the good news, you can still compute the PMF via the mean forces. Average the forces in pullf (after some equilibration), and integrate the mean forces (e.g. with g_analyze), giving the potential of mean force (PMF). That technique is called something like constrained something calculation or so, don't remember exactly. If you still want to do umbrella sampling, you'll have to do the simulation again with pull = umbrella and then use g_wham to get the PMF. Best wishes, Jochen I have attached my original pull .mdp file, and the .mdp file used in the 14 equilibration runs. I appreciate any help. Thanks, Jenny -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- -- 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] valgrind warnigs with git mdrun
) ==6218==by 0x5378A2: init_par (main.c:413) ==6218==by 0x41D27F: main (mdrun.c:393) ==6218== ==6218== 2,259 bytes in 42 blocks are definitely lost in loss record 905 of 1,032 ==6218==at 0x4A05140: calloc (vg_replace_malloc.c:418) ==6218==by 0x5546CA: save_calloc (smalloc.c:157) ==6218==by 0x555BD3: mk_desc (statutil.c:620) ==6218==by 0x556C2D: parse_common_args (statutil.c:863) ==6218==by 0x41D342: main (mdrun.c:412) ==6218== ==6218== 16,032 bytes in 1 blocks are possibly lost in loss record 919 of 1,032 ==6218==at 0x4A05E1C: malloc (vg_replace_malloc.c:195) ==6218==by 0x46246C: make_nbf_tables (forcerec.c:1040) ==6218==by 0x464ABC: init_forcerec (forcerec.c:1539) ==6218==by 0x4128C8: mdrunner (runner.c:508) ==6218==by 0x411972: mdrunner_threads (runner.c:196) ==6218==by 0x41DAC0: main (mdrun.c:515) ==6218== ==6218== 32,048 bytes in 1 blocks are possibly lost in loss record 923 of 1,032 ==6218==at 0x4A05E1C: malloc (vg_replace_malloc.c:195) ==6218==by 0x46242B: make_nbf_tables (forcerec.c:1034) ==6218==by 0x464ABC: init_forcerec (forcerec.c:1539) ==6218==by 0x4128C8: mdrunner (runner.c:508) ==6218==by 0x411972: mdrunner_threads (runner.c:196) ==6218==by 0x41DAC0: main (mdrun.c:515) ==6218== ==6218== 48,064 bytes in 1 blocks are possibly lost in loss record 929 of 1,032 ==6218==at 0x4A05E1C: malloc (vg_replace_malloc.c:195) ==6218==by 0x4D4883: make_tables (tables.c:921) ==6218==by 0x4623CB: make_nbf_tables (forcerec.c:1020) ==6218==by 0x464ABC: init_forcerec (forcerec.c:1539) ==6218==by 0x4128C8: mdrunner (runner.c:508) ==6218==by 0x411972: mdrunner_threads (runner.c:196) ==6218==by 0x41DAC0: main (mdrun.c:515) ==6218== ==6218== 48,064 bytes in 1 blocks are possibly lost in loss record 930 of 1,032 ==6218==at 0x4A05E1C: malloc (vg_replace_malloc.c:195) ==6218==by 0x4D4883: make_tables (tables.c:921) ==6218==by 0x464EF1: init_forcerec (forcerec.c:1574) ==6218==by 0x4128C8: mdrunner (runner.c:508) ==6218==by 0x411972: mdrunner_threads (runner.c:196) ==6218==by 0x41DAC0: main (mdrun.c:515) ==6218== ==6218== 262,408 bytes in 1 blocks are possibly lost in loss record 968 of 1,032 ==6218==at 0x4A05E1C: malloc (vg_replace_malloc.c:195) ==6218==by 0x4CCC1D4: MPIDI_CH3I_SHM_Get_mem_shm (ch3_shm_memory.c:1015) ==6218==by 0x4CAC05A: MPIDI_CH3_SHM_Init (ch3_init.c:1894) ==6218==by 0x4CA5294: MPIDI_CH3_Init (ch3_init.c:189) ==6218==by 0x4D4F2D8: MPIDD_Init (mpid_init.c:96) ==6218==by 0x4E0DF82: MPID_Init (wrap_adi3.c:334) ==6218==by 0x4D414D4: MPIR_Init_thread (initthread.c:277) ==6218==by 0x4D391AE: PMPI_Init (init.c:117) ==6218==by 0x5437D7: gmx_setup (network.c:92) ==6218==by 0x5378A2: init_par (main.c:413) ==6218==by 0x41D27F: main (mdrun.c:393) ==6218== ==6218== 2,649,952 bytes in 1 blocks are possibly lost in loss record 1,025 of 1,032 ==6218==at 0x4A05E1C: malloc (vg_replace_malloc.c:195) ==6218==by 0x4FE31D: gmx_alloc_aligned (fftgrid.c:73) ==6218==by 0x4FE6AF: mk_fftgrid (fftgrid.c:164) ==6218==by 0x4B2899: gmx_pme_init (pme.c:1818) ==6218==by 0x412E3E: mdrunner (runner.c:609) ==6218==by 0x411972: mdrunner_threads (runner.c:196) ==6218==by 0x41DAC0: main (mdrun.c:515) ==6218== ==6218== 2,649,952 bytes in 1 blocks are possibly lost in loss record 1,026 of 1,032 ==6218==at 0x4A05E1C: malloc (vg_replace_malloc.c:195) ==6218==by 0x4FE31D: gmx_alloc_aligned (fftgrid.c:73) ==6218==by 0x4FE80E: mk_fftgrid (fftgrid.c:181) ==6218==by 0x4B2899: gmx_pme_init (pme.c:1818) ==6218==by 0x412E3E: mdrunner (runner.c:609) ==6218==by 0x411972: mdrunner_threads (runner.c:196) ==6218==by 0x41DAC0: main (mdrun.c:515) ==6218== ==6218== LEAK SUMMARY: ==6218==definitely lost: 2,300 bytes in 47 blocks ==6218==indirectly lost: 0 bytes in 0 blocks ==6218== possibly lost: 5,709,202 bytes in 12 blocks ==6218==still reachable: 87,724,883 bytes in 4,653 blocks ==6218== suppressed: 0 bytes in 0 blocks ==6218== Reachable blocks (those to which a pointer was found) are not shown. ==6218== To see them, rerun with: --leak-check=full --show-reachable=yes ==6218== ==6218== For counts of detected and suppressed errors, rerun with: -v ==6218== ERROR SUMMARY: 252186 errors from 21 contexts (suppressed: 4 from 4) -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- -- 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
[gmx-users] linking gromcs to efence
Hi, I am trying to link mdrun with efence, but don't really know how. I have been trying to add the -lefence to the CFLAGS or to the LDFLAGS, but that doesn't seem to work. Any help would be appreciated. Thanks in advance, Jochen -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- -- 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] New tutorial available - umbrella sampling
Hi Justin, I think you did a great job with that tutorial, a lot of people will benefit from it. I have just 2 additional suggestions: 1) Maybe you can comment on the issue of equilibration, especially since you took your initial frames from a non-equilibrium pulling. In such cases you probably want to play with the -b option of g_wham an generate a series of PMFs with different equilibration times, such as for b in 100 200 300 400 ... ; do g_wham -b $b -o prof.b$b -hist hist.b$b ... done and compare the profiles. This way one can check how long you need to equilibrate. As long as the PMF changes with b you may have an equilibration issue. 2) Concerning the histogram plot. That is actually a good example where one needs more umbrella windows since there is hardly any overlap between some of the histograms, between green and blue for instance. Maybe you can point that out in the tutorial. But hey, great job, Jochen Justin A. Lemkul wrote: Hi all, I've been working on an umbrella sampling/PMF tutorial for some time now, and I have just added it to the Tutorials page on the Gromacs site. As with my previous tutorials, I would welcome anyone to look through it and give me any feedback you may have on making it better; feel free to email me on-list or off. http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html Since use of the pull code seems to be a common inquiry across the list, I hope this instructional material will help out. -Justin -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- -- 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] Error while pulling a settled tip4p water molecule
chris.ne...@utoronto.ca wrote: I have done a similar thing in the past (without using the pull code), renaming the crystal waters around the protein so that they were easier to track. I eventually figured out that it was necessary for me to place the waters sequentially in the .top file. e.g: ; This is OK Protein 1 SOL 999 XSOL 1 ; This crashed SOL 999 Protein 1 XSOL 1 I realize that I was getting different errors than you are, but it's worth checking if this fix works for you. My old post is here http://lists.gromacs.org/pipermail/gmx-users/2006-September/024003.html although it doesn't contain any relevant information other than what I have mentioned above. Ah thanks. For me it was already fine to replace the settle-line by 3 constraints: ; [ settles ] ; OWfunct dohdhh ; 1 1 0.095720.15139 [ constraints ] ; turned settle into normal constraint 1 2 1 0.09572 1 3 1 0.09572 2 3 1 0.15139 Jochen Chris. --- original message --- Berk Hess wrote: Hi, I don't understand why you got this error message. Do you have two different types of water molecules with different geometries? In that case Gromacs would give this error message, because currently only one geometry is supported for settle, so you'll have to replace the others by 3 normal constraints. Ah, all right. I have indeed a separate topology for the water used in the pulling (to be able to give it a different residue name). I have replaced the settle by 3 constraints and now everything works fine. But if the you make the geometry identical, it should still work with settle, since then the two settle geometries are identical. Berk Then there is something odd. The two settles are definitely identical since I simply copied the tip4p.itp. I also just rechecked with xxdiff, the two settle lines are the same. Jochen -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- -- 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] Error while pulling a settled tip4p water molecule
Hi, I am doing umbrella simulations of a water molecule, using complete tip4p molecules as pull groups (or alternatively using only the three masses of the tip4p as pull group). When doing so, mdrun exits with the error: --- Program mdrun, VERSION 4.0.5 Source code file: constr.c, line: 841 Fatal error: More than one settle type. Suggestion: change the least use settle constraints into 3 normal constraints. --- Does that mean that I cannot pull a settled water molecule? Actually I do not really understand the suggestions, change the least use settle constraints into 3 normal constraints, why do I have to replace the settle constraint? Cheers, Jochen -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- -- 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] Error while pulling a settled tip4p water molecule
Berk Hess wrote: Hi, I don't understand why you got this error message. Do you have two different types of water molecules with different geometries? In that case Gromacs would give this error message, because currently only one geometry is supported for settle, so you'll have to replace the others by 3 normal constraints. Ah, all right. I have indeed a separate topology for the water used in the pulling (to be able to give it a different residue name). I have replaced the settle by 3 constraints and now everything works fine. Thanks! Jochen Berk Date: Thu, 14 Jan 2010 14:07:04 +0100 From: joc...@xray.bmc.uu.se To: gmx-users@gromacs.org Subject: [gmx-users] Error while pulling a settled tip4p water molecule Hi, I am doing umbrella simulations of a water molecule, using complete tip4p molecules as pull groups (or alternatively using only the three masses of the tip4p as pull group). When doing so, mdrun exits with the error: --- Program mdrun, VERSION 4.0.5 Source code file: constr.c, line: 841 Fatal error: More than one settle type. Suggestion: change the least use settle constraints into 3 normal constraints. --- Does that mean that I cannot pull a settled water molecule? Actually I do not really understand the suggestions, change the least use settle constraints into 3 normal constraints, why do I have to replace the settle constraint? Cheers, Jochen -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- -- 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 New Windows 7: Simplify what you do everyday. Find the right PC for you. http://windows.microsoft.com/shop -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- -- 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] Error while pulling a settled tip4p water molecule
Berk Hess wrote: Date: Thu, 14 Jan 2010 14:20:48 +0100 From: joc...@xray.bmc.uu.se To: gmx-users@gromacs.org Subject: Re: [gmx-users] Error while pulling a settled tip4p water molecule Berk Hess wrote: Hi, I don't understand why you got this error message. Do you have two different types of water molecules with different geometries? In that case Gromacs would give this error message, because currently only one geometry is supported for settle, so you'll have to replace the others by 3 normal constraints. Ah, all right. I have indeed a separate topology for the water used in the pulling (to be able to give it a different residue name). I have replaced the settle by 3 constraints and now everything works fine. But if the you make the geometry identical, it should still work with settle, since then the two settle geometries are identical. Berk Then there is something odd. The two settles are definitely identical since I simply copied the tip4p.itp. I also just rechecked with xxdiff, the two settle lines are the same. Jochen -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- -- 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] water molecule not settled.........
YOu have atomic overlaps or not energy minimized your starting structure. Best, Jochen pavan payghan wrote: hi ... while running mdrun im getting an error water molecule is not settled there is only single such water molecule what should be possible way out...? the same system when i run in previous version of gromacs it showed wrote pdb files with previous current coordinates segmentation fault, what is the reason behind this difference in error ? -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- -- 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] Simulation at unrealistic temperatures
Possibly your water is boiling? YOu could try with NVT. Neha Bharat Gajaria wrote: Dear List, I m trying to run an NPT simulation at 600K which looks unrealistic. I m running minimization followed by anealing and then NPT simulation (mdp files are attached). The job keeps running but after 162 ps, the CPU usage gradually decreases to 26% without any further output. Your help is very much appreciated. Regards, Neha Gandhi Gajaria, School of Biomedical Sciences, Curtin University of Technology, GPO Box U1987 Perth, Western Australia 6845 -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- -- 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] Disulfide bridge formation between A and B state
Hi, I have yesterday already started a topic, but I think I was a bit unclear about what is the problem. I want to have a disulfide bridge in the B state, but not in the A state. And I have not found a way to get the Coulomb interaction between the two sulfurs (and other nearby atoms) right in the A and in the B state. A-state: ...C-S-H H-S-C... B-state: ... C-S-S-C | | H H (where these two H are dummies in B) To close the S-S bond smoothly by going from lambda=0 to 1, I have added a bond type 6 (harmonic potential) [ bonds ] S-nr S-nr 6 b0 k and, a bond type 5 (connection without interaction) S-nr Snr 5 That is required since otherwise, I will have full LJ interaction in B state between, e.g. between the two sulfurs. To have correct LJ interaction in A, I have added pairs between all required atoms, so the LJ should be fine. But what about the charges? If I have a connection between, e.g., sulfur1 and sulfur2, I will never have a coulomb interaction. The problem seems that there is no way to scale a coulomb interaction between two atoms between A and B. There is a pair type 2, that apparently allows to add 1-4 charge interactions, but the parameters cannot be scaled between state A and B (manual table 5.4). I feel that forming a bond with the FEP should be more or less common thing, that's why I am surprised that there seems to be no solution for that. Or am I missing something here? Any ideas? Thanks a lot, Jochen -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- -- 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] Disulfide bridge formation between A and B state
Hi Berk, thanks a lot for the comment. Actually I have found a solution which is good enough for what I am planing to do. I have placed a dummy onto the sulfur which is turned on while the sulfur is tuned off. And I switch on a bond between the dummys when switching from A to B. Then I have added all the necessary exclusions and pairs between the dummy and the nearby atoms, and the new angles and dihedrals due to the S-S bond. The only issue which is now not exact are the 1-4 coulomb interactions of the dummies in the B state. They are computed completely instead of being scaled down by 1.2. So for a real FEP calculation that might be a problem, but for me it is fine. Cheers, Jochen Berk Hess wrote: Hi, I would say that it is very uncommon to form a bond during free energy calculations. To make this work easily we would need to introduce a pair interaction with all parameters explicit that can be perturbed. For the moment you should be able to get it to work using tabulated bonded interactions. The only thing that is not supported through that are soft-core interactions, but I guess those will not be necessary for 1-4 interactions. Berk Date: Fri, 20 Nov 2009 14:01:28 +0100 From: joc...@xray.bmc.uu.se To: gmx-users@gromacs.org Subject: [gmx-users] Disulfide bridge formation between A and B state Hi, I have yesterday already started a topic, but I think I was a bit unclear about what is the problem. I want to have a disulfide bridge in the B state, but not in the A state. And I have not found a way to get the Coulomb interaction between the two sulfurs (and other nearby atoms) right in the A and in the B state. A-state: ...C-S-H H-S-C... B-state: ... C-S-S-C | | H H (where these two H are dummies in B) To close the S-S bond smoothly by going from lambda=0 to 1, I have added a bond type 6 (harmonic potential) [ bonds ] S-nr S-nr 6 b0 k and, a bond type 5 (connection without interaction) S-nr Snr 5 That is required since otherwise, I will have full LJ interaction in B state between, e.g. between the two sulfurs. To have correct LJ interaction in A, I have added pairs between all required atoms, so the LJ should be fine. But what about the charges? If I have a connection between, e.g., sulfur1 and sulfur2, I will never have a coulomb interaction. The problem seems that there is no way to scale a coulomb interaction between two atoms between A and B. There is a pair type 2, that apparently allows to add 1-4 charge interactions, but the parameters cannot be scaled between state A and B (manual table 5.4). I feel that forming a bond with the FEP should be more or less common thing, that's why I am surprised that there seems to be no solution for that. Or am I missing something here? Any ideas? Thanks a lot, Jochen -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- -- 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 New Windows 7: Find the right PC for you. Learn more. http://windows.microsoft.com/shop -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- -- 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] FEP with bond formation, pair problem
Hi, how can I use different coulomb 1-4 interactions in the A and B state. The Manual just says [ pairs ] : LJ and Coulomb 1-4 interactions but, I far as I could see, did not give an example how the coulomb 1-4 interaction can be explicitly given. Thanks a lot for any help, Jochen -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- -- 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] FEP with bond formation, pair problem
David van der Spoel wrote: Berk Hess wrote: Hi, There are automatically different, since they are based on the A and B state charges and the A and B state atom types. But the problem is more complicated: Let's say there is a Butane radical C4H9. that you want to bond to another butane radical to form octane (C8H18). Then the interactions that are non-bonded in the A state are excluded in the B state and replaced by pair interactions. Is this supported in some way? Actually for the LJ part that is supported. The solution is to turn the normal non-bonded LJ in part A into pairs and explicitly give the standart sigma/epsion as A, and zero sigma/epsilon (for 1-2 and 1-3 in B), or scaled (for 1-4 in B) as B state parameters. So far so good. But can the same be done for the colomb 1-4 interactions in the B state? The problem arises since the 1-4 coulomb interactions are scaled down by 1.2 in the AMBER FF, so I need different 1-4 coulomb interactions in A and B. In principle that problem should be in any FEP calculation which includes the formation of a bond. Jochen Berk Date: Thu, 19 Nov 2009 16:15:52 +0100 From: joc...@xray.bmc.uu.se To: gmx-users@gromacs.org Subject: [gmx-users] FEP with bond formation, pair problem Hi, how can I use different coulomb 1-4 interactions in the A and B state. The Manual just says [ pairs ] : LJ and Coulomb 1-4 interactions but, I far as I could see, did not give an example how the coulomb 1-4 interaction can be explicitly given. Thanks a lot for any help, Jochen -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- -- 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 Express yourself instantly with MSN Messenger! MSN Messenger http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/ -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- -- 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] vsites and lincs-order
Berk Hess wrote: Date: Wed, 7 Oct 2009 15:51:00 +0200 From: joc...@xray.bmc.uu.se To: gmx-users@gromacs.org Subject: Re: [gmx-users] vsites and lincs-order All right, thanks! Since you mention energy conservation, maybe it would be worth adding notes or a warnings into pdb2gmx if the time step is large. First, if lincs-order is 4 (instead of 6) and second (more important), if nstlist is not reduced with increasing dt. I strongly feel that most people who use vsites forget to reduce nstlist accordingly. grompp you mean, I guess? I have played a bit with timestep and nstlist and checked the energy drift - apparently neighbor searching should be done at least every 20fs. With less frequent neighbor searching the energy drift increases drastically (with PME and LJ-cutoff, what people typically use). Now imagine a time step of 5fs, with the standard nstlist=10, yields neighbor searching only every 50fs. In my test system that increased the energy drift by a factor of 10-20 compared to the case where neighbor searching was done every 20fs. We can not do such things. Gromacs is not a atomistic, protein specific simulations package. For other systems, masses, etc. such settings could be fine. Moreover, grompp can not easily check for this specific type of vsite use. TIP4p, for instance, also contains a vsite. It has happened that someone put in similar checks in grompp, but this can be EXTREMELY annoying when you use different systems. I see... Jochen Berk Jochen Berk Hess wrote: My P-Lincs paper http://dx.doi.org/10.1021/ct700200b shows that with order 6 and a time step of 4 fs you get roughly the same constraint accuracy and energy conservation as without v-sites and a 2 fs time step. With order 4 and a 4 fs time step the energy drift is 2.2 times higher than with order 6 (not mentioned in the paper). This is not a very large difference. I recall that some time ago I decided to change the default lincs order to 6 (I have not done this yet), but unfortunately now I don't recall what issue made me decide that the current default accuracy is not high enough. Berk Date: Wed, 7 Oct 2009 13:16:52 +0200 From: joc...@xray.bmc.uu.se To: gmx-users@gromacs.org Subject: [gmx-users] vsites and lincs-order Hi, the manual suggests lincs-order = 6 when using large time steps (4-5 fs, with vsites). Has anyone experience how severe that issue is. Has anyone observed artefacts with lincs-order=4 and large time steps? Thanks a lot, Jochen -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- ___ 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 What can you do with the new Windows Live? Find out http://www.microsoft.com/windows/windowslive/default.aspx ___ 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 -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- ___ 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 What can you do with the new Windows Live? Find out http://www.microsoft.com/windows/windowslive/default.aspx
Re: [gmx-users] LINCS error
= 1 qm_opts: ngQM = 0 Table routines are used for coulomb: TRUE Table routines are used for vdw: FALSE Will do PME sum in reciprocal space. PLEASE READ AND CITE THE FOLLOWING REFERENCE U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen A smooth particle mesh Ewald method J. Chem. Phys. 103 (1995) pp. 8577-8592 --- Thank You --- Using a Gaussian width (1/beta) of 0.320163 nm for Ewald Cut-off's: NS: 1 Coulomb: 1 LJ: 2 System total charge: -0.000 Generated table with 1500 data points for Ewald. Tabscale = 500 points/nm Generated table with 1500 data points for LJ6. Tabscale = 500 points/nm Generated table with 1500 data points for LJ12. Tabscale = 500 points/nm Configuring nonbonded kernels... Testing AMD 3DNow support... not present. Testing ia32 SSE support... present. Removing pbc first time Initializing LINear Constraint Solver PLEASE READ AND CITE THE FOLLOWING REFERENCE B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije LINCS: A Linear Constraint Solver for molecular simulations J. Comp. Chem. 18 (1997) pp. 1463-1472 --- Thank You --- The number of constraints is 5500 Center of mass motion removal mode is Linear We have the following groups for center of mass motion removal: 0: rest PLEASE READ AND CITE THE FOLLOWING REFERENCE G. Bussi, D. Donadio and M. Parrinello Canonical sampling through velocity rescaling J. Chem. Phys. 126 (2007) pp. 014101 --- Thank You --- There are: 5600 Atoms Max number of connections per atom is 4 Total number of connections is 11000 Max number of graph edges per atom is 4 Total number of graph edges is 11000 Constraining the starting coordinates (step 0) Constraining the coordinates at t0-dt (step 0) RMS relative constraint deviation after constraining: 6.33e-04 Initial temperature: 306.393 K Started mdrun on node 0 Thu Oct 8 09:58:49 2009 Step Time Lambda 00.00.0 Grid: 25 x 25 x 25 cells --- Program mdrun, VERSION 4.0.2 Source code file: constr.c, line: 136 Fatal error: Too many LINCS warnings (3821) If you know what you are doing you can adjust the lincs warning threshold in your mdp file or set the environment variable GMX_MAXCONSTRWARN to -1, but normally it is better to fix the problem --- Can anyone help me to navigate this issue? Thanks -- Yongchul Greg Chung Graduate Student Dept. of Chemical Engineering, Case Western Reserve University ___ 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 -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- ___ 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] vsites and lincs-order
Hi, the manual suggests lincs-order = 6 when using large time steps (4-5 fs, with vsites). Has anyone experience how severe that issue is. Has anyone observed artefacts with lincs-order=4 and large time steps? Thanks a lot, Jochen -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- ___ 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] vsites and lincs-order
All right, thanks! Since you mention energy conservation, maybe it would be worth adding notes or a warnings into pdb2gmx if the time step is large. First, if lincs-order is 4 (instead of 6) and second (more important), if nstlist is not reduced with increasing dt. I strongly feel that most people who use vsites forget to reduce nstlist accordingly. I have played a bit with timestep and nstlist and checked the energy drift - apparently neighbor searching should be done at least every 20fs. With less frequent neighbor searching the energy drift increases drastically (with PME and LJ-cutoff, what people typically use). Now imagine a time step of 5fs, with the standard nstlist=10, yields neighbor searching only every 50fs. In my test system that increased the energy drift by a factor of 10-20 compared to the case where neighbor searching was done every 20fs. Jochen Berk Hess wrote: My P-Lincs paper http://dx.doi.org/10.1021/ct700200b shows that with order 6 and a time step of 4 fs you get roughly the same constraint accuracy and energy conservation as without v-sites and a 2 fs time step. With order 4 and a 4 fs time step the energy drift is 2.2 times higher than with order 6 (not mentioned in the paper). This is not a very large difference. I recall that some time ago I decided to change the default lincs order to 6 (I have not done this yet), but unfortunately now I don't recall what issue made me decide that the current default accuracy is not high enough. Berk Date: Wed, 7 Oct 2009 13:16:52 +0200 From: joc...@xray.bmc.uu.se To: gmx-users@gromacs.org Subject: [gmx-users] vsites and lincs-order Hi, the manual suggests lincs-order = 6 when using large time steps (4-5 fs, with vsites). Has anyone experience how severe that issue is. Has anyone observed artefacts with lincs-order=4 and large time steps? Thanks a lot, Jochen -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- ___ 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 What can you do with the new Windows Live? Find out http://www.microsoft.com/windows/windowslive/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 -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- ___ 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] large VCM(group rest)
Carla Jamous wrote: Hi, when I get the error message: water molecule cannot be settled,does it have to do with the SETTLE parameter in gromacs? If yes, does anyone know how to fix this? No, that probably means that you have clashes (atomic overlaps) in your system which cause huge forces. Track down which atoms cause the error message and remove the clashes. If that error message appeares during energy minimization, using flexible water may help. Define -DFLEXIBLE in the mdp file, and check in the spc/itp4p/tip3p.itp file if flexible water molecules are actually defined. Good luck, Jochen Carla On Thu, Oct 1, 2009 at 4:46 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Carla Jamous wrote: Hi, I have a problem, I'm running EM, it works but when it comes to doing position-restrained MD, it gives me this error message: Segmentation fault Large VCM(group System): -1293135642624.0, 358859374592.0, -846768177152.0, T-cm: 6.13428e+26 I searched the archives, it says to check-out: oldwiki.gromacs.org http://oldwiki.gromacs.org http://oldwiki.gromacs.org but this site doesn't exist anymore. All of the content has been moved to the new site, albeit a very different organization system. You should still be able to find it with a bit of digging. So please can anyone give me the answer to this problem? The problem is that your system is suddenly moving very fast, probably blowing up. Without a further description of the system and seeing your .mdp file, it's hard to say what the root problem is. -Justin Cheers, Carla ___ gmx-users mailing listgmx-users@gromacs.org mailto: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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org mailto: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 mailto: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 -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- ___ 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] vsites, ffamber, charge groups, N-terminus, and crashes
Berk, I just found that the simulation with a separate CG on each atom also crashed, but much later (after 11ns), that why I just noticed that. I have repeated the simulations now to make really sure that the crashes are reproducible. Jochen Jochen Hub wrote: I have only tested on 8 nodes, and 4 x 2 x 1 DD. Should I try someting else? Jochen Berk Hess wrote: Hi, One question: Are these crashes single processor, with domain decomposition, or both? Berk Date: Wed, 30 Sep 2009 15:35:42 +0200 From: joc...@xray.bmc.uu.se To: gmx-users@gromacs.org Subject: [gmx-users] vsites, ffamber, charge groups, N-terminus, and crashes Hi, I have been trying to use vsites with AMBER99SB, but the simulation frequently cashes after a few hundred ps with the suspects (lincs warnings, 1-4 distance error). I could pinpoint the problem to erroneous charge group assignments generated by pdb2gmx at the NH3 group at the N-terminus. The following charge group assignments caused the error: ; nr type resnr residue atom cgnr charge mass 1 MNH3 1 NASN MN1 1 0 8.517 ; qtot 0 2 MNH3 1 NASN MN2 1 0 8.517 ; qtot 0 3 amber99_39 1 NASN N 1 0.1801 0 ; qtot 0.1801 4 amber99_17 1 NASN H1 2 0.1921 0 ; qtot 0.3722 5 amber99_17 1 NASN H2 2 0.1921 0 ; qtot 0.5643 6 amber99_17 1 NASN H3 2 0.1921 0 ; qtot 0.7564 7 amber99_11 1 NASN CA 3 0.0368 13.018 ; qtot 0.7932 ... The NH3 groups in the lysines were fine and did not cause any error. The only difference compared to the N-terminus is that each of the three H in the NH3 has its own charge group, but the vsites and the N are still in the same CG: 30 amber99_11 2 LYP CE 29 -0.0143 14.026 ; qtot 0.9937 31 amber99_28 2 LYP HE1 30 0.1135 0 ; qtot 1.107 32 amber99_28 2 LYP HE2 31 0.1135 0 ; qtot 1.221 33 MNH3 2 LYP MNZ1 32 0 8.517 ; qtot 1.221 34 MNH3 2 LYP MNZ2 32 0 8.517 ; qtot 1.221 35 amber99_39 2 LYP NZ 32 -0.3854 0 ; qtot 0.8353 36 amber99_17 2 LYP HZ1 33 0.34 0 ; qtot 1.175 37 amber99_17 2 LYP HZ2 34 0.34 0 ; qtot 1.515 38 amber99_17 2 LYP HZ3 35 0.34 0 ; qtot 1.855 Alternatively, I have also tried to give every single atom (including the vsites MN??) a separate charge group, which also worked fine. 1) So, is there any reason why the dummies should be in the same CG as the nitrogen? Or should it be fine just to assign a separate CG to every atom? 2) Is a bug report appreciated on that issue? Best, Jochen -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- ___ 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 See all the ways you can stay connected to friends and family http://www.microsoft.com/windows/windowslive/default.aspx ___ 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 -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755
Re: [gmx-users] vsites, ffamber, charge groups, N-terminus, and crashes
Berk Hess wrote: Hi, I just ran pdb2gmx (4.0.5 and git master) with AMBER on a test di-peptide. But for me all H's in the NH3 terminus always end up in different charge-groups. No matter if I use v-sites or not and if use -ignh or not. So I don't understand how you managed to get the H's in the same charge group. Weird, I always get the H's in separate charge groups. I tried with older and newer pdb2gmx, amber03, amber99sb. I and compared with some older stuff from 1-2 years ago. I had the H's in the terminal always in separate charge groups... But I don't think it will make a difference, so I'll just stick to these CGs. Btw, the bug seemed to have fixed the problem, the simulations running now for a couple of ns. So thanks again for the bugfix. Jochen Berk Date: Wed, 30 Sep 2009 18:14:06 +0200 From: joc...@xray.bmc.uu.se To: gmx-users@gromacs.org Subject: Re: [gmx-users] vsites, ffamber, charge groups, N-terminus, and crashes Berk Hess wrote: Hi, Are you 100% sure you have no other charge groups in your system that consist of only virtual sites, but at least with 2 virtual sites? Ah, you're right. One of the CG which caused the crash is the following, with 2 H's in one CG: 1 amber99_39 1 NPRO N 1 -0.202 16.026 ; qtot -0.202 2 amber99_17 1 NPRO H1 2 (!) 0.312 0 ; qtot 0.11 3 amber99_17 1 NPRO H2 2 (!) 0.312 0 ; qtot 0.422 4 amber99_11 1 NPRO CD 3 -0.012 14.026 ; qtot 0.41 Note however, that the CG which also caused crashes was different, with 2 vsites and 1 heavy atom in the same group, plus a separate CG with 3 hydrogens. According to the lincs warning and 1-4 distance error, the hydrogens seemed to be involved. Typically the warning/error mentioned the hydrogen to have moved/rotated too much: 1 MNH3 1 NASN MN1 1 0 8.517 ; qtot 0 2 MNH3 1 NASN MN2 1 0 8.517 ; qtot 0 3 amber99_39 1 NASN N 1 0.1801 0 ; qtot 0.1801 4 amber99_17 1 NASN H1 2 0.1921 0 ; qtot 0.3722 5 amber99_17 1 NASN H2 2 0.1921 0 ; qtot 0.5643 6 amber99_17 1 NASN H3 2 0.1921 0 ; qtot 0.7564 7 amber99_11 1 NASN CA 3 0.0368 13.018 ; qtot 0.7932 I just fixed a bug with this situation for 4.0.6 and 4.1. You can try the git master or 4.0 release branch. I will get the lates gmx with your bugfix and write back if the crashes still appear. I don't understand why only your terminal NH3 becomes a single charge group, unless the hydrogens were generated with the .hdb file, while they were present for all other NH3 groups. I don't understand that either. The result is the same no matter if I use -ignh, or if the hydrogens are present in the input gro file or not. For examle, using pdb2gmx -f asn[-h].gro -ff amber99sb [-ignh] with asn-h.gro or asn.gro are just the ASN at the N-terminus (with or without hydrogens), e.g. asn-h.gro: Gallium Rubidium Oxygen Manganese Argon Carbon Silicon 8 97NASN N 1423 0.062 -1.317 1.235 97NASN CA 1427 0.109 -1.209 1.154 97NASN CB 1429 0.233 -1.249 1.073 97NASN CG 1432 0.213 -1.368 0.981 97NASN OD1 1433 0.263 -1.478 1.005 97NASN ND2 1434 0.143 -1.345 0.867 97NASN C 1437 0.003 -1.148 1.068 97NASN O 1438 0.033 -1.090 0.964 0.0 0.0 0.0 The written topology is: [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 amber99_39 1 NASN N 1 0.1801 14.01 ; qtot 0.1801 2 amber99_17 1 NASN H1 2 0.1921 1.008 ; qtot 0.3722 3 amber99_17 1 NASN H2 2 0.1921 1.008 ; qtot 0.5643 4 amber99_17 1 NASN H3 2 0.1921 1.008 ; qtot 0.7564 5 amber99_11 1 NASN CA 3 0.0368 12.01 ; qtot 0.7932 6 amber99_28 1 NASN HA 4 0.1231 1.008 ; qtot 0.9163 ... Weird. The same thing happens by the way with a proline N-terminus, no matter if hydrogens are present before pdb2gmx or not. So thanks a lot for the help, Jochen Berk Date: Wed, 30 Sep 2009 16:45:39 +0200 From: joc...@xray.bmc.uu.se To: gmx-users@gromacs.org Subject: Re: [gmx-users] vsites, ffamber, charge groups, N-terminus, and crashes Hey Berk, I just found that the simulation with a separate CG on each atom also crashed, but much later (after 11ns), that why I just noticed that. I have repeated the simulations now to make really sure that the crashes are reproducible. Jochen Jochen Hub wrote: I have only tested on 8 nodes, and 4 x 2 x 1 DD. Should I try someting else? Jochen Berk Hess wrote: Hi, One question: Are these crashes single processor, with domain decomposition, or both? Berk Date: Wed, 30 Sep 2009 15:35:42 +0200 From: joc...@xray.bmc.uu.se To: gmx-users@gromacs.org Subject: [gmx-users] vsites, ffamber, charge groups, N-terminus, and crashes Hi, I have been trying to use vsites with AMBER99SB, but the simulation frequently cashes after a few hundred ps with the suspects (lincs warnings, 1-4 distance error). I could pinpoint the problem
[gmx-users] vsites, ffamber, charge groups, N-terminus, and crashes
Hi, I have been trying to use vsites with AMBER99SB, but the simulation frequently cashes after a few hundred ps with the suspects (lincs warnings, 1-4 distance error). I could pinpoint the problem to erroneous charge group assignments generated by pdb2gmx at the NH3 group at the N-terminus. The following charge group assignments caused the error: ; nr type resnr residue atom cgnr charge mass 1 MNH3 1 NASNMN1 1 0 8.517 ; qtot 0 2 MNH3 1 NASNMN2 1 0 8.517 ; qtot 0 3 amber99_39 1 NASN N 1 0.1801 0 ; qtot 0.1801 4 amber99_17 1 NASN H1 2 0.1921 0 ; qtot 0.3722 5 amber99_17 1 NASN H2 2 0.1921 0 ; qtot 0.5643 6 amber99_17 1 NASN H3 2 0.1921 0 ; qtot 0.7564 7 amber99_11 1 NASN CA 3 0.0368 13.018 ; qtot 0.7932 ... The NH3 groups in the lysines were fine and did not cause any error. The only difference compared to the N-terminus is that each of the three H in the NH3 has its own charge group, but the vsites and the N are still in the same CG: 30 amber99_11 2LYP CE 29-0.0143 14.026 ; qtot 0.9937 31 amber99_28 2LYPHE1 30 0.1135 0 ; qtot 1.107 32 amber99_28 2LYPHE2 31 0.1135 0 ; qtot 1.221 33 MNH3 2LYP MNZ1 32 0 8.517 ; qtot 1.221 34 MNH3 2LYP MNZ2 32 0 8.517 ; qtot 1.221 35 amber99_39 2LYP NZ 32-0.3854 0 ; qtot 0.8353 36 amber99_17 2LYPHZ1 33 0.34 0 ; qtot 1.175 37 amber99_17 2LYPHZ2 34 0.34 0 ; qtot 1.515 38 amber99_17 2LYPHZ3 35 0.34 0 ; qtot 1.855 Alternatively, I have also tried to give every single atom (including the vsites MN??) a separate charge group, which also worked fine. 1) So, is there any reason why the dummies should be in the same CG as the nitrogen? Or should it be fine just to assign a separate CG to every atom? 2) Is a bug report appreciated on that issue? Best, Jochen -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- ___ 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] vsites, ffamber, charge groups, N-terminus, and crashes
Hi Berk, thanks a lot for the quick response. Please let me know if you require a topology/mdp-file/starting structure of the crashing simulation. Concerning pdb2gmx, there is however and issue with the charge group assignments. In my ffamber99sb.rtp, the H's in the N-terminal are set into *separate* charge groups: [ NASN ] [ atoms ] Namber99_39 0.18010 1 H1amber99_17 0.19210 2 -- ! H2amber99_17 0.19210 3 -- ! H3amber99_17 0.19210 4 -- ! CAamber99_11 0.03680 5 In the generated topology, however, the H are merged into the same CG (but not together with the nitrogen): ; nr type resnr residue atom cgnr charge mass t 1 MNH3 1 NASNMN1 1 0 8.517 ; qtot 0 2 MNH3 1 NASNMN2 1 0 8.517 ; qtot 0 3 amber99_39 1 NASN N 1 0.1801 0 ; qtot 0.1801 4 amber99_17 1 NASN H1 2 (!)0.1921 0 ; qtot 0.3722 5 amber99_17 1 NASN H2 2 (!) 0.1921 0 ; qtot 0.5643 6 amber99_17 1 NASN H3 2 (!)0.1921 0 ; qtot 0.7564 7 amber99_11 1 NASN CA 3 0.0368 13.018 ; qtot 0.7932 8 amber99_28 1 NASN HA 4 0.1231 0 ; qtot 0.9163 That does not happen at the lysines. Is there a specific reason why pdb2gmx overrules the parameters in the rtp file (only at the terminus)? (By the way, the charge group generation at the terminus is not affected by vsites, the H's are in the same CG also without vsites.) I feel that even if separate charge groups for each atom is not the gromacs philosophy, pdb2gmx should stick to the rtp file, shouldn't it? Best, Jochen Berk Hess wrote: Hi, There are two separate issues here. One is the charge groups assignment with AMBER. I think that in Gromacs we, in general, do not want all atoms in separate charge groups, but we want to include at least the hydrogens in a charge group with the heavy atom. We would also like the option to make every atom a single charge group, but pdb2gmx of 4.1 already has an option for this. Since the AMBER force fields are currently not in the Gromacs package, we don't have control over the charge group assignment. The second issue is the crashing of the simulations. I don't see why simulations would crash with the slightly strange charge group assignment. But it sounds like there is a bug somewhere. I suspect it could happen when an NH3 group is partially over a box edge. This is strange though, since I think I check all nasty combinations of vsite generation and charge groups. I already got such a file from Bert. Berk Date: Wed, 30 Sep 2009 15:35:42 +0200 From: joc...@xray.bmc.uu.se To: gmx-users@gromacs.org Subject: [gmx-users] vsites, ffamber, charge groups, N-terminus, and crashes Hi, I have been trying to use vsites with AMBER99SB, but the simulation frequently cashes after a few hundred ps with the suspects (lincs warnings, 1-4 distance error). I could pinpoint the problem to erroneous charge group assignments generated by pdb2gmx at the NH3 group at the N-terminus. The following charge group assignments caused the error: ; nr type resnr residue atom cgnr charge mass 1 MNH3 1 NASN MN1 1 0 8.517 ; qtot 0 2 MNH3 1 NASN MN2 1 0 8.517 ; qtot 0 3 amber99_39 1 NASN N 1 0.1801 0 ; qtot 0.1801 4 amber99_17 1 NASN H1 2 0.1921 0 ; qtot 0.3722 5 amber99_17 1 NASN H2 2 0.1921 0 ; qtot 0.5643 6 amber99_17 1 NASN H3 2 0.1921 0 ; qtot 0.7564 7 amber99_11 1 NASN CA 3 0.0368 13.018 ; qtot 0.7932 ... The NH3 groups in the lysines were fine and did not cause any error. The only difference compared to the N-terminus is that each of the three H in the NH3 has its own charge group, but the vsites and the N are still in the same CG: 30 amber99_11 2 LYP CE 29 -0.0143 14.026 ; qtot 0.9937 31 amber99_28 2 LYP HE1 30 0.1135 0 ; qtot 1.107 32 amber99_28 2 LYP HE2 31 0.1135 0 ; qtot 1.221 33 MNH3 2 LYP MNZ1 32 0 8.517 ; qtot 1.221 34 MNH3 2 LYP MNZ2 32 0 8.517 ; qtot 1.221 35 amber99_39 2 LYP NZ 32 -0.3854 0 ; qtot 0.8353 36 amber99_17 2 LYP HZ1 33 0.34 0 ; qtot 1.175 37 amber99_17 2 LYP HZ2 34 0.34 0 ; qtot 1.515 38 amber99_17 2 LYP HZ3 35 0.34 0 ; qtot 1.855 Alternatively, I have also tried to give every single atom (including the vsites MN??) a separate charge group, which also worked fine. 1) So, is there any reason why the dummies should be in the same CG as the nitrogen? Or should it be fine just to assign a separate CG to every atom? 2) Is a bug report appreciated on that issue? Best, Jochen -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755
Re: [gmx-users] vsites, ffamber, charge groups, N-terminus, and crashes
I have only tested on 8 nodes, and 4 x 2 x 1 DD. Should I try someting else? Jochen Berk Hess wrote: Hi, One question: Are these crashes single processor, with domain decomposition, or both? Berk Date: Wed, 30 Sep 2009 15:35:42 +0200 From: joc...@xray.bmc.uu.se To: gmx-users@gromacs.org Subject: [gmx-users] vsites, ffamber, charge groups, N-terminus, and crashes Hi, I have been trying to use vsites with AMBER99SB, but the simulation frequently cashes after a few hundred ps with the suspects (lincs warnings, 1-4 distance error). I could pinpoint the problem to erroneous charge group assignments generated by pdb2gmx at the NH3 group at the N-terminus. The following charge group assignments caused the error: ; nr type resnr residue atom cgnr charge mass 1 MNH3 1 NASN MN1 1 0 8.517 ; qtot 0 2 MNH3 1 NASN MN2 1 0 8.517 ; qtot 0 3 amber99_39 1 NASN N 1 0.1801 0 ; qtot 0.1801 4 amber99_17 1 NASN H1 2 0.1921 0 ; qtot 0.3722 5 amber99_17 1 NASN H2 2 0.1921 0 ; qtot 0.5643 6 amber99_17 1 NASN H3 2 0.1921 0 ; qtot 0.7564 7 amber99_11 1 NASN CA 3 0.0368 13.018 ; qtot 0.7932 ... The NH3 groups in the lysines were fine and did not cause any error. The only difference compared to the N-terminus is that each of the three H in the NH3 has its own charge group, but the vsites and the N are still in the same CG: 30 amber99_11 2 LYP CE 29 -0.0143 14.026 ; qtot 0.9937 31 amber99_28 2 LYP HE1 30 0.1135 0 ; qtot 1.107 32 amber99_28 2 LYP HE2 31 0.1135 0 ; qtot 1.221 33 MNH3 2 LYP MNZ1 32 0 8.517 ; qtot 1.221 34 MNH3 2 LYP MNZ2 32 0 8.517 ; qtot 1.221 35 amber99_39 2 LYP NZ 32 -0.3854 0 ; qtot 0.8353 36 amber99_17 2 LYP HZ1 33 0.34 0 ; qtot 1.175 37 amber99_17 2 LYP HZ2 34 0.34 0 ; qtot 1.515 38 amber99_17 2 LYP HZ3 35 0.34 0 ; qtot 1.855 Alternatively, I have also tried to give every single atom (including the vsites MN??) a separate charge group, which also worked fine. 1) So, is there any reason why the dummies should be in the same CG as the nitrogen? Or should it be fine just to assign a separate CG to every atom? 2) Is a bug report appreciated on that issue? Best, Jochen -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- ___ 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 See all the ways you can stay connected to friends and family http://www.microsoft.com/windows/windowslive/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 -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- ___ 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] vsites, ffamber, charge groups, N-terminus, and crashes
Hey Berk, I just found that the simulation with a separate CG on each atom also crashed, but much later (after 11ns), that why I just noticed that. I have repeated the simulations now to make really sure that the crashes are reproducible. Jochen Jochen Hub wrote: I have only tested on 8 nodes, and 4 x 2 x 1 DD. Should I try someting else? Jochen Berk Hess wrote: Hi, One question: Are these crashes single processor, with domain decomposition, or both? Berk Date: Wed, 30 Sep 2009 15:35:42 +0200 From: joc...@xray.bmc.uu.se To: gmx-users@gromacs.org Subject: [gmx-users] vsites, ffamber, charge groups, N-terminus, and crashes Hi, I have been trying to use vsites with AMBER99SB, but the simulation frequently cashes after a few hundred ps with the suspects (lincs warnings, 1-4 distance error). I could pinpoint the problem to erroneous charge group assignments generated by pdb2gmx at the NH3 group at the N-terminus. The following charge group assignments caused the error: ; nr type resnr residue atom cgnr charge mass 1 MNH3 1 NASN MN1 1 0 8.517 ; qtot 0 2 MNH3 1 NASN MN2 1 0 8.517 ; qtot 0 3 amber99_39 1 NASN N 1 0.1801 0 ; qtot 0.1801 4 amber99_17 1 NASN H1 2 0.1921 0 ; qtot 0.3722 5 amber99_17 1 NASN H2 2 0.1921 0 ; qtot 0.5643 6 amber99_17 1 NASN H3 2 0.1921 0 ; qtot 0.7564 7 amber99_11 1 NASN CA 3 0.0368 13.018 ; qtot 0.7932 ... The NH3 groups in the lysines were fine and did not cause any error. The only difference compared to the N-terminus is that each of the three H in the NH3 has its own charge group, but the vsites and the N are still in the same CG: 30 amber99_11 2 LYP CE 29 -0.0143 14.026 ; qtot 0.9937 31 amber99_28 2 LYP HE1 30 0.1135 0 ; qtot 1.107 32 amber99_28 2 LYP HE2 31 0.1135 0 ; qtot 1.221 33 MNH3 2 LYP MNZ1 32 0 8.517 ; qtot 1.221 34 MNH3 2 LYP MNZ2 32 0 8.517 ; qtot 1.221 35 amber99_39 2 LYP NZ 32 -0.3854 0 ; qtot 0.8353 36 amber99_17 2 LYP HZ1 33 0.34 0 ; qtot 1.175 37 amber99_17 2 LYP HZ2 34 0.34 0 ; qtot 1.515 38 amber99_17 2 LYP HZ3 35 0.34 0 ; qtot 1.855 Alternatively, I have also tried to give every single atom (including the vsites MN??) a separate charge group, which also worked fine. 1) So, is there any reason why the dummies should be in the same CG as the nitrogen? Or should it be fine just to assign a separate CG to every atom? 2) Is a bug report appreciated on that issue? Best, Jochen -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- ___ 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 See all the ways you can stay connected to friends and family http://www.microsoft.com/windows/windowslive/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 -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- ___ 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] vsites, ffamber, charge groups, N-terminus, and crashes
Berk Hess wrote: Hi, Are you 100% sure you have no other charge groups in your system that consist of only virtual sites, but at least with 2 virtual sites? Ah, you're right. One of the CG which caused the crash is the following, with 2 H's in one CG: 1 amber99_39 1 NPRO N 1 -0.202 16.026 ; qtot -0.202 2 amber99_17 1 NPRO H1 2 (!) 0.312 0 ; qtot 0.11 3 amber99_17 1 NPRO H2 2 (!)0.312 0 ; qtot 0.422 4 amber99_11 1 NPRO CD 3 -0.012 14.026 ; qtot 0.41 Note however, that the CG which also caused crashes was different, with 2 vsites and 1 heavy atom in the same group, plus a separate CG with 3 hydrogens. According to the lincs warning and 1-4 distance error, the hydrogens seemed to be involved. Typically the warning/error mentioned the hydrogen to have moved/rotated too much: 1 MNH3 1 NASNMN1 1 0 8.517 ; qtot 0 2 MNH3 1 NASNMN2 1 0 8.517 ; qtot 0 3 amber99_39 1 NASN N 1 0.1801 0 ; qtot 0.1801 4 amber99_17 1 NASN H1 2 0.1921 0 ; qtot 0.3722 5 amber99_17 1 NASN H2 2 0.1921 0 ; qtot 0.5643 6 amber99_17 1 NASN H3 2 0.1921 0 ; qtot 0.7564 7 amber99_11 1 NASN CA 3 0.0368 13.018 ; qtot 0.7932 I just fixed a bug with this situation for 4.0.6 and 4.1. You can try the git master or 4.0 release branch. I will get the lates gmx with your bugfix and write back if the crashes still appear. I don't understand why only your terminal NH3 becomes a single charge group, unless the hydrogens were generated with the .hdb file, while they were present for all other NH3 groups. I don't understand that either. The result is the same no matter if I use -ignh, or if the hydrogens are present in the input gro file or not. For examle, using pdb2gmx -f asn[-h].gro -ff amber99sb [-ignh] with asn-h.gro or asn.gro are just the ASN at the N-terminus (with or without hydrogens), e.g. asn-h.gro: Gallium Rubidium Oxygen Manganese Argon Carbon Silicon 8 97NASN N 1423 0.062 -1.317 1.235 97NASNCA 1427 0.109 -1.209 1.154 97NASNCB 1429 0.233 -1.249 1.073 97NASNCG 1432 0.213 -1.368 0.981 97NASN OD1 1433 0.263 -1.478 1.005 97NASN ND2 1434 0.143 -1.345 0.867 97NASN C 1437 0.003 -1.148 1.068 97NASN O 1438 0.033 -1.090 0.964 0.0 0.0 0.0 The written topology is: [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB 1 amber99_39 1 NASN N 1 0.1801 14.01 ; qtot 0.1801 2 amber99_17 1 NASN H1 2 0.1921 1.008 ; qtot 0.3722 3 amber99_17 1 NASN H2 2 0.1921 1.008 ; qtot 0.5643 4 amber99_17 1 NASN H3 2 0.1921 1.008 ; qtot 0.7564 5 amber99_11 1 NASN CA 3 0.0368 12.01 ; qtot 0.7932 6 amber99_28 1 NASN HA 4 0.1231 1.008 ; qtot 0.9163 ... Weird. The same thing happens by the way with a proline N-terminus, no matter if hydrogens are present before pdb2gmx or not. So thanks a lot for the help, Jochen Berk Date: Wed, 30 Sep 2009 16:45:39 +0200 From: joc...@xray.bmc.uu.se To: gmx-users@gromacs.org Subject: Re: [gmx-users] vsites, ffamber, charge groups, N-terminus, and crashes Hey Berk, I just found that the simulation with a separate CG on each atom also crashed, but much later (after 11ns), that why I just noticed that. I have repeated the simulations now to make really sure that the crashes are reproducible. Jochen Jochen Hub wrote: I have only tested on 8 nodes, and 4 x 2 x 1 DD. Should I try someting else? Jochen Berk Hess wrote: Hi, One question: Are these crashes single processor, with domain decomposition, or both? Berk Date: Wed, 30 Sep 2009 15:35:42 +0200 From: joc...@xray.bmc.uu.se To: gmx-users@gromacs.org Subject: [gmx-users] vsites, ffamber, charge groups, N-terminus, and crashes Hi, I have been trying to use vsites with AMBER99SB, but the simulation frequently cashes after a few hundred ps with the suspects (lincs warnings, 1-4 distance error). I could pinpoint the problem to erroneous charge group assignments generated by pdb2gmx at the NH3 group at the N-terminus. The following charge group assignments caused the error: ; nr type resnr residue atom cgnr charge mass 1 MNH3 1 NASN MN1 1 0 8.517 ; qtot 0 2 MNH3 1 NASN MN2 1 0 8.517 ; qtot 0 3 amber99_39 1 NASN N 1 0.1801 0 ; qtot 0.1801 4 amber99_17 1 NASN H1 2 0.1921 0 ; qtot 0.3722 5 amber99_17 1 NASN H2 2
Re: [gmx-users] vsites, ffamber, charge groups, N-terminus, and crashes
Ups, sorry, the other CG which caused the crashes (with 3 H's) was of course also in your category and not different. I think I should go home for today... :-) So thanks again for the bugfix! Jochen Berk Hess wrote: Hi, Are you 100% sure you have no other charge groups in your system that consist of only virtual sites, but at least with 2 virtual sites? I just fixed a bug with this situation for 4.0.6 and 4.1. You can try the git master or 4.0 release branch. I don't understand why only your terminal NH3 becomes a single charge group, unless the hydrogens were generated with the .hdb file, while they were present for all other NH3 groups. Berk Date: Wed, 30 Sep 2009 16:45:39 +0200 From: joc...@xray.bmc.uu.se To: gmx-users@gromacs.org Subject: Re: [gmx-users] vsites, ffamber, charge groups, N-terminus, and crashes Hey Berk, I just found that the simulation with a separate CG on each atom also crashed, but much later (after 11ns), that why I just noticed that. I have repeated the simulations now to make really sure that the crashes are reproducible. Jochen Jochen Hub wrote: I have only tested on 8 nodes, and 4 x 2 x 1 DD. Should I try someting else? Jochen Berk Hess wrote: Hi, One question: Are these crashes single processor, with domain decomposition, or both? Berk Date: Wed, 30 Sep 2009 15:35:42 +0200 From: joc...@xray.bmc.uu.se To: gmx-users@gromacs.org Subject: [gmx-users] vsites, ffamber, charge groups, N-terminus, and crashes Hi, I have been trying to use vsites with AMBER99SB, but the simulation frequently cashes after a few hundred ps with the suspects (lincs warnings, 1-4 distance error). I could pinpoint the problem to erroneous charge group assignments generated by pdb2gmx at the NH3 group at the N-terminus. The following charge group assignments caused the error: ; nr type resnr residue atom cgnr charge mass 1 MNH3 1 NASN MN1 1 0 8.517 ; qtot 0 2 MNH3 1 NASN MN2 1 0 8.517 ; qtot 0 3 amber99_39 1 NASN N 1 0.1801 0 ; qtot 0.1801 4 amber99_17 1 NASN H1 2 0.1921 0 ; qtot 0.3722 5 amber99_17 1 NASN H2 2 0.1921 0 ; qtot 0.5643 6 amber99_17 1 NASN H3 2 0.1921 0 ; qtot 0.7564 7 amber99_11 1 NASN CA 3 0.0368 13.018 ; qtot 0.7932 ... The NH3 groups in the lysines were fine and did not cause any error. The only difference compared to the N-terminus is that each of the three H in the NH3 has its own charge group, but the vsites and the N are still in the same CG: 30 amber99_11 2 LYP CE 29 -0.0143 14.026 ; qtot 0.9937 31 amber99_28 2 LYP HE1 30 0.1135 0 ; qtot 1.107 32 amber99_28 2 LYP HE2 31 0.1135 0 ; qtot 1.221 33 MNH3 2 LYP MNZ1 32 0 8.517 ; qtot 1.221 34 MNH3 2 LYP MNZ2 32 0 8.517 ; qtot 1.221 35 amber99_39 2 LYP NZ 32 -0.3854 0 ; qtot 0.8353 36 amber99_17 2 LYP HZ1 33 0.34 0 ; qtot 1.175 37 amber99_17 2 LYP HZ2 34 0.34 0 ; qtot 1.515 38 amber99_17 2 LYP HZ3 35 0.34 0 ; qtot 1.855 Alternatively, I have also tried to give every single atom (including the vsites MN??) a separate charge group, which also worked fine. 1) So, is there any reason why the dummies should be in the same CG as the nitrogen? Or should it be fine just to assign a separate CG to every atom? 2) Is a bug report appreciated on that issue? Best, Jochen -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- ___ 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 See all the ways you can stay connected to friends and family http://www.microsoft.com/windows/windowslive/default.aspx ___ 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 -- --- Dr. Jochen Hub Molecular
[gmx-users] read_eigenvectors not in libgmxana
Hi, I am writing a tool which requires the read_eigenvectors routine from tools/eigio.c. Apparently, this function is not in any gromacs library, as I am getting a link error, such as Undefined symbols: _read_eigenvectors, referenced from: ... As a workaround, I am directly linking to eigio.o and eigenvectors.o, which is, however, less convenient... Is there a special reason why the routines from eigio.c and eigenvectors.c are not in any library? Or do I miss something here? Best, Jochen -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- ___ 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_wham error
Ragnarok sdf wrote: While trying to analyse my several windows with g_wham the following error appears : Fatal error: Pull geometry direction not supported The pull geometry direction has unfortunatly been forgotten in g_wham by, well, myself (shame on me :-) ). I can add the geometry to the g_wham code if desired. However, it is straigh-forward to make a gromacs 3 style pdo file out of your pullx files. Probably, that is a 10-liner awk script or similar. Then, feed the pdo files into g_wham with g_wham -ip. Best, Jochen -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- ___ 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] ffgmx:diffusion of oxygen
Could it be that you have not removed the jumps due to the periodic boudary conditions before using g_msd? Try trjconv -pbc nojump Jochen Sunil Thapa wrote: Respectable Justin/David/Mark I used ffgmx force field thinking it as suitable for bonds in the oxygen molecule. And yes it gives diffusion coefficient of SPC water to be 3.5 which matches with that given in the gromacs manual. After equilibrating my system of 1 oxygen and 255 water molecules in NPT ensemble at 1 bar and 298 K i subjected it to the NVT ensemble for about 50 ns. The msd is not a straight line. It increases linearly for first 20 ns and after some ns it decreases linearly giving negative diffusion coefficient. Could you help me out with it? The model contains L-J interaction between oxygen and water molecule. The mdp file used for production run is as follows: ;RUN CONTROL parameters. integrator = md dt = 0.002 ; ps ! nsteps = 5000 ; total 1 ns. nstcomm = 1 ;LANGEVIN DYNAMICS parameters have not been specified as the integrator is ;md ;OUPUT CONTROL parameters. nstxout = 250 nstvout = 1000 nstfout = 0 nstlog = 100 nstenergy = 100 energygrps = OMOL SOL ;NEIGHBOUR SEARCHING parameters. nstlist = 10 ns_type = grid rlist = 0.9 ;initially 1 I modified to 0.9 ;ELECTROSTATIC and VdW parameters. rcoulomb = 0.9 rvdw = 0.9 epsilon-r = 1 ;BERENDSEN TEMPERATURE COUPLING is on in two groups Tcoupl = berendsen tc-grps = OMOL SOL tau_t = 0.001 0.01 ref_t = 298 298 ;PRESSURE COUPLING is on Pcoupl = no;berendsen; berendsen exponential relaxation coupling tau_p = 0.1;modified from 0.5 compressibility = 4.6e-5 ref_p = 1.0 ;SIMULATED ANNEALING parameters are not specified. ;GENERATE VELOCITIES is on at 298 K. gen_vel = no; ; generate initially gen_temp = 298 gen_seed = 173529 ;give different values for different trials. ;BONDS parameters constraints = all-bonds constraint-algorithm = shake unconstrained-start = yes and the msd curve is attached in the next mail due to insufficient space Your help is necessary for me. Sunil Kumar Thapa Tribhuvan University, Nepal ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] intermolecular distance restraint
Hi Warren, if you want to use distance restraints, the two proteins must be in the same gromacs molecule. AFAIK, it is impossible to use distance restraints between atoms of different molecules. Altermatively, you may want to consider bonds of type 6 (not subject to lincs). pdb2gmx -merge is useful to create the topology of a molecule that actually contains 2 proteins. If the two proteins must be in different gromacs molecules, you would have to use the pull code. Best, Jochen warren deng wrote: Hi Gromacs users, In my simulation, I need to restrain distances between atoms on two protein molecules. But the Gromacs manual on NOE seems to imply that the atom indices belong to the same molecule type. So I am wondering whether it is possible to create distance restraint between two molecule types in Gromacs? Many thanks, Warren ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] how to define the dummy atoms in gromacs
He, Yang wrote: Hi all users, I need to add some dummy atoms in my case. I know that I need to include the section [virtual_sites] in the top file but I am not sure how to define them in the itp file .Do I need to list these atoms in the section[atoms] ? Can anyone of you give me some suggestions about that? Define them in the atoms section and list them as dummies in the dummie section. Check the manual for detail. Jochen Thank you in advance. Yang ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 . -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] how to save grace out put to jpeg or grafifal pic
Homa Azizian wrote: hi my ques. dose not exactly relate to the gromacs while it is about how I can save the resulting plot from grace in to the jpeg or other picture file. thanks -- Tehran University of Medical Sciences www.tums.ac.ir One also gets pretty results when first printing to eps, and then using the imagemagick command convert -density 100 plot.eps plot.png jochen -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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_wham
Hi, sorry for the late answer. But there is a completely new g_wham in the most recent gmx version 4.xx. With this one, the error This does not appear to be a valid pdo file does not occur any more. And the new g_wham provides a lot of new featues, too. Best, Jochen anirban polley wrote: Hi all, Could you please tell me why g_wham does not give the correct result? After doing umbrella sampling with mdrun, I got the .pdo file which is like # UMBRELLA 3.0 # Component selection: 0 0 1 # nSkip 1 # Ref. Group 'DPP' # Nr. of pull groups 1 # Group 1 'PIP' Umb. Pos. 3.388542 Umb. Cons. 100.00 # 0.001.650988 0.0020001.650989 0.0040001.651020 0.0060001.651055 0.0080001.651139 . Now, when I try to analysis it by g_wham, I have stuck. Could you please tell me the right method? 1. g_wham -max 1.7779 -min .8988 -temp 310 -o pull_pip2_dppc.pdo. The error message is: --- Program g_wham, VERSION 3.3.3 Source code file: gmx_wham.c, line: 313 Fatal error: You need to specify a series of pdo files as input --- Question: How can I get the series of pdo file? Did it mean that I have to vary the Umb. const. and run it many times and get many .pdo files? 2. g_wham pull_pip2_dppc.pdo -max 1.7779 -min .8988 -temp 310 -o -hist The error is : Opening file pull_pip2_dppc.pdo. gzip: stdin: not in gzip format --- Program g_wham, VERSION 3.3.3 Source code file: gmx_wham.c, line: 89 Fatal error: This does not appear to be a valid pdo file --- 3. Now, I tried it by converting .gz file as an input g_wham pull_pip2_dppc.pdo.gz -max 1.7779 -min .8988 -temp 310 -o The error is: Opening file pull_pip2_dppc.pdo.gz. --- Program g_wham, VERSION 3.3.3 Source code file: gmx_wham.c, line: 89 Fatal error: This does not appear to be a valid pdo file --- Could you please tell me why it gives error again and again? What is the wrong that I have done? How Can I get the correct answer? Please, tell me the answer? I am eagerly waiting for your advise. Regards, Anirban ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] Rugged dgdl curve in turning off/on the charge for Leu
friendli wrote: Dear all, When I performing mutation free energy calculation from Leu to Ala, I first turn off the charge on the side chain of Leu. As I read from the GMX archive, the dG/dl curve should be rather smooth for turning off the partial charge. In this step(charge off/on), however, I can not obtain the expected smooth dGdl curve.(see the attachment). I did not use soft-core in this step. Is this normal because the mutation is relatively large? If not, what could be the problem? The partial charges of the sidechaines of apolar AA (such as Leu) are almost zero, that's why your dGdl is almost zero. Only because of the small dgdl your curve looks non-smooth, but that's just a scale issue here. Best, Jochen the following is part of the topology file. 17 opls_238 2LEU N 7 -0.514.0067 ; qtot 0.5 18 opls_241 2LEU H 70.3 1.008 ; qtot 0.8 19 opls_224B 2LEU CA 7 0.14 12.011 ; qtot 0.94 20 opls_140 2LEU HA 7 0.06 1.008 ; qtot 1 21 opls_136 2LEU CB 8 -0.12 12.011 opls_1360 12.011 ; qtot 0.88 22 opls_140 2LEUHB1 8 0.06 1.008 opls_1400 1.008 ; qtot 0.94 23 opls_140 2LEUHB2 8 0.06 1.008 opls_1400 1.008 ; qtot 1 24 opls_137 2LEU CG 9 -0.06 12.011 opls_1370 12.011 ; qtot 0.94 25 opls_140 2LEU HG 9 0.06 1.008 opls_1400 1.008 ; qtot 1 26 opls_135 2LEUCD1 10 -0.18 12.011 opls_1350 12.011 ; qtot 0.82 27 opls_140 2LEU HD11 10 0.06 1.008 opls_1400 1.008 ; qtot 0.88 28 opls_140 2LEU HD12 10 0.06 1.008 opls_1400 1.008 ; qtot 0.94 29 opls_140 2LEU HD13 10 0.06 1.008 opls_1400 1.008 ; qtot 1 30 opls_135 2LEUCD2 11 -0.18 12.011 opls_1350 12.011 ; qtot 0.82 31 opls_140 2LEU HD21 11 0.06 1.008 opls_1400 1.008 ; qtot 0.88 32 opls_140 2LEU HD22 11 0.06 1.008 opls_1400 1.008 ; qtot 0.94 33 opls_140 2LEU HD23 11 0.06 1.008 opls_1400 1.008 ; qtot 1 34 opls_235 2LEU C 120.5 12.011 ; qtot 1.5 35 opls_236 2LEU O 12 -0.515.9994 ; qtot 1 thank you Qiang ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] error in parallel mdrun
hazizian wrote: hi I want to use mdrun, when i use It as one job it goes on. but when i use as parallel job grompp -np 4 -f md300.mdp -c pr.pdb -p topol.top -o md300.tpr then mpirun -np 4 mdrungromacs_mpi -nice 0 -v -s md300.tpr -o md300.trr -c md300.pdb -e md300.edr -g md300.log the following error apear: starting mdrun 'SWISS-MODEL SERVER (http:' 1 steps, 1.0 ps. step 0 Warning: 1-4 interaction between 1 and 8 at distance 247185117020282387238658576035127661536052825745545652719669759062373813704493551571478495838644038086589824739452834743244657492619860086077032362651572801981421019014673105813372306735907332585544062133537655269329581179473829805619840403813960735860655676896572043357093782778978904568459302010880.000 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation ** This usually means your system is exploding, ^^ That is what is probably happening. check your starting structure and to an energy minimization. Best, Jochen if not, you should increase table-extension in your mdp file --- Program mdrungromacs_mpi, VERSION 3.3.3 Source code file: nsgrid.c, line: 220 Fatal error: Number of grid cells is zero. Probably the system and box collapsed. --- Everything Must Go (Red Hot Chili Peppers) Error on node 0, will try to stop all the nodes Halting parallel program mdrungromacs_mpi on CPU 0 out of 4 any help would be appriciated. thanks -- Tehran University of Medical Sciences www.tums.ac.ir -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Bugs in gromacs 4
Jelger Risselada wrote: Finally had a look through the gromacs 4.0 source code. Don't know if this bug/points already have been reported and changed in 4.0.2: 1) There is never memory allocated for the pointers to the user defined groups: mdatoms-cU1 etc. I'm not sure, but there is a /* The user should fix this */ if (FALSE) srenew(md-cU1,md-nalloc); if (FALSE) srenew(md-cU2,md-nalloc); in ./src/mdlib/mdatom.c. You can remove the FALSE and get the memory allocation, I guess. Jochen These pointers will stay NULL when a user defined group is defined in the mdp file. I find these groups normally a pretty useful interface for simple fast implementations. 2) The pull code has indeed completely changed, however to me the questionable factor 0.5 remained the same: In pull.c: /* Add the pull contribution to the virial */ vir[j][m] += 0.5*f[j]*r_ij[g][m]; I do agree with the positive sign of the summation, but why is there a factor 0.5 to correct for double counting included in the summation. The summation is already ordered as r_ij and f[j] is the distance vector and force between the particle and the equilibrium position of the spring and therefore double counting cannot occur. Ofcourse it's possible that this factor 0.5 is not meant as a double counting correction factor, but then I don't see where it does come from. If this factor is indeed incorrect it might affect the pressure significantly in case a large pulling group is used. greetings Jelger ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problems with editconf 4.0
Hey Alan, I think there is a litle bug in editconf. If you add a CRYST1 line with some random numbers into the first Complex.pdb, editconf works fine adds the corret CRYST1 line according to your option (-d and -bt). Best, Jochen Alan wrote: Hello, So this command used to work fine: editconf -bt triclinic -f Complex.pdb -o Complex.pdb -d 1.0 Now, with gmx 4.0 (from fink for Mac Intel Leopard), I got a warning: WARNING: No boxtype specified - distance condition applied in each dimension. (no box information is inserted in the pdb file as it used to do in gmx 3) and then when I try: genbox -cp Complex.pdb -cs ffamber_tip3p.gro -o Complex_b4ion.pdb -p Complex.top I get this error: --- Program genbox, VERSION 4.0 Source code file: gmx_genbox.c, line: 744 Fatal error: Undefined solute box. Create one with editconf or give explicit -box command line option --- If I change '-o Complex.pdb' to '-o Complex.gro' and so on (i.e, if I use gro instead of pdb), all work fine. So, pdb format is not ok anymore with gmx commands or there's a bug here? Many thanks in advance, Alan ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Misunderstandings with g_rms
DimitryASuplatov wrote: Hello, I am sorry for this stupid question. Lets say I have an index file of all chain A atoms. I want to calculate RMS of chain A _backbone_ only. I run g_rms. It asks two questions: 1/ Select group for least squares fit 2/ Select group for RMSD calculation To the best of my understanding, I should answer BACKBONE to the first question and enter group number corresponding to chain A index file to the second one. In your case you need to make an index file with a group of the backbone of chain a, do something like make_ndx -f x.gro chain a ChA Backbone q then run g_rms with -n And give the ChainA-backbone group twice to g_rms. Best, Jochen Is that correct? Thank you. SDA ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Repeating the simulation
Q. Y. HUAN wrote: Dear all gmx-users and developers, I have completed a simulation, and get all the results. Just asking you guys for your opinion whether I should repeat the simulation again 1 or 2 times in order to make sure the simulation results are valid for my work even thought I have equilibrate my system before running the production simulation or I just need to do it ONCE? That depends very much on the observable that you measure and on the amount of statistics you can extract from your single simulation. E.g., if you want to compute the RDF of water moleucles in a pure water simulation, the single simulation is certainly enough. If you observed some transition in a protein simulation only once in your simulation, it is highly advisable to repeat the simulation a couple of times to make sure that your observation is significant. Best, Jochen Thanks for any comments and suggestions. QIU YI HUAN DEPARTMENT OF CHEMISTRY, FACULTY OF SCIENCE, UNIVERSITY PUTRA MALAYSIA, MALAYSIA. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem in prest.mdp file
Bhawana Gupta wrote: hello everybody, I m sending this mail just to ask u problem which i m facing which using command for grompp prest.mdp Error is Program grompp, VERSION 4.0 Source code file: futil.c, line: 527 Fatal error: Library file posre.itp not found in current dir nor in default directories. (You can set the directories to search with the GMXLIB path variable) You probably try to include a posre.itp in your topology (check for #include posre.itp) but it is not present in the current directory. They are also saying that NOTE 1 [file *_md_water_prest.mdp, line unknown]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. Better use the V-rescale thermostad. Best, Jochen Please Please help me as soon as possible. With Regards Bhawana Gupta ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Warning with L-BFGS minimization
Sorry, I haven't read the thread for a couple of days...too many
projects in parallel, I guesss. :)
Thanks a lot for your answers!
It was indeed the LJ cutoff which caused the error. With the following
settings, the L-BFGS minimization went allright:
vdwtype = Shift
rlist= 1.2
rvdw = 1.0
rvdw-switch = 0.8
coulombtype = PME
rcoulomb = 1.2
Btw, I've had quit good experience with the l-bfgs minimizer. In some
cases, where cg or steep failed, l-bfgs was succeessful.
Thanks again,
jochen
Tsjerk Wassenaar wrote:
Hi Jochen,
It's probably the rvdw cutoff (from readir.c):
if (ir-eI == eiLBFGS (ir-coulombtype==eelCUT || ir-vdwtype==evdwCUT)
ir-rvdw != 0) {
warning(For efficient BFGS minimization, use switch/shift/pme
instead of cut-off.);
}
Bummer!
Tsjerk
On 10/24/08, Jochen Hub [EMAIL PROTECTED] wrote:
Hi,
with l-bfgs minimzation, grompp always reports
WARNING 1 [file em.mdp, line unknown]:
For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
even if the mdp gives
; Method for doing electrostatics
coulombtype = PME
rcoulomb_switch = 0
rcoulomb = 1.
I could't find anything on that in the archive. Is that a known issue?
Cheers,
Jochen
--
Dr. Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
Tel.: +49 (0)551 201-2312
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--
Dr. Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
Tel.: +49 (0)551 201-2312
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Re: [gmx-users] Is it the correct label on Y axis ( density graph)
Mark Abraham wrote: Jochen Hub wrote: huan wrote: Dear all, I am wondering that is it the correct label of y axis in the density graph which i obtained using g_energy? because it is not a density unit but is labeled as kJ/mol Dear huan, 1) I would encourage you to read a few reviews on MD and the gromacs manual carfully. 2) g_energy doesn't write densities, but box vectors which you can use to compute your density. mdrun calculates densities for simulations with non-constant volume, and g_energy will show and plot these. Ah, right, I didn't know that (yet :) )! Thanks! Jochen Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] density graph ( density vs time)
huan wrote: Dear all gmx-users and developers. I wish to get a density graph with density versus time instead of nm, so how can i obtained this? You could extract the box vectors with g_energy and compute the density from the volume. Best, Jochen Thanks. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] density graph ( density vs time)
huan wrote: I used g_energy before but i just obtained density (y-axis) versus box length (x axis). huan wrote: Previously i obtained a density (y-axis) versus box length (x axis) using g_density.. Sounds like a contradition to me... :-) thanks --- On Tue, 10/28/08, Justin A. Lemkul [EMAIL PROTECTED] wrote: From: Justin A. Lemkul [EMAIL PROTECTED] Subject: Re: [gmx-users] density graph ( density vs time) To: [EMAIL PROTECTED], Discussion list for GROMACS users gmx-users@gromacs.org Date: Tuesday, October 28, 2008, 11:31 PM huan wrote: Dear all, Previously i obtained a density (y-axis) versus box length (x axis) using g_density.. So now i wonder is it there is another way that we can use other way to obtain a density (y axis) versus time length (x-axis). Use g_energy. -Justin Thanks.. --- On Tue, 10/28/08, Mark Abraham [EMAIL PROTECTED] wrote: From: Mark Abraham [EMAIL PROTECTED] Subject: Re: [gmx-users] density graph ( density vs time) To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Tuesday, October 28, 2008, 4:46 PM huan wrote: Dear all gmx-users and developers. I wish to get a density graph with density versus time instead of nm, so how can i obtained this? Please ask a more specific question. We can't tell whether your problem is knowing what tool to use, how to use it, how to label axes of plots or something else. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users]Simulated annealing
858.75 40.00 872.787048 41.04 843.033813 42.04 874.984009 43.04 845.272583 44.04 822.993713 45.04 863.116455 46.04 865.640198 47.04 873.489563 48.04 849.170776 49.04 861.631958 50.04 860.39 51.04 834.341003 52.04 864.601196 53.04 838.268372 54.04 842.860046 55.04 837.590332 56.04 855.985046 57.04 836.168030 58.04 862.147644 59.04 869.183044 60.04 873.057556 61.04 871.051636 62.04 857.647217 63.04 857.834106 64.00 871.380981 65.00 850.045654 66.00 880.142456 67.00 844.183350 68.00 850.980042 69.00 854.431091 70.00 847.898743 71.00 859.750488 72.00 852.219910 73.00 854.833984 74.00 851.676514 75.00 866.519287 76.00 861.120605 77.00 857.873230 78.00 845.287720 79.00 874.60 80.00 854.244751 81.08 864.049561 82.08 892.515991 83.08 855.164734 84.08 867.054077 85.08 862.560059 86.08 829.368469 87.08 864.729553 88.08 882.954102 89.08 865.048401 90.08 864.581848 91.08 870.596619 92.08 856.474976 93.08 861.473450 94.08 838.902344 95.08 896.907715 96.08 865.042480 97.08 877.761292 98.08 877.356750 99.08 855.421753 100.08 863.720398 -- Could anyone tell me what changes I should make in the parameter file? Many thanks, Jes. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Warning with L-BFGS minimization
Hi, with l-bfgs minimzation, grompp always reports WARNING 1 [file em.mdp, line unknown]: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. even if the mdp gives ; Method for doing electrostatics coulombtype = PME rcoulomb_switch = 0 rcoulomb = 1. I could't find anything on that in the archive. Is that a known issue? Cheers, Jochen -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Warning with L-BFGS minimization
Mark Abraham wrote: Jochen Hub wrote: Hi, with l-bfgs minimzation, grompp always reports WARNING 1 [file em.mdp, line unknown]: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. even if the mdp gives ; Method for doing electrostatics coulombtype = PME rcoulomb_switch = 0 rcoulomb = 1. I could't find anything on that in the archive. Is that a known issue? Maybe it's case-sensitive... try pme No, same warning. :-( Jochen Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] spliting clusters.pdb
Abu Naser wrote: Hi All, I have been wondering whether there is any tools for spliting clusters.pdb file into individual snapshots. If there is a TER between the structures, the shell command csplit may be useful for you. Jochen With regards, Abu _ Win an Xbox 360 or £200 Top Shop Vouchers http://clk.atdmt.com/GBL/go/115454062/direct/01/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] trjconv in Parallel run
sudheer babu wrote: Hi all, I have been running mdrun in Parallel for few hours due to full disk it crashed in between, later when I use trjconv command trjconv -f .trr -o xtc for convert .trr to .xtc its showing Program trjconv, VERSION 3.3.1 Source code file: trnio.c, line: 66 File input/output error: Can not determine precision of trn file have you tried trjconv -ndec ? Jochen cant I make .trr to .xtc? what may be the problem how can I remedy this error. Any suggestions would be appreciated Thanks in advance ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
