Re: [gmx-users] Simulation of charged systems (2)
Hi, thanks to Justin for the pointer to the list archive I searched before with net charge, but without getting useful results. For the sake of clarity, I am not referring to the neutralizing plasma or neutralizing background charge used implicitly with PME, but to an additional net-charge correction implemented for example in CHARMM to avoid, at least partly, the artifacts produced by that neutralizing background charge in net-charged systems, which are sometimes unavoidable (s., eg., Bogusz S, Cheatham TE, Brooks BR. Removal of pressure and free energy artifacts in charged periodic systems via net charge corrections to the ewald potential. Journal of Chemical Physics. 1998;108(17):7070-84. http://jcp.aip.org/jcpsa6/v108/i17/p7070_s1). Felipe On 11/05/2012 02:27 PM, Justin Lemkul wrote: On 11/5/12 8:16 AM, Felipe Pineda, PhD wrote: Hi again! many thanks to Xavier for his response, the only one I got so far ... I had the same impression, but I'm seeking for theoretically/technically more funded statements. My impression is also that there are different kind of equations depending of the treatment of long-range electrostatic interactions. My concrete question is now: are net charge corrections to the Ewald potential implemented in Gromacs? http://lists.gromacs.org/pipermail/gmx-users/2006-April/020821.html Searching the list archive for neutralizing background charge turns up a large number of results. This is a fairly common question, and there are many replies with varying degrees of detail. -Justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: NPT with md-vv + Nose-Hoover + Parinello-Rehman
Hi Tarak, I have had the same problem. As far as I know, it is not possible to use Nose-Hoover + Parrinello-Rahman in combination with the md-vv integrator. I am using md (leap-frog) in combination with Nose-Hoover + Parrinello-Rahman, this is working fine. I guess it would be great to get a confirmation by the developers. Daniel -- View this message in context: http://gromacs.5086.n6.nabble.com/NPT-with-md-vv-Nose-Hoover-Parinello-Rehman-tp5002701p5002702.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] PCA
Hi Tuba, I guess you have to create an index for each peptide and then extracting covariance matrix on each peptide using the new indexes. Francesco 2012/11/6 Tuba Kilinc tkil...@gmail.com hi all, i would like to apply PCA (principal component analysis) for my peptides that i simulated. i do know PCA for one trajectory but what if i have more than one peptide ? how can i apply pca for example 10 peptides in a box ? typically, i start with a PCA on the simulation with g_covar -s protein.pdb -f traj.xtc -v eigenvec.trr and i create projections on PCA vectors using g_anaeig i have to extract a trajectory for each peptide and concatenate those trajectories and i need to make an index group for each peptide in each system that i include but i couldnt figure out extract a trajectory for each group for each system? Could you help me please ? thanks -- 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 -- Cordiali saluti, Dr.Oteri Francesco -- 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: NPT with md-vv + Nose-Hoover + Parinello-Rehman
On 11/6/12 3:56 AM, dakoenig wrote: Hi Tarak, I have had the same problem. As far as I know, it is not possible to use Nose-Hoover + Parrinello-Rahman in combination with the md-vv integrator. I am using md (leap-frog) in combination with Nose-Hoover + Parrinello-Rahman, this is working fine. I guess it would be great to get a confirmation by the developers. This is correct. Not all combinations of .mdp parameters work; there are methodological and algorithmic constraints (no pun intended) on some of them. -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
[gmx-users] Re: charge groups
Dear Justin, Thank you for the answer. I'm using OPLS force field but I calculated the partial charges of the atoms from the HF geometry optimization. Do you have any idea if I should arrange the charge groups in this case or not? Regards, Akn. -- View this message in context: http://gromacs.5086.n6.nabble.com/charge-groups-tp5002681p5002705.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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:Ka/Kd
Thank you for the reply, Figured. Needless to say though, the software using the pulled gives about the same as by hand (although diffusion constants are also guessed but fit into what the computer calculates as compared on a scale of lysozyme,,, xxx, Fab fragments) but can not do the forward/backward (values of -65000.045/-74967.031), while the one way and integral give reasonable values, and the caculated (via g_hbond or g_hbond-g_analyze) DelG fits well also... grüess Stephan Original-Nachricht Datum: Mon, 05 Nov 2012 18:14:36 -0500 Von: Justin Lemkul jalem...@vt.edu An: Discussion list for GROMACS users gmx-users@gromacs.org Betreff: Re: [gmx-users] Re:Ka/Kd On 11/5/12 9:59 AM, lloyd riggs wrote: Quick question, I went and calculated the Ka/Kd with the g_hbond -- -g_analyze and just wondered, if all my simulations are pulled, does it in the end make any sense, or is there ways to compensate for this. I assume the h_bond life would be meaningless, as under a normal situation, 2 proteins h-bond lifes could stretch into the seconds (minus fluctuation around a very small bound area)... Extracting equilibrium properties from a non-equilibrium simulation is dicey, indeed. I've never attempted such a thing myself, but I would think determining Kd from deltaG would be more reliable, at least inasmuch as the deltaG estimate is reliable (i.e., from umbrella sampling and a proper assessment of errors). -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 -- 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
Re: [gmx-users] Re: Diatomic in MeCN NPT (NH and PR) simulation segfaults after 1 us
On 11/5/12 11:25 PM, benjfitz wrote: Justin, thank you for reminding me that I need to adhere to sane parameters. I do have a few clarifying points, as it were. I tried these simulations again, but with a larger box and 0.9 nm cutoffs, and received a segfault at the same simulation time. The model I am using, from the user contributed downloads section, does make use of virtual sites (virtual2). The choice for the masses and diatomic bond length always seemed strange to me (9 and 33 amu) b/c one could use almost identical masses. This would make setting up the virtual sites far more intuitive. I did this, after going through your tutorial for CO2, and this adaptation of the MeCN model suffers the same instability. I then took your CO2 model and modified it to CS2 using the proper LJ parameters from Madden's 1981 model that doesn't have charges. I ran this using coulombtype=cutoff and the 2 us simulation completed without any problems. I gave small (-0.01 for S and 0.02 for C) charges to the atoms and ran using PME, which crashed at 1.07 us. Do these results shed any new light on what is happening with my NPT simulations? The fact that any system crashes at 1.07 us (either CS2 or MeCN) suggests that the problem is external to your molecule's topology. It seems too coincidental that the times are the same, almost as if your system is running out of memory or there is some nefarious error accumulating a problem. Unfortunately, I suspect this will be really hard to debug, especially given the fact that it takes a very long time for the error to occur. If you're interested in trying to debug it yourself, change algorithms one by one, i.e. tcoupl and pcoupl methods, and see if the situation improves. This may not be how you want to do your data collection, but it would either rule out or identify which algorithm might be failing. -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
Re: [gmx-users] Creating layers of atoms in the BOX
On 11/5/12 11:52 PM, harshaljain950 wrote: Dear all, I am a final year undergrauate student and a novice in GROMACS. I want 3-4 layers of Carbon atoms to be added one over the other in my box starting from Z=0 to Z=(3-4 carbon diameter). How can I do that. Please help me out genconf -nbox can be used to create grids of atoms, and editconf -center can be used to place any sets of atoms at any given location in the box. -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
Re: [gmx-users] Re: charge groups
On 11/6/12 6:56 AM, akn wrote: Dear Justin, Thank you for the answer. I'm using OPLS force field but I calculated the partial charges of the atoms from the HF geometry optimization. Do you have any idea if I should arrange the charge groups in this case or not? My intuition says that a group-based approach is correct, not an atom-based assignment. Parameterization of the OPLS-AA force field was done using model compounds that were then used as building blocks, so I believe that is where the multi-atom charge groups (as implemented in Gromacs) come from. -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
[gmx-users] Re: Diatomic in MeCN NPT (NH and PR) simulation segfaults after 1 us
Thanks for the suggestion, I should have mentioned Tcoupl and Pcoupl in my previous post. I changed them from Nose-Hoover/Parrinello-Rahman to V-rescale/Berendsen and one permutation mixing the two, but it crashed all the same. The nodes have at least 8 GB of ram and free -m shows that I'm not running out, even when it gets close to the magical 1.07 us. I'm currently running a 2 us NVT simulation with CS2 and PME. Do you have any other thoughts as to options I can change to narrow this down? Perhaps a third coulombtype? Thanks in advance. -- View this message in context: http://gromacs.5086.n6.nabble.com/Diatomic-in-MeCN-NPT-NH-and-PR-simulation-segfaults-after-1-us-tp5001845p5002711.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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: Diatomic in MeCN NPT (NH and PR) simulation segfaults after 1 us
On 11/6/12 9:01 AM, benjfitz wrote: Thanks for the suggestion, I should have mentioned Tcoupl and Pcoupl in my previous post. I changed them from Nose-Hoover/Parrinello-Rahman to V-rescale/Berendsen and one permutation mixing the two, but it crashed all the same. The nodes have at least 8 GB of ram and free -m shows that I'm not running out, even when it gets close to the magical 1.07 us. I'm currently running a 2 us NVT simulation with CS2 and PME. Do you have any other thoughts as to options I can change to narrow this down? Perhaps a third coulombtype? Thanks in advance. Rather than run the entire job in one sitting, I would suggest running in smaller chunks of time (e.g. 500 ns or so) and restarting from checkpoints as necessary to reach the desired 2 us. It would be interesting to see if there is some accumulated error that arises from a very long simulation that is mitigated or fixed by using smaller increments of time. -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
Re: [gmx-users] g_wham with pull_geometry=position
Hi, thanks for your response, Since I'm using pull_geometry=position I was under the impression that defining pull_dim was not necessary. Instead, I defined pull_vec to specify that the protein should be pulled along 0 0 1 I was previously using pull_geometry=distance with pull_dim= N N Y but found that at slow pull_rates the protein actually moved in the opposite direction that I wanted. I am using a negative pull_k but from what I've read that is fine. I will try to use pull_dim along with the pull_vec definition while using pull_geometry=position, I just thought the two were mutually exclusive. Thanks, David On Tue, Nov 6, 2012 at 8:08 AM, Jochen Hub j...@gwdg.de wrote: 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/ http://cmb.bio.uni-goettingen.de/ --**- -- David Peeler http://www.linkedin.com/pub/david-peeler/3b/b4b/123 President,* *Society of Biological Engineers University of Maryland, College Park '13 -- 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] PCA
use make_ndx to create a new group, then use the -n index.ndx option with g_covar Date: Tue, 6 Nov 2012 09:58:51 +0200 From: tkil...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] PCA hi all, i would like to apply PCA (principal component analysis) for my peptides that i simulated. i do know PCA for one trajectory but what if i have more than one peptide ? how can i apply pca for example 10 peptides in a box ? typically, i start with a PCA on the simulation with g_covar -s protein.pdb -f traj.xtc -v eigenvec.trr and i create projections on PCA vectors using g_anaeig i have to extract a trajectory for each peptide and concatenate those trajectories and i need to make an index group for each peptide in each system that i include but i couldnt figure out extract a trajectory for each group for each system? Could you help me please ? thanks -- 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 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] gromos 45a3 ff
On 11/6/12 12:12 PM, Ali Alizadeh wrote: Dear All users 1- Do these parameters strongly impact on my final results? rlist rcoulomb rvdw Yes, potentially very strongly. 2- Are these parameters independent from type of system and only dependent to type of the force fields? Yes. 3- I want to use gromos 45a3 ff but i do not know these parameters, Have you read the article in which 45A3 was derived? It spells out precisely what you need to do. http://onlinelibrary.wiley.com/doi/10.1002/jcc.1078/abstract -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
Re: [gmx-users] Converting trajectory into tpr file
I wasn't outputting an arbitrary configuration - the timestep at 1000 was the last frame of my equilibration. On 5 November 2012 16:37, Justin Lemkul jalem...@vt.edu wrote: On 11/5/12 7:25 PM, rainy908 wrote: Fellow Gromacs users: Suppose I run a 1 ns equilibration on my protein system prior to molecular dynamics, and I am converting the equilibration trajectory to a TPR file. Correct me if I'm wrong here - I'd like to confirm that I can generate a TPR file by using frames accessed in the ENTIRE trajectory, or just certain frame(s), i.e. last snapshot. grompp does no such thing. If given multiple frames, it uses the first frame it encounters. grompp will use the last frame of a trajectory provided with -t, unless overridden by the -time option, in which case it uses the frame that most closely corresponds to that time value, per the printed documentation. 1. trjconv -f protein_equil.xtc -s protein_equil.tpr -o protein_b4md.gro 2. grompp -f md.mdp -c protein_b4md.gro -p topol.top -o protein_md.tpr 3. editconf -f protein_md.tpr -n index.ndx -o protein_md.pdb As compared to using the very last frame in the equilibrated trajectory: 1. trjconv -f protein_equil.xtc -s protein_equil.tpr -o protein_b4md_1ns.gro -b 1000 -e 1000 2. grompp -f md.mdp -c protein_b4md_1ns.gro -p topol.top -o protein_md_1ns.tpr 3. editconf -f protein_md_1ns.tpr -n index.ndx -o protein_md_1ns.pdb Does the former method output a structure that is an ensemble average based off of the equilibration time? If it is indeed an average, should I use RMSD clustering to extract an actual structure accessed in the trajectory that is closest to the ensemble average? Any suggestions would be greatly appreciated here. There is no ensemble averaging in this protocol. I'm not sure why you're trying to re-start a simulation from some arbitrary configuration during equilibration. If you use some frame from within the equilibration, you'll have to start a new simulation from this point, which destroys the previous equilibration. -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
Re: [gmx-users] Converting trajectory into tpr file
On 11/6/12 1:14 PM, rainy908 wrote: I wasn't outputting an arbitrary configuration - the timestep at 1000 was the last frame of my equilibration. I was replying to your question regarding the choice of configuration, whether or not you needed to do any sort of RMSD clustering. -Justin On 5 November 2012 16:37, Justin Lemkul jalem...@vt.edu wrote: On 11/5/12 7:25 PM, rainy908 wrote: Fellow Gromacs users: Suppose I run a 1 ns equilibration on my protein system prior to molecular dynamics, and I am converting the equilibration trajectory to a TPR file. Correct me if I'm wrong here - I'd like to confirm that I can generate a TPR file by using frames accessed in the ENTIRE trajectory, or just certain frame(s), i.e. last snapshot. grompp does no such thing. If given multiple frames, it uses the first frame it encounters. grompp will use the last frame of a trajectory provided with -t, unless overridden by the -time option, in which case it uses the frame that most closely corresponds to that time value, per the printed documentation. 1. trjconv -f protein_equil.xtc -s protein_equil.tpr -o protein_b4md.gro 2. grompp -f md.mdp -c protein_b4md.gro -p topol.top -o protein_md.tpr 3. editconf -f protein_md.tpr -n index.ndx -o protein_md.pdb As compared to using the very last frame in the equilibrated trajectory: 1. trjconv -f protein_equil.xtc -s protein_equil.tpr -o protein_b4md_1ns.gro -b 1000 -e 1000 2. grompp -f md.mdp -c protein_b4md_1ns.gro -p topol.top -o protein_md_1ns.tpr 3. editconf -f protein_md_1ns.tpr -n index.ndx -o protein_md_1ns.pdb Does the former method output a structure that is an ensemble average based off of the equilibration time? If it is indeed an average, should I use RMSD clustering to extract an actual structure accessed in the trajectory that is closest to the ensemble average? Any suggestions would be greatly appreciated here. There is no ensemble averaging in this protocol. I'm not sure why you're trying to re-start a simulation from some arbitrary configuration during equilibration. If you use some frame from within the equilibration, you'll have to start a new simulation from this point, which destroys the previous equilibration. -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
Re: [gmx-users] gromos 45a3 ff
On 11/6/12 1:21 PM, Ali Alizadeh wrote: Dear Justin Thank you for your reply On 11/6/12 12:12 PM, Ali Alizadeh wrote: Dear All users 1- Do these parameters strongly impact on my final results? rlist rcoulomb rvdw Yes, potentially very strongly. 2- Are these parameters independent from type of system and only dependent to type of the force fields? Yes. 3- I want to use gromos 45a3 ff but i do not know these parameters, Have you read the article in which 45A3 was derived? It spells out precisely what you need to do. Yes, i studied and i understand, So as you said, I do not need to change rcoulomb and rvdw, is it true? Change from what? You should use the settings described in the paper unless there is newer evidence that the force field is equivalently (or more) effective using some different settings. -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
Re: [gmx-users] Converting trajectory into tpr file
I was making a clarification regarding the equilibration, not the RMSD clustering. On 6 November 2012 10:16, Justin Lemkul jalem...@vt.edu wrote: On 11/6/12 1:14 PM, rainy908 wrote: I wasn't outputting an arbitrary configuration - the timestep at 1000 was the last frame of my equilibration. I was replying to your question regarding the choice of configuration, whether or not you needed to do any sort of RMSD clustering. -Justin On 5 November 2012 16:37, Justin Lemkul jalem...@vt.edu wrote: On 11/5/12 7:25 PM, rainy908 wrote: Fellow Gromacs users: Suppose I run a 1 ns equilibration on my protein system prior to molecular dynamics, and I am converting the equilibration trajectory to a TPR file. Correct me if I'm wrong here - I'd like to confirm that I can generate a TPR file by using frames accessed in the ENTIRE trajectory, or just certain frame(s), i.e. last snapshot. grompp does no such thing. If given multiple frames, it uses the first frame it encounters. grompp will use the last frame of a trajectory provided with -t, unless overridden by the -time option, in which case it uses the frame that most closely corresponds to that time value, per the printed documentation. 1. trjconv -f protein_equil.xtc -s protein_equil.tpr -o protein_b4md.gro 2. grompp -f md.mdp -c protein_b4md.gro -p topol.top -o protein_md.tpr 3. editconf -f protein_md.tpr -n index.ndx -o protein_md.pdb As compared to using the very last frame in the equilibrated trajectory: 1. trjconv -f protein_equil.xtc -s protein_equil.tpr -o protein_b4md_1ns.gro -b 1000 -e 1000 2. grompp -f md.mdp -c protein_b4md_1ns.gro -p topol.top -o protein_md_1ns.tpr 3. editconf -f protein_md_1ns.tpr -n index.ndx -o protein_md_1ns.pdb Does the former method output a structure that is an ensemble average based off of the equilibration time? If it is indeed an average, should I use RMSD clustering to extract an actual structure accessed in the trajectory that is closest to the ensemble average? Any suggestions would be greatly appreciated here. There is no ensemble averaging in this protocol. I'm not sure why you're trying to re-start a simulation from some arbitrary configuration during equilibration. If you use some frame from within the equilibration, you'll have to start a new simulation from this point, which destroys the previous equilibration. -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 -- 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] EM and an error: Water molecule starting at atom 5113 can not be settled.
On 11/6/12 1:37 PM, Ali Alizadeh wrote: Dear All users 1- I got an error when i wanted to perform EM, my emtol = 100 but it did not converge Water molecule starting at atom 5113 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. ... I saw the pdb files and understood what did the happen, For solving this error, so i want to perform EM with emtol=1000 What did you do to fix the problem? it converged, in next step i got em.gro as a input file and perform another EM with emtol=900 It converged , and i continued to emtol=100 Did it work the second time? Is my method true? I do not know my energy profile(i got by this method) is correct, 2- Does this parameter affect on my md production? (when i use emtol=1000 or emtol=100) The tolerance setting the desired value of Fmax. If the EM algorithm reaches a force below the tolerance, it finishes. Without knowing what your system is or what you intend to do, it's impossible to state what level of emtol is sufficient. -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
Re: [gmx-users] Water molecule starting at atom 5113 can not be settled.
On 11/6/12 2:10 PM, Ali Alizadeh wrote: Dear Justin What did you do to fix the problem? it converged, in next step i got em.gro as a input file and perform another EM with emtol=900 It converged , and i continued to emtol=100 Did it work the second time? Yes, But i got a lot of errors in my md run, in your opinion, how can i solve this error? I reduced my dt, My system is biphasic(water and methane and propane and methane in 300 bar and 240 k, ff is gromos45a3) If mdrun fails to converge, then you shouldn't proceed to MD, since the system is not at a stable minimum. The most common cause of EM failing is bad atomic clashes, which means you need more careful system preparation or more delicate minimization. -Justin Is my method true? I do not know my energy profile(i got by this method) is correct, 2- Does this parameter affect on my md production? (when i use emtol=1000 or emtol=100) The tolerance setting the desired value of Fmax. If the EM algorithm reaches a force below the tolerance, it finishes. Without knowing what your system is or what you intend to do, it's impossible to state what level of emtol is sufficient. -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
Re: [gmx-users] Water molecule starting at atom 5113 can not be settled.
On 11/6/12 2:19 PM, Ali Alizadeh wrote: Dear Justin I added this line to my minim.mdp file and i solved the error, define = -DFLEXIBLE Why did this line affect to em convergence? Do you know what this setting does? -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
[gmx-users] Problem building Gromacs-4.5.5 on BlueGene/Q
Hi all, I'm trying to build the mdrun binary for the BGQ system with the following commands (current dir is /scratch/dlin13/gromacs/gromacs-4.5.5/backend) : ../configure --prefix=/scratch/dlin13/gromacs/gromacs-4.5.5/backend \ --build=powerpc64-bgq-linux \ --enable-bluegene \ --with-fft=fftw3 \ --enable-float \ --enable-mpi \ --enable-shared=no \ --without-dlopen \ --disable-threads \ --program-suffix=_mpi_bg \ CC=mpixlc CFLAGS=-O3 -qarch=450d -qtune=450 \ CXX=mpixlcxx CXXFLAGS=-O3 -qarch=450d -qtune=450 \ CPPFLAGS=-I/scratch/dlin13/fftw/fftw-3.3.2-mpi/include \ F77=mpixlf77 FFLAGS=-O3 -qarch=auto -qtune=auto \ LDFLAGS=-L/scratch/dlin13/fftw/fftw-3.3.2-mpi/lib \ LIBS=-lmass make mdrun The build generate some errors in the middle: ../../../../../src/gmxlib/nonbonded/nb_kernel_bluegene/nb_kernel_gen_bluegene.h, line 259.13: 1506-1231 (S) The built-in function __fpadd is not valid for the target architecture. make[3]: *** [nb_kernel010_bluegene.lo] Error 1 make[3]: Leaving directory `/scratch/dlin13/gromacs/gromacs-4.5.5/backend/src/gmxlib/nonbonded/nb_kernel_bluegene' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/scratch/dlin13/gromacs/gromacs-4.5.5/backend/src/gmxlib/nonbonded' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/scratch/dlin13/gromacs/gromacs-4.5.5/backend/src/gmxlib' (cd ./src/mdlib make ; exit 0) and it finally stop at: :0 -L/scratch/dlin13/fftw/fftw-3.3.2-mpi/lib -o libgmxpreprocess_mpi.la -rpath /scratch/dlin13/gromacs/gromacs-4.5.5/backend/lib add_par.lo compute_io.lo convparm.lo fflibutil.lo gen_ad.lo gen_vsite.lo genhydro.lo gpp_atomtype.lo gpp_bond_atomtype.lo h_db.lo hackblock.lo hizzie.lo pdb2top.lo pgutil.lo readir.lo readpull.lo resall.lo sorting.lo specbond.lo ter_db.lo tomorse.lo topdirs.lo topexcl.lo topio.lo toppush.lo topshake.lo toputil.lo tpbcmp.lo vsite_parm.lo xlate.lo ../mdlib/libmd_mpi.la -lnsl -lm -lmass mkdir .libs libtool: link: cannot find the library `../mdlib/libmd_mpi.la' or unhandled argument `../mdlib/libmd_mpi.la' make[1]: *** [libgmxpreprocess_mpi.la] Error 1 make[1]: Leaving directory `/scratch/dlin13/gromacs/gromacs-4.5.5/backend/src/kernel' But if I leave out the --enable-bluegene option and configure otherwise the same way as I showed, it works. Does anyone have any suggestion? Thanks, Dejun-- 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] A charge group moved too far between two domain decomposition steps
On 11/6/12 10:42 PM, Ali Alizadeh wrote: Dear All users I used OPLS ff for my system and I did not break my bonds, When i use gromos96 45a3 after minimizing my bonds break(i can see em.gro) but i do not get any errors in this step Bonds do not break during MD. Probably what you're seeing is a periodicity effect. After md production i get this error: Fatal error: A charge group moved too far between two domain decomposition steps This usually means that your system is not well equilibrated Lots of information on the Gromacs website: http://www.gromacs.org/Documentation/Errors#A_charge_group_moved_too_far_between_two_domain_decomposition_steps. ...and also in the list archive. -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
[gmx-users] What algorithm does g_sas use?
Dear gmx users: So sorry for bother you. Does any one know what algorithm g_sas use? There is no information about algorithm in help file, man page, and code. I think gromos use naccess method but not sure gromacs use the same one. Regards ZhiGuang Jia -- 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] What algorithm does g_sas use?
On 11/7/12 1:18 AM, jia jia wrote: Dear gmx users: So sorry for bother you. Does any one know what algorithm g_sas use? There is no information about algorithm in help file, man page, and code. I think gromos use naccess method but not sure gromacs use the same one. References are printed in the screen output when running g_sas. -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
Re: [gmx-users] What algorithm does g_sas use?
Thanks! I've checked gromacs v 4.5.5 and got it. Seems all version before 4.0.5 doen't have that information.. Cheers Guang 2012/11/7, Justin Lemkul jalem...@vt.edu: On 11/7/12 1:18 AM, jia jia wrote: Dear gmx users: So sorry for bother you. Does any one know what algorithm g_sas use? There is no information about algorithm in help file, man page, and code. I think gromos use naccess method but not sure gromacs use the same one. References are printed in the screen output when running g_sas. -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 -- 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
