Re: [gmx-users] Conceptual question: Why are MD production simulations usually run in the NVT ensemble?
On 7/14/12 11:06 AM, Andrew DeYoung wrote: Hi, I'm not sure if this is an appropriate question for the Gromacs users' mailing list. If it isn't, please forgive me and disregard this message. I asked this question on Physics Stack Exchange: Why is the canonical (NVT) ensemble often used for molecular dynamics (MD) simulations? My question and an answer are posted here: http://physics.stackexchange.com/questions/31997/why-is-the-canonical-nvt-en semble-often-used-for-classical-molecular-dynam My question is, do you agree with the answer? I'm not sure that I do. The responder seems to imply that it is practically impossible to use periodic boundary conditions in an NPT simulation. But, I think that the algorithms in Gromacs do just this; am I correct in this belief? I also disagree with the answer you got, on several grounds. I will admit that I have never gone into the code for how boxes are scaled and how this is all done in terms of bookkeeping, but I think there is plenty of evidence that we have decent barostat algorithms. The response you got seemed to just say "it's all too inconvenient to try to think about, so we shouldn't do it." Part of the response was simply that if you increase the system size, the ensembles become the same, which may be true in a theoretical sense (since P fluctuations decrease proportionally with system size) but it becomes totally impractical for doing simulations. How then, does one account for heterogeneous systems like I've got with a membrane, protein, water, and maybe small molecules? I can't just keep scaling that up and assume that the relative majority of water molecules is going to make everything happy. That, and the lipid model was parameterized for NPT... People do often run _equilibration_ simulations in the NPT ensemble, I think. They do this usually, I think, to obtain the proper density -- the code changes the box dimensions until the proper average pressure is reached. Then, for _production_ simulations, people usually use the NVT ensemble, where the dimensions of the simulation box are held fixed. My question here is, why is the NVT ensemble, rather than the NPT ensemble, typically used for production MD simulations? I disagree with this premise as well. The vast majority of all biological simulations I see are done under NPT conditions. I think the heart of the issue is the discipline you're studying and what is commonly done. Maybe in pure physics or chemistry simulations, NVT is more common because the experiments are done that way. For us in biological science, the NVT ensemble is less relevant than NPT because we are studying processes that go on in cells, within membranes, or even just in solution an open-topped test tube or flask that is under atmospheric pressure. The general advice from many on this list has always been, "pick an ensemble that models the reality of your system best." If it makes sense to switch back to NVT from NPT for whatever you're doing, by all means do it. Do you have any suggestions for helpful reading that I can do on this topic? Thank you for your time! I think it's a philosophical discussion, but comes down to what it is you're modeling and what the most appropriate conditions are. Knowing the ins and outs of thermostat and barostat algorithms would be very important in debating these issues. -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 * 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] (no subject)
On 7/14/12 3:34 AM, sara elham wrote: Dear Gromacs users I want to find the solution for my problem from mailing list, but it give me this massage: "Timeout expired. The timeout period elapsed prior to completion of the operation or the server is not responding." The website experiences intermittent issues. Hopefully they will be sorted out soon. I tried to registration again, but in the section " Type the characters you see in the image below " , it isn't shown anything!!! You don't need to register to search the mailing 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 * 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] Re: Melting simulations - regd
On 7/14/12 1:02 AM, rapolu sukumar wrote: Dear Justin, Thank you for your reply, here I have one more doubt, I am using 'pcoupltype= anisotropic' in my simulationa as the polymers are aniostropic, I have searched for compressibility values of system but i couldn't find is there any generalized way to set up compressibility values. Most simulations probably just use the compressibility of water. As for the accuracy of your simulation if you do this, I cannot say. -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 * 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] g_saltbr speed
On 7/13/12 12:05 PM, Kavyashree M wrote: Its 50ns 25000 frames. the xtc file is 695MB. it has 16GB RAM. So will that be insufficient? I have previously run other analysis which used to take huge memory, for eg. covariance analysis, in a system with much lesser memory even though CPU usage was low the job used to finish. But in this case its not so. I can't see a reason why the file itself would present a problem. I have run g_saltbr on similarly sized systems. Sorry, I can't offer an explanation as to why it's stopping prematurely. -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 * 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] g_saltbr speed
On 7/13/12 11:50 AM, Kavyashree M wrote: Dear users, Its the continuation of the question I asked yesterday, Inorder to reduce the memory usage during g_saltbr calculations i got the trajectory of only protein, and tpr file without water and was able to successfully run it. But unfortunately this again got stopped at 36ns as it had stopped when i was using the whole trajectory. I tried with -dt 2, still the same problem exists. Kindly suggest a way out of this situation. How long is the trajectory? How many frames? What is the size of the file on disk? It sounds to me like you're simply exhausting available memory, so the only advice is in the link I posted before - use fewer frames or use a machine that has more memory to do the analysis. -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 * 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] Re: Error in Membrane simulations with POPC bilayer
On 7/13/12 6:44 AM, J Peterson wrote: Thanks Justin, The explanations are very very useful during my course of simulating a protein with POPC. I also would like to get explanation on how to simulate a protein which has only its N-terminal region embedded in the membrane but the rest in solvent. What is the easy and accurate way to do it? Position the protein with editconf -center and follow all the other steps in the same way. The dimensions of the box become quite important in such a case. There are some general tips on such placement in another of my tutorials: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/biphasic/03_tricks.html -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 * 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] Melting simulations - regd
On 7/13/12 2:27 AM, sukumar rapolu wrote: Hello gmx users, I am doing melting simulations of a polymer in gromacs, for this am giving output from a production run of particular temperature as the input for equilibration at next temperature and generating velocities in equilibration at each temperature by using gen_vel = yes. Here my doubt is, as I am using output from production as input for equilibration so do I have to use continuation= yes in my equilibration mdp file or as I am generating velocities at each temperature during equilibration do I have to use continuation= no ? If you're using the structure from a previous run that used constraints, the difference between these two settings should be minimal. But since you're basically starting totally new simulations, you can't go wrong with "continuation = no." -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 * 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] Re: Error in Membrane simulations with POPC bilayer
On 7/13/12 4:14 AM, J Peterson wrote: Hi Justin, I have another doubt on the strong posres that was included in the topology file. When do we need to remove that position restraint? Does it really affect at point of time the system? The strong restraints are only needed for InflateGRO. During equilibration, position restraints with a normal magnitude are appropriate. -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 * 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] Re: Error in Membrane simulations with POPC bilayer
On 7/13/12 1:44 AM, J Peterson wrote: Thanks for the comment. By the way how to make a bigger box at this time of the tutorial without affecting any part of the system. Can I use editconf with slightly bigger number for z-axis (something like 6.7 which was 5.7 before)? The box should be sufficiently large so as to avoid spurious interactions across periodic boundaries. The size is thus motivated by the length of the cutoffs used. Increasing the box by 1.0 nm might be just enough, but you should calculate this very carefully. -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 * 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] Re: Final state not reached in pulling simulation
On 7/13/12 2:32 AM, Neeru Sharma wrote: Dear Justin, Thanks for the suggestion regarding the pull force. 1)I will try by reducing the pull force to 1000 and 100 KJmol/nm2 now. Regarding the force being applied in z-direction, after visualizing my trajectory i thought it would work by providing force in z-direction. 2)Regarding the protein rotation, it does not rotate over the time. There are just some localized changes in it. 3)Regarding the distance measurement, I am measuring the distance between the specific atoms of the residue and the atoms of the GTP. Till now, these distances as well as the overall protein geometry is maintained well in the range too. 4)If this kind of pulling does not work out in my case, I will again try it with using "position" geometry too with pull_vec1. Can you suggest why have I not reached the final distance at the end of the simulation? Is it because of the geometry that I have used, because the force constant is already too high in this case? I don't know why this is happening. That's why you need to try more things to see if you can root out the issue. There are a whole host of factors that can act against the pulling force. You're not using any sort of position restraints, are you? The other thing to keep in mind is that if your initial distance is 0.7 nm, and you pull for 10 ns at 0.05 nm/ns, you should in theory end up with a distance of 0.2 nm, not 0.3 nm. That is, assuming that the pulled group is free to move and thus smoothly goes along with the spring. Other forces within the structure may act in opposition. -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 * 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] Re: Error in Membrane simulations with POPC bilayer
On 7/13/12 12:24 AM, J Peterson wrote: Hi Justin, I followed your comments and now at the stage of adding solvents. I wonder to see the protein after shrinking step to have no SOL molecules as there were SOL molecules in the source popc128b.pdb. Had we removed all the original SOL molecules anywhere during the course of tutorial? InflateGRO removes all solvent molecules. I also see one of the POPC molecules standing out (upside down) of the bilayer area. How would that be adjusted? http://gromacs.5086.n6.nabble.com/file/n4999393/POPC..jpg You need a bigger box. The lipids are moving into a neighboring periodic cell, which in itself is not a problem, but I suspect you'll have inadequate hydration and thus you'll be calculating headgroup-headgroup interactions across periodic boundaries, which you probably want to avoid. -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 * 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] Re: Error in Membrane simulations with POPC bilayer
On 7/12/12 10:23 PM, J Peterson wrote: Hi Justin, Thanks for the suggestion I got it solved somehow. The main problem was in the popc128b.pdb itself, it has first 64 lipids and half of the SOl molecules followed by rest of the POPC and SOL molecules. When I rearranged them the error was solved. But now another thing I would like to confirm with you. During shrinking stage, I get the following notes, please tell me are they OK at this stage, NOTE 1 [file topol.top, line 3070]: System has non-zero total charge: 5.00e+00 Assuming this is the net charge on your protein, there's nothing wrong here. Analysing residue names: There are:46Protein residues There are: 126 Other residues Analysing Protein... Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Number of degrees of freedom in T-Coupling group rest is 21063.00 Largest charge group radii for Van der Waals: 0.249, 0.247 nm Largest charge group radii for Coulomb: 0.249, 0.247 nm Calculating fourier grid dimensions for X Y Z Using a fourier grid of 160x160x48, spacing 0.110 0.114 0.119 Estimate for the relative computational load of the PME mesh part: 0.92 NOTE 2 [file em_st.mdp]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing PME load for EM runs is usually irrelevant. During actual MD, you'd strive for better balance, but since an inflated lipid system in vacuo is rather weird, you can ignore this as well. -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 * 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] Final state not reached in pulling simulation
On 7/12/12 3:43 PM, lloyd riggs wrote: your pull force looks insanly high especially if your pulling a small piece of residue? But for a whole protein of averidge 40 KDa, or 350 amino acids its around 2000 to 3000 from liturature (only about 6 that I could find anyways). I might thus be wrong, but wounder if you have a pull rate and force what one wins? The force constant and pull rate do not compete. The pull rate governs how fast the virtual particle is pulled (at constant velocity) and the stiffness of the spring dictates the response of the pulled group to which it is attached. I agree that the force constant seems excessive. I also wonder why the pulling is only being applied in the z-direction. To the OP - are the GTP and chosen residue completely linear in the z-direction? Does the protein structure rotate over time? If it does, then you're doing nonproductive pulling. How are you measuring the distance (achieved and desired)? Is it the z-component of the distance only, or the complete distance? I would also note that one-dimensional pulling using the "distance" geometry is relatively inflexible. Using "direction" or "position" geometries in concert with pull_vec1 and/or more sophisticated index groups may be more appropriate. -Justin Original-Nachricht Datum: Thu, 12 Jul 2012 18:15:53 +0200 Von: Thomas Schlesier An: gmx-users@gromacs.org Betreff: [gmx-users] Final state not reached in pulling simulation It could be possible tht you do not pull into the 'right' direction. if there is another group between 'GTP' and 'Residue' you will get clashes and 'Residue' won't move further (could be a water molecule, or some other part of 'GTP'). If this happens you should observe an increase in the force due to the umbrella potential. If the problems are due to waters molecules which block the 'pathway' you could just delete them. If another group is in the way, you might want to change the pull-vector (and if lucky find the right one). But don't know what would be the best strategy in this case. Maybe you can look into what docking-people do, seems to me that your simulation is related to what they do (but myself has absolute no knowledge about docking simulations). greetings thomas Am 12.07.2012 17:26, schrieb gmx-users-requ...@gromacs.org: Hello all, I m performing a pulling simulation on my Protein-Mg-GTP complex. I have considered pulling between the GTP and a residue of protein. The pull code in the .mdp file im using is as follows: ; Pull code pull= umbrella pull_geometry = distance ; simple distance increase pull_dim= N N Y pull_start = yes ; define initial COM distance> 0 pull_ngroups= 1 pull_group0 = GTP pull_group1 = Residue pull_rate1 = -0.5 ; 0.5 nm per ps = .05 nm per ns pull_k1 = 1 ; kJ mol^-1 nm^-2 The initial distance between GTP and the residue was 7 A and the desired one was 3A. After the completion of run (10ns), I could get a trajectory where the final distance was still 4.25 A. I tried to continue the simulation for another 10ns with the same value for pull_k1 parameter and one by increasing the value to 100,000 also. In both of the case, the trajectories showed the distance stabilized near _4.25 A only. Can anyone please tell me the reason behind it? What should I do, so that I could get the desired distance ? Any suggestion and help is welcome !!! Thanks, Neeru Sharma -- 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 -- 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 * 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] more than one protonation per residue with pdb2gmx
On 7/12/12 9:00 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Can you please give me an example of such a modeling software? I tried it with PYMOL but the results are not very good. And I also found several programs but the are all not free. http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources -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 * 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] g_saltbr speed
On 7/12/12 8:31 AM, Kavyashree M wrote: Ok may be i need to specify an index file. I will try that. And regarding the WARNING: this .tpx file is not fully functional. I hope it will work fine enough to finish g_saltbr calculation? In principle, you should be prompted to choose a default group, but you can also use a custom index group as needed. The warning message is intended to note that the .tpr file you produce will not likely work for running an actual simulation. It should be fine for analysis. -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 * 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] g_saltbr speed
On 7/12/12 8:15 AM, Kavyashree M wrote: Dear Sir, I had a problem again during g_saltbr calculation it needs .xtc and .tpr file, I can reduce the .xtc file to have only protein but .tpr file will have water also in it. inorder to generate new tpr file without water using grompp, i need topology file without water .. so do you suggest me to go this way.. it appears quite complicated! In fact, it's quite easy with tpbconv. From tpbconv -h: "3. by creating a .tpx file for a subset of your original tpx file, which is useful when you want to remove the solvent from your .tpx file, or when you want to make e.g. a pure Calpha .tpx file. Note that you may need to use -nsteps -1 (or similar) to get this to work. WARNING: this .tpx file is not fully functional." -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 * 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] water bridge
On 7/12/12 8:02 AM, Raj wrote: Hi all, I have an protein and drg complex. I've done the MD in SPC water environment. Now I would like to check number of hydrogen bond formed between the drug and protein, water as well. What will the right command for me to analyse. Thanks in advance g_hbond with suitable index groups. If you're looking for water-mediated hydrogen bonds, there are numerous discussions about ways to accomplish that if you search the mailing 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 * 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] g_saltbr speed
On 7/12/12 6:38 AM, Kavyashree M wrote: Dear Sir, That is true as the number of the frames increased the memory had almost reached 95% but still it has been in 95% since long and CPU usage drops down to 1.5 -2 % but in many cases i have seen that still it will run (off course slowly) and finish. But this was too long. So any suggestions? http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume -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 * 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] more than one protonation per residue with pdb2gmx
On 7/12/12 6:12 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi Justin, so you mean that I first have to add the capping groups to my structure and then run pdb2gmx with the -ter function? Yes. The capping groups (see your force field's .rtp file for available entries) are treated as any other residue. Gromacs will not magically build them; they need to be present. But how can I add the capping groups to the structure? You'll have to use some external modeling software for that. -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 * 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] Re: Error in Membrane simulations with POPC bilayer
On 7/12/12 4:59 AM, J Peterson wrote: Hi Justin, Thanks for the effort to help me. I still no out of the error. The following is the content of my topol_popc.top ; Include chain topologies #include "gromos53a6_lipid.ff/forcefield.itp" #include "popc.itp" ; Include water topology #include "gromos53a6_lipid.ff/spc.itp" ; Include ion topologies #include "gromos53a6_lipid.ff/ions.itp" ; System specifications [ system ] 128-Lipid POPC Bilayer [ molecules ] ; molecule name nr. POPC 128 SOL 2460 And the following is the first part of my popc128b.gro file Alm on surf + relaxed popc 14036 1POP C11 0.253 5.425 1.688 1POP C22 0.428 5.314 1.792 1POP C33 0.334 5.243 1.571 1POP N44 0.378 5.352 1.660 1POP C55 0.474 5.439 1.590 1POP C66 0.606 5.390 1.531 1POP O77 0.692 5.366 1.643 1POP P88 0.834 5.316 1.587 1POP O99 0.800 5.197 1.505 1POPO10 10 0.903 5.435 1.533 1POPO11 11 0.890 5.266 1.729 1POPC12 12 0.823 5.142 1.753 1POPC13 13 0.836 5.086 1.895 1POPO14 14 0.766 4.964 1.924 1POPC15 15 0.632 4.959 1.944 1POPO16 16 0.555 5.019 1.869 1POPC17 17 0.589 4.833 2.020 1POPC18 18 0.615 4.703 1.944 1POPC19 19 0.595 4.575 2.025 1POPC20 20 0.625 4.467 1.920 1POPC21 21 0.677 4.340 1.987 1POPC22 22 0.813 4.357 2.055 1POPC23 23 0.848 4.223 2.120 1POPC24 24 0.884 4.121 2.012 1POPC25 25 0.957 4.013 2.043 1POPC26 26 0.994 3.986 2.189 1POPC27 27 1.069 3.853 2.202 1POPC28 28 0.967 3.739 2.204 1POPC29 29 1.012 3.593 2.202 1POPC30 30 0.916 3.478 2.169 1POPC31 31 0.869 3.518 2.029 1POPC32 32 0.801 5.205 1.983 . . . . . What are the parts mismatching in these files? From what's shown, it's impossible to tell. Based on this information, everything lines up. I'm assuming the original coordinate file and the popc.itp topology came from Tieleman's site? Since it says the atom names from the top file will be used, is it safe to ignore this warning too? No. The naming mismatches imply that grompp is trying to map parameters for lipids onto water molecules. The resulting simulation will be nonsense and will probably crash immediately. -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 * 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] g_saltbr speed
On 7/12/12 4:51 AM, Kavyashree M wrote: Dear Gromacs users, I was running the saltbridge calculations for a dimeric protein simulation using g_saltbr, But its taking very long time, almost four days still its not completed. Could anyone has suggestion regarding this issue? I am using the same system - Intel(R) Core(TM) i7-2600 CPU @ 3.40GHz where i ran MD. Please give some suggestion as to how to increase the speed of calculation. Command i issued was: g_saltbr -f ../traj.xtc -s md.tpr -t 0.4 -sep g_saltbr calculates properties of all possible ionic pairs in the system, so if there are many, the calculation might take a long time. Four days sounds ridiculous, and perhaps the program has frozen by exhausting the available memory. -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 * 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] more than one protonation per residue with pdb2gmx
On 7/12/12 4:37 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: I have another question about the option -ter of the pdb2gmx command. I choose it because I thought that this is a way that I can determine what shell happen with the termini but I was not ask anything by the program. My aim is it to block the termini with a neutral group. Is there a way to do this with gromacs? Yes. You need to build the appropriate groups onto your protein's structure using normal capping groups present within the force field (ACE, NME, NH2, etc) and choose "None" for the termini when running pdb2gmx so that no additional protons are added or removed; the first and last amino acids are then treated as internal residues with normal peptide bonds. -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 * 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] pH and protein
On 7/12/12 1:42 AM, tarak karmakar wrote: Dear All, I am simulating a protein in gromacs with amber force field. The protein shows maximum biological activity at pH 5.0 and at pH 7.4 it shows no activity. So whichever biological process I am going to model should be at the biologically active pH . So can anyone suggest me 1) how to get the protonation state of each and every residues present in the protein at that particular pH [i.e. at pH 5.00] ? Should I look into the pKa values of each and every residues from standard table to or is there any software to find the same ? pKa values can vary greatly depending on the local environment of the residue. You should find a method to calculate the pKa values. One possibility: http://biophysics.cs.vt.edu/ 2) how to get the net charge of the protein at that particular pH ? [ Protein Calculator !! ] The net charge is printed in the topology produced by pdb2gmx. -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 * 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] More accurate potential energy in output?
On 7/11/12 3:14 PM, Markus Kaukonen wrote: Dear Gromacs, I'm trying to build a QM/MM with gromacs as MM. The thing would be run by ASE-simulation environment (https://wiki.fysik.dtu.dk/ase/). Question: I'm trying to get the potential energy of a single atomic configutation. Is it possible to get the potential energy of a given configuration with more than 5 digits? Compile and run in double precision. -Justin Both the log file and gmxdump -e give me only 5 digits. The .mdp file I used is below. terveisin, Markus ;=== ;Gromacs input file ;Created using the Atomic Simulation Environment (ASE) ;=== rlist = 0.0 ; nstlist = 1 ; pbc = no ; integrator = md ; md: molecular dynamics(Leapfrog), rvdw= 0.0 ; nstlog = 1 ; nstenergy = 1 ; rcoulomb= 0.0 ; energygrps = System ; ns_type = grid ; nsteps = 0 ; nstfout = 1 ; define = -DFLEXIBLE ; flexible/ rigid water -- ==== 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 * 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] Time for NPT or NVT equilibration
On 7/11/12 2:08 PM, Shima Arasteh wrote: Dear gmx friends,How much time should have been spent in NPT equilibrium for a system composed of protein and water? In Justin's tutorial, I saw it is 100 ps for a system composed of Lysozym and water. Long enough for the observables of interest to converge. -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 * 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] Forcefield parameters for AcetylCoA
Please keep the discussion on the gmx-users mailing list. On 7/11/12 10:43 AM, panbazha wrote: Dear Justin, That file was generated by me in ATB, The issue is when i looked into the united atom itp file, I found many bonds and angles has not determined. So, just wondering if there are any published reports to edit it manually. A quick literature search should turn something up. Google returns lots of results if you search "Gromos96 acetyl CoA" (without the quotes). I looked at the missing bonded parameters and they should all be quite easy to define based on known values in ffbonded.itp - it is not clear to me why they are missing. Most, if not all, of the missing bonds are between OA and H atoms, which are simple alcohol groups (bond type gb_1). -Justin Best regards Quoting "Justin A. Lemkul" : On 7/11/12 8:18 AM, Padmanabhan Anbazhagan wrote: Dear All, Could anyone please suggest me some article or information that contains force field parameters (gromacs53A6) for acetyl Coenzyme A Google turned up: http://compbio.biosci.uq.edu.au/atb/download.py?molid=5470 -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 * 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 -- ======== 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 * 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] more than one protonation per residue with pdb2gmx
On 7/11/12 10:24 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I wanted to ask if there is a possibility to tell pdb2gmx which residues I want to be protonated or not. So that I can for example say HIS at position 29 shell be protonated twice. I need this for further electrostatic analysis. Please read pdb2gmx -h. There are tons of available options to control protonation of any and all titratable residues. -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 * 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] Forcefield parameters for AcetylCoA
On 7/11/12 8:18 AM, Padmanabhan Anbazhagan wrote: Dear All, Could anyone please suggest me some article or information that contains force field parameters (gromacs53A6) for acetyl Coenzyme A Google turned up: http://compbio.biosci.uq.edu.au/atb/download.py?molid=5470 -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 * 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] question about the output of minimization
On 7/11/12 7:34 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Yes I tried the command you wrote but it is still in the corner of the box. Is there anything else I can do? The coordinates I used to center the protein are the ones which are in the last line of the .gro file. The last line of the .gro file are the box vectors, not the center of the system, so you are not, in fact, centering the protein. You are placing it in the corner of the box yourself. The -center option overrides the -c option. If you want the protein centered, omit -center in your editconf command. -Justin Thank you On 7/11/12 7:12 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi Justin, ah okey. Thank you. And I have another question. Why is the protein in the corner of the box and not in the middle? I thought I centered it with the command: editconf -f wholeProtein.gro -o 3m71_box.gro -center 4.59340 4.59470 5.17330 -c -bt dodecahedron -d 1.0 2>>logErr 1>>logOut Or not? Have you tried trjconv -pbc mol -ur compact? The "center" of an infinite system is an arbitrary location; you have to re-wrap the unit cell to achieve the expected outcome. It's centered, it just may not look like it in the current representation. -Justin On 7/11/12 6:13 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I did a minimization of my structure. But the output seems a bit strange for me, since my input was the protein with its membrane in a box like this: # = box P = Protein M=Membrane # # # # MM# # # # # # # # But the output of the minimization looks like this # ## #M M # # # ## ## ## How can that be? It's a triclinic representation of the unit cell. Nothing is wrong. My box was created with: editconf -f wholeProtein.gro -o 3m71_box.gro -center 4.59340 4.59470 5.17330 -c -bt dodecahedron -d 1.0 2>>logErr 1>>logOut Is a dodecahedral box appropriate for a protein in a membrane? The inherent symmetry of a slab of any sort dictates that you should be using a cubic or rectangular box. Dodecahedral and octahedral boxes are better for systems with spherical symmetry, like globular proteins in water. I put solvent in it with: genbox -cp 3m71_box.gro -cs spc216.gro -p 3m71.top -o 3m71_water.gro 2>>logErr 1>>logOut The mdp file for the minimization looks like this: define = -DPOSRES integrator = steep emtol = 10 nsteps = 1500 nstenergy = 1 energygrps = System coulombtype = PME rcoulomb= 0.9 rvdw= 0.9 rlist = 0.9 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 pbc = xyz Can you please tell me how I can prevent my box to shift? There is no box shift; it's just a visual representation of the dodecahedral box. You can "correct" it (for visualization purposes) by running trjconv -pbc mol -ur compact. -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 * 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 -- 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 * 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 -- 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-user
Re: [gmx-users] question about the output of minimization
On 7/11/12 7:12 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi Justin, ah okey. Thank you. And I have another question. Why is the protein in the corner of the box and not in the middle? I thought I centered it with the command: editconf -f wholeProtein.gro -o 3m71_box.gro -center 4.59340 4.59470 5.17330 -c -bt dodecahedron -d 1.0 2>>logErr 1>>logOut Or not? Have you tried trjconv -pbc mol -ur compact? The "center" of an infinite system is an arbitrary location; you have to re-wrap the unit cell to achieve the expected outcome. It's centered, it just may not look like it in the current representation. -Justin On 7/11/12 6:13 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I did a minimization of my structure. But the output seems a bit strange for me, since my input was the protein with its membrane in a box like this: # = box P = Protein M=Membrane # # # # MM# # # # # # # # But the output of the minimization looks like this # ## #M M # # # ## ## ## How can that be? It's a triclinic representation of the unit cell. Nothing is wrong. My box was created with: editconf -f wholeProtein.gro -o 3m71_box.gro -center 4.59340 4.59470 5.17330 -c -bt dodecahedron -d 1.0 2>>logErr 1>>logOut Is a dodecahedral box appropriate for a protein in a membrane? The inherent symmetry of a slab of any sort dictates that you should be using a cubic or rectangular box. Dodecahedral and octahedral boxes are better for systems with spherical symmetry, like globular proteins in water. I put solvent in it with: genbox -cp 3m71_box.gro -cs spc216.gro -p 3m71.top -o 3m71_water.gro 2>>logErr 1>>logOut The mdp file for the minimization looks like this: define = -DPOSRES integrator = steep emtol = 10 nsteps = 1500 nstenergy = 1 energygrps = System coulombtype = PME rcoulomb= 0.9 rvdw= 0.9 rlist = 0.9 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 pbc = xyz Can you please tell me how I can prevent my box to shift? There is no box shift; it's just a visual representation of the dodecahedral box. You can "correct" it (for visualization purposes) by running trjconv -pbc mol -ur compact. -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 * 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 -- 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 * 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] (no subject)
On 7/11/12 6:19 AM, amir abbasi wrote: Thanks Justin, But I want to neutralize my system in implicit solvent. In Amber I had use Debye screening but in gromacs I don't know what should I do. From my understanding, this remains an unresolved issue. -Justin On Wed, Jul 11, 2012 at 2:45 PM, Justin A. Lemkul wrote: On 7/11/12 6:00 AM, amir abbasi wrote: Hi All! I want to use Implicit solvent to simulate a nucleic acid sequence. How can I do it? I use this command: genion -s ions.tpr -o nucleic_ions.gro -p nucleic.top -pname K+ -nname CL -neutral -conc 0.1 ions.tpr file is same as umbrella sampling tutorial. I got this error message: Fatal error: Your solvent group size (2898) is not a multiple of 31 what should I do? One does not typically add explicit ions in an implicit solvent system. genion fails because it appears you are trying to replace parts of your nucleic acid with ions. -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 * 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 -- ============ 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 * 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] question about the output of minimization
On 7/11/12 6:13 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I did a minimization of my structure. But the output seems a bit strange for me, since my input was the protein with its membrane in a box like this: # = box P = Protein M=Membrane # # # # MM# # # # # # # # But the output of the minimization looks like this # ## #M M # # # ## ## ## How can that be? It's a triclinic representation of the unit cell. Nothing is wrong. My box was created with: editconf -f wholeProtein.gro -o 3m71_box.gro -center 4.59340 4.59470 5.17330 -c -bt dodecahedron -d 1.0 2>>logErr 1>>logOut Is a dodecahedral box appropriate for a protein in a membrane? The inherent symmetry of a slab of any sort dictates that you should be using a cubic or rectangular box. Dodecahedral and octahedral boxes are better for systems with spherical symmetry, like globular proteins in water. I put solvent in it with: genbox -cp 3m71_box.gro -cs spc216.gro -p 3m71.top -o 3m71_water.gro 2>>logErr 1>>logOut The mdp file for the minimization looks like this: define = -DPOSRES integrator = steep emtol = 10 nsteps = 1500 nstenergy = 1 energygrps = System coulombtype = PME rcoulomb= 0.9 rvdw= 0.9 rlist = 0.9 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 pbc = xyz Can you please tell me how I can prevent my box to shift? There is no box shift; it's just a visual representation of the dodecahedral box. You can "correct" it (for visualization purposes) by running trjconv -pbc mol -ur compact. -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 * 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] (no subject)
On 7/11/12 6:00 AM, amir abbasi wrote: Hi All! I want to use Implicit solvent to simulate a nucleic acid sequence. How can I do it? I use this command: genion -s ions.tpr -o nucleic_ions.gro -p nucleic.top -pname K+ -nname CL -neutral -conc 0.1 ions.tpr file is same as umbrella sampling tutorial. I got this error message: Fatal error: Your solvent group size (2898) is not a multiple of 31 what should I do? One does not typically add explicit ions in an implicit solvent system. genion fails because it appears you are trying to replace parts of your nucleic acid with ions. -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 * 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] sovation with tip3p
On 7/11/12 5:36 AM, Shima Arasteh wrote: Hi all, I'm going to do the step 3 in Justin's tutorial (Lysozyme in water) . In this step, the solvation is accomplished through this command: genbox -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top in which that spc216.gro is used. In first step I had used the TIP3P water model, here I'd rather to call TIP3P too. But there is not tip3p.gro in share/top . I would appreciate you if you give me any suggestion. http://www.gromacs.org/Documentation/How-tos/TIP3P_coordinate_file -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 * 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] refcoord_scaling
On 7/10/12 5:48 PM, Katie Maerzke wrote: Hi all - I'm new to Gromacs (and MD). I can't figure out whether or not refcoord_scaling is important for an NpT simulation. In an MC simulation, when the volume changes, the coordinates of the molecules are also scaled. Does refcoord_scaling control how to handle scaling the molecular coordinates (e.g., scale all coordinates or scale based on COM), or does it do something else? Is it even important? I've searched the manual and the user forum, but I haven't found an answer to my question. The important distinction is between reference coordinates and the actual coordinates of the atoms. When employing position restraints, the restraint potential is based on the reference positions of the atoms. It is these that are updated based on the refcoord_scaling option. In most cases, the box shouldn't change drastically, and if it does, you have bigger problems. Thus, I imagine the contribution to energy is likely small, but I have never tested this myself. In theory, if the reference coordinates are not updated correctly, you will get incorrect contributions to the virial and thus some errors in pressure calculation. This is my understanding of the implementation; if it is incorrect or incomplete, hopefully someone will chime in. -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 * 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] POPC in water
On 7/10/12 6:09 AM, Shima Arasteh wrote: Dear gmx users, I want to simulate a protein in bilayer. The chosen bilayer is POPC. According to Justin's tutorial about KALP15 in DPPC, I would simulate the protein in lipid bilayer and water. In this tutorial I didn't find the simulation of bilayer in water seperately and it is just going through the simulation with protein. See part 1 of step 3: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html It's not a full simulation of a membrane, but it presents all the essential elements - coordinate file, topology (very simple), and .mdp (though it is for EM, not an MD simulation). I need to say that I got the POPC.itp and .top through the link sent me by dear Peter. Now I'm wondering if POPC is needed to simulate in water before applying in simulation of protein in POPC? The answer depends on how well equilibrated the starting structure is. If you're going to be putting a protein in it, you'll have to re-equilibrate that new system for a considerable amount of time, so simulating the membrane beforehand may or may not be relevant, but a thoroughly equilibrated membrane will reduce the time needed in equilibrating the membrane protein system. -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 * 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] node decomposition' problem
On 7/9/12 4:25 PM, Justin A. Lemkul wrote: On 7/9/12 4:23 PM, Thales Kronenberger wrote: I'm trying to run a kinase (what means that I had ATP - large charged group) energy minimization and then MD. But when I put my protein together with its ligands I gotcha the follow error message: "There is no domain decomposition for 6 nodes that is compatible with the given box and a minimum cell size of 6.47943 nm Change the number of nodes or mdrun option -rdd Look in the log file for details on the domain decomposition" I read about in gromacs forums and I can force the thing's running with the option nt 1 (one node...). My problem is that I still want to run in parallel. Is it still that possible for my system or I'm doomed to the 1 core simulation The minimum charge group size depends on a whole host of factors: *Edit* "minimum domain decomposition cell" - I don't know where "charge group" came from... http://www.gromacs.org/Documentation/Errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm The large size you have obtained indicates there are likely problems with the .mdp file, topology, or both. -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 * 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] node decomposition' problem
On 7/9/12 4:23 PM, Thales Kronenberger wrote: I'm trying to run a kinase (what means that I had ATP - large charged group) energy minimization and then MD. But when I put my protein together with its ligands I gotcha the follow error message: "There is no domain decomposition for 6 nodes that is compatible with the given box and a minimum cell size of 6.47943 nm Change the number of nodes or mdrun option -rdd Look in the log file for details on the domain decomposition" I read about in gromacs forums and I can force the thing's running with the option nt 1 (one node...). My problem is that I still want to run in parallel. Is it still that possible for my system or I'm doomed to the 1 core simulation The minimum charge group size depends on a whole host of factors: http://www.gromacs.org/Documentation/Errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm The large size you have obtained indicates there are likely problems with the .mdp file, topology, or both. -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 * 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] Re: DNA simulations
On 7/9/12 4:07 PM, SatyaK wrote: Hello, I followed below steps using VMD and GROMACS but something went wrong in using GROMACS which I am not able to figure out. Appreciate your help. 1. editconf -f initialfile.pdb -o initialfile.gro -d 0.2 2. VMD: within 5 of nucleic $sel writepdb initialfile_updated.pdb $sel delete (initialfile_updated.pdb has only those molecules that are at a distance of 5A) 3. I used GROMACS to convert back to .gro:editconf -f initialfile_updated.pdb -o initialfile_updated.gro -d 0.2 The coordinates in ininitialfile.gro and initialfile_updared.gro are different. I quite don't understand the reason for the same. You are resetting the box by invoking the -d option with editconf. If initialfile.gro had all the original atoms and initialfile_updated.gro has significantly fewer (due to the selection made in VMD), then the size associated with the system is much smaller. Using -d re-centers the system within the defined box, thus shifting the coordinates. -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 * 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 field parametrs for Mn2+
On 7/9/12 1:21 PM, tarak karmakar wrote: Oh !! nice work Thanks a lot for the quick reply. But I'm very sorry to inform you that whichever table [supplementary table S4] you are specifying in the supporting info, I couldn't find anywhere. So, may be I'm finding my way in wrong track. Can you please provide me the link and / the table containing the parameters for the Manganese ? It's on p. 11 of the supplement. http://onlinelibrary.wiley.com/store/10.1002/anie.201202032/asset/supinfo/anie_201202032_sm_miscellaneous_information.pdf?v=1&s=cff1986017d1843da85eb75dbd174c8e11727dc8 -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 * 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] Reg dimers
On 7/9/12 9:48 AM, Ramya LN wrote: Dear all, I have done protein-ligand dynamics.I got the final gro file.When converted to PDB, i observed that my active site has ligand but two chains of teh protein got separated. What might be the reason for this?should i consider this as an error in my simulation???kindly help me in this regard. http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions -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 * 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] error in mdrun
On 7/9/12 9:46 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: With the mentioned below options I get the following error: Fatal error: 1 particles communicated to PME node 1 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated. But it does not occur immediatly but only at step Step 695, time 1.39 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 2.011725, max 78.611298 (between atoms 3778 and 3781) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3782 3785 92.21.3061 0.2785 0.1090 3782 3784 93.00.1055 0.2552 0.1090 3782 3783 91.00.1062 0.3086 0.1090 3204 3206 89.60.1449 1.0256 0.1449 3204 3205 89.70.1010 0.9949 0.1010 Is there something wrong with my temperature coupling? I doubt it. Decrease your timestep (as I've said twice now) and try again with something sensible for dt. -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 * 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] error in mdrun
On 7/9/12 9:40 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi Justin, okey then I will try it with this timestep. No it is not my goal to do a NVE. I already had temperature coupling options in my .mdp file but on the blowing up side was written "you are using inappropriate temperature coupling" so I thought that that might be the reason and deleted it from my .mdp file. Temperature coupling in itself is not the source of the problem, but what is stated on the wiki is that inappropriate use of it can lead to instability. The settings below look fine. I think your biggest problem is the large timestep. -Justin I had the following temperature coupling options: tcoupl = V-rescale tc-grps = Protein Non-Protein tau_t = 0.1 0.1 ref_t = 298 298 pcoupl = no Thank you for your answer. Eva On 7/9/12 9:25 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I want to do a md for a protein with a membrane around it. I already minimised the energy of the protein. Output of the minimization: ^MStep= 812, Dmax= 1.4e-06 nm, Epot= -7.59283e+05 Fmax= 3.59781e+02, atom= 1653 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 10 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 813 steps, but did not reach the requested Fmax < 10. Potential Energy = -7.5928356e+05 Maximum force = 3.6197971e+02 on atom 1653 Norm of force = 2.6517429e+00 In my eyes this output was okey so I went on with the md. And here I get the error: Fatal error: A charge group moved too far between two domain decomposition steps This usually means that your system is not well equilibrated I already read the error page for this error and also the blowing up page but I still do not know what to do now. My .mdp file for the md runs looks like this: define = -DPOSRES integrator = md dt = 0.005 This timestep is huge. Even with constraints, you probably can't exceed 2 fs stably (0.002 ps). nsteps = 2000 nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 1000 nstxtcout = 0 nstenergy = 5 energygrps = Protein Non-Protein nstcalcenergy = 5 nstlist = 10 ns-type = Grid pbc = xyz rlist = 0.9 coulombtype = PME rcoulomb= 0.9 rvdw= 0.9 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 gen_vel = yes gen_temp= 200.0 gen_seed= constraints = all-bonds Are here any optinos which can cause the error? In the absence of temperature and/or pressure coupling, the ensemble you're trying to simulate is NVE, which is very tricky to get stabilized. http://www.gromacs.org/Documentation/Terminology/NVE If you're not going for an NVE ensemble, you need several adjustments in the .mdp file. See any basic tutorial for examples of how to simulate other ensembles, if this is your goal. -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 * 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 -- ============ 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 * 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] error in mdrun
On 7/9/12 9:25 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I want to do a md for a protein with a membrane around it. I already minimised the energy of the protein. Output of the minimization: ^MStep= 812, Dmax= 1.4e-06 nm, Epot= -7.59283e+05 Fmax= 3.59781e+02, atom= 1653 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 10 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 813 steps, but did not reach the requested Fmax < 10. Potential Energy = -7.5928356e+05 Maximum force = 3.6197971e+02 on atom 1653 Norm of force = 2.6517429e+00 In my eyes this output was okey so I went on with the md. And here I get the error: Fatal error: A charge group moved too far between two domain decomposition steps This usually means that your system is not well equilibrated I already read the error page for this error and also the blowing up page but I still do not know what to do now. My .mdp file for the md runs looks like this: define = -DPOSRES integrator = md dt = 0.005 This timestep is huge. Even with constraints, you probably can't exceed 2 fs stably (0.002 ps). nsteps = 2000 nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 1000 nstxtcout = 0 nstenergy = 5 energygrps = Protein Non-Protein nstcalcenergy = 5 nstlist = 10 ns-type = Grid pbc = xyz rlist = 0.9 coulombtype = PME rcoulomb= 0.9 rvdw= 0.9 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 gen_vel = yes gen_temp= 200.0 gen_seed= constraints = all-bonds Are here any optinos which can cause the error? In the absence of temperature and/or pressure coupling, the ensemble you're trying to simulate is NVE, which is very tricky to get stabilized. http://www.gromacs.org/Documentation/Terminology/NVE If you're not going for an NVE ensemble, you need several adjustments in the .mdp file. See any basic tutorial for examples of how to simulate other ensembles, if this is your goal. -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 * 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] large radius problem
On 7/9/12 7:09 AM, siddhant jain wrote: I was performing simulations on urea unfolding of protein. I performed one set of simulation for 50 ns with a velocity (set by gen_seed) and it went fine. Now when I am doing simulation using a different gen_seed from 10 to 20 ns many long bonds are formed. I could visualize them in vmd. Subsequently rmsd and radius of gyration plots also show the large change. But, energy is almost constant during the whole time period. Also after 20 ns this problem goes by itself and all bonds become normal. Why it could be so and how could I correct it. These bonds are so long that radius of gyration changes from 1.2 nm to 3.5 nm. That sounds like a PBC issue to me. http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions -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 * 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] Peptide folding simulation
On 7/9/12 12:02 AM, bharat gupta wrote: Hi, I have been trying to study folding of a peptide 24 residues long. I did a simulation of 50 ns with explicit solvent, CHARMM FF, but I was not able to find even a single folding event. Then I decided use explicit solvent for simulation and I again simulated the peptide for 100 ns . This time again I ended with no folding events. I know that in case of explicit solvent , a 50ns simulation time is not enough to observe anything. But I did it to see the initial behavior of the peptide in water. In take many random like conformation but doesnot fold into a desired beta-hairpin. For the explicit solvent simulation, I followed the lysozyme tutorial parameters. You shouldn't. The .mdp settings are appropriate for OPLS-AA, not CHARMM. For implicit solvent simulation, I used the following parameters for Energy minimization : define = -DFLEXIBLE constraints = none integrator = steep dt = 0.001; ps nsteps = 3 vdwtype = cut-off coulombtype = cut-off pbc = no nstlist = 0 ns_type = simple rlist = 0 ; this means all-vs-all (no cut-off), which gets expensive for bigger systems rcoulomb= 0 rvdw= 0 comm-mode = angular comm-grps = Protein optimize_fft= yes ; ; Energy minimizing stuff ; emtol = 5.0 emstep = 0.01 ; ; Implicit solvent ; implicit_solvent= GBSA gb_algorithm= Still ; HCT ; OBC nstgbradii = 1 rgbradii= 0 ; [nm] Cut-off for the calculation of the Born radii. Currently must be equal to rlist gb_epsilon_solvent = 80; Dielectric constant for the implicit solvent ; gb_saltconc = 0 ; Salt concentration for implicit solvent models, currently not used sa_algorithm= Ace-approximation sa_surface_tension = -1 For MD I used the following : - define = -DPOSRESHELIX ; -DFLEXIBLE -DPOSRES constraints = none integrator = md dt = 0.001 ; ps nsteps = 10 ; 10 ps = 100 ns nstcomm = 10 nstcalcenergy = 10 nstxout = 1000 ; frequency to write coordinates to output trajectory nstvout = 0 ; frequency to write velocities to output trajectory; the last velocities are always written nstfout = 0 ; frequency to write forces to output trajectory nstlog = 1000 ; frequency to write energies to log file nstenergy = 1000 ; frequency to write energies to edr file vdwtype = cut-off coulombtype = cut-off pbc = no nstlist = 0 ns_type = simple rlist = 0 ; this means all-vs-all (no cut-off), which gets expensive for bigger systems rcoulomb= 0 rvdw= 0 comm-mode = angular comm-grps = system optimize_fft= yes ; V-rescale temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 tc_grps = system ref_t = 300 ; Pressure coupling is off Pcoupl = no ; Generate velocites is on gen_vel = yes gen_temp= 300 gen_seed= -1 ; ; Implicit solvent ; implicit_solvent= GBSA gb_algorithm= Still ; HCT ; OBC nstgbradii = 1 rgbradii= 0 ; [nm] Cut-off for the calculation of the Born radii. Currently must be equal to rlist gb_epsilon_solvent = 80; Dielectric constant for the implicit solvent ; gb_saltconc = 0 ; Salt concentration for implicit solvent models, currently not used sa_algorithm= Ace-approximation sa_surface_tension = -1 So, finally I want to know where have I gone in my simulation experiments, both implicit and explicit ?? ... Please reply . What evidence do you have that you should expect to see a folding event in such a short time? Most people will use more extensive sampling methods like REMD to observe peptide folding. -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 * 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 t
Re: [gmx-users] Re: Two questions about index files
On 7/8/12 4:14 PM, Andrew DeYoung wrote: Hi, Thanks, Justin! Do you by any chance have any experience with the "expect" tool (http://www.nist.gov/el/msid/expect.cfm)? I have never used it. I guess that this may not help in this case because, of course, the printing of selections is due to Gromacs. But I wonder if there is any way that "expect" can be used in tandem with modification of the source code to run the Gromacs utility in the background. No, I've never used it. I think there has been some mention across the list, but I don't know how it would be necessary (or exceptionally useful) here. Maybe someone with more experience with it can comment. I certainly doubt it will suppress Gromacs screen output. -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 * 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] define a new residue
On 7/8/12 12:43 PM, Shima Arasteh wrote: OK. What about generating an output file through CGenFF by the first 3 residues of the protein, rather thn the first 2 (formyl+valine)? Maybe. Try it and see, rather than waiting a few hours for someone to get around to replying :) -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 * 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] Two questions about index files
On 7/8/12 3:59 PM, Andrew DeYoung wrote: Hi, I hope that all is well. If you have time, I have two questions about index files: (1) Do you know if there is a limit on the number of entries an index file can have? I am trying to write a shell script which would allow me to run g_traj 20 times, feeding a different index entry to it on each iteration. This is because I have used g_select to (dynamically) pick out atoms that meet certain criteria. I have 20 time steps in my trajectory, so I have 20 entries in my index file. I will try this, but do you have any experience with this about whether such a large index file will work? The only limitation here is disk space and available memory, both of which are external to Gromacs. (2) Normally, when I call any Gromacs program with the -n switch, the program prints to the screen all of the choices available in the index file. I am planning to use the "<http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts#Withi n_Script This works, but the problem is that the program still prints all of the index file selections to the screen, even though the input is now automated from the shell script. This means that the program insists upon printing out all 20 index selections on each of my 20 calls to the program, and this can take a lot of time. Do you know if there is a way to suppress the printing of the index files selections and somehow feed input to the program in the background/invisibly? Simply putting & at the end of the command does not seem to work. In other words, is there a way to make commands non-interactive _in the background_? Thank you! I don't think so. There is a hidden option called -quiet that reduces some screen output, but since selections are dependent upon user choice, they can't be suppressed, at least in the quick trials I just did. I suppose you could modify the source to prevent this printing, but whether or not that's worth the effort is up to you. -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 * 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] define a new residue
On 7/8/12 11:29 AM, Shima Arasteh wrote: Thanks all. So if I find a protein which is parametrized by CHARMM and then find the valine residue there, I might use the parameters of side chains of it in my own rtp file. Right? You can look this up in the force field's .rtp file. For full parameterization procedures, refer to the primary literature for CHARMM. It should detail how to derive parameters for new species. -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 * 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] Re: Re: g_sham problem
On 7/8/12 9:39 AM, siddhant jain wrote: Thanks Justin Also I wanted to ask that to know my structure which has minimum energy, can I take the corresponding values of principle components, look at the time at which they occur simultaneously, and hence note the structure corresponding to that time. Will it be reasonable enough or its vague. You can certainly identify structures within different regions of the free energy surface in this way. Just be careful about saying any structure has a particular "energy" value, since this can mean a number of different things. -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 * 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] g_sham problem
On 7/8/12 9:16 AM, siddhant jain wrote: I used the g_sham command to get 2-d energy field where the two components are eigenvector 1 and 2. The graph is fine but it has no labelling along the axis. I used g_sham -f proj124.xvg -ls 124.xpm -notime I want the labels along the axes so that i can comprehend it better. Use the -xmin and -xmax options to set suitable values. g_sham tries to guess, but in my experience, does a poor job of it and I usually have to set everything manually. -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 * 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] Crashes during protein-ligand simulation
On 7/8/12 6:57 AM, James Starlight wrote: Justin, unfortunately my last system have also been crashed after 35ns of simulation with the links warnings accompanied by the error Fatal error: A charge group moved too far between two domain decomposition steps This usually means that your system is not well equilibrated For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors This time I've devided all functional groups of my ADENOSINE ligand into separate charge groups in topol.itp. Note that these charges are not the same as the adenosine moiety of ATP, which is standard in the Gromos96 force fields. Perhaps you should re-evaluate some charges (see aminoacids.rtp for the existing ATP implementation). ; nr type resnr resid atom cgnr chargemasstotal_charge 1NT1ADN N61 -0.844 14.0067 2 H1ADNH1110.422 1.0080 3 H1ADNH1210.422 1.0080 ; 0.000 4 C1ADN C820.097 12.0110 5HC1ADNH0120.177 1.0080 6NR1ADN N32 -0.642 14.0067 7 C1ADN C420.175 12.0110 8 C1ADN C520.092 12.0110 9NR1ADN N72 -0.556 14.0067 10 C1ADN C620.657 12.0110 ; 0.000 11 C1ADNC5'3 -0.677 12.0110 12 C1ADNC4'30.834 12.0110 13OE1ADNO4'3 -0.248 15.9994 14 C1ADNC1'3 -0.558 12.0110 15 C1ADNC2'40.603 12.0110 16 C1ADNC3'5 -0.212 12.0110 17NR1ADN N930.415 14.0067 18OA1ADNO2'4 -0.606 15.9994 19 H1ADNH0840.482 1.0080 20OA1ADNO3'5 -0.606 15.9994 21 H1ADNH0650.482 1.0080 22OA1ADNO5'3 -0.246 15.9994 23 H1ADNH0330.337 1.0080 ; -0.000 24 C1ADN C260.502 12.0110 25HC1ADNH1060.106 1.0080 26NR1ADN N16 -0.608 14.0067 ; 0.000 Also I've done proper equilibration in tho steps (I've used 1fs integrator steps on both stages of equilibration) 1- I've made equilibration with posres ( 500ps) on protein backbone atoms as well as ligand with x-ray water 2- The next step (5ns) was done without posres only with smaller integrator steps. What another possible sollutions could be ? Try some diagnostics: http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System If simulations of the same system without a ligand run fine, then the error is still related to the ligand, either its topology or placement. -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 * 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] error in grompp
On 7/8/12 6:02 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi Justin, thank you for your answer. Now I tried it with two different restraint .itp files. One for the protein and one for the dummy atoms. But still it doesn't work. Now the error is: [ file posre_memb.itp, line 5 ]: Atom index (4942) in position_restraints out of bounds (1-1). This probably means that you have inserted topology section "position_restraints" in a part belonging to a different molecule than you intended to. In that case move the "position_restraints" section to the right molecule. But I think I included it the right way: ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif ; Include water topology #include "amber03.ff/tip3p.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include "amber03.ff/ions.itp" #include "amber03.ff/dum.itp" #ifdef POSRES #include "posre_memb.itp" #endif In my coordiate file the difference between them look like this: 313LEU HD23 4938 3.813 4.505 3.308 313LEU C 4939 3.435 4.335 3.190 313LEUOC1 4940 3.429 4.330 3.090 313LEUOC2 4941 3.337 4.305 3.259 314DUMDUM 4942 1.996 2.371 6.171 314DUMDUM 4943 1.996 2.371 6.271 314DUMDUM 4944 1.996 2.471 6.171 314DUMDUM 4945 1.996 2.471 6.271 my restraint file for the protein looks like this: ; position restraints for Protein-H of GROup of MAchos and Cynical Suckers [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 41 1000 1000 1000 71 1000 1000 1000 101 1000 1000 1000 131 1000 1000 1000 and my restraint file for the dummy atoms look like this: ; position restraints for Protein-H of GROup of MAchos and Cynical Suckers [ position_restraints ] ; i funct fcxfcyfcz 49421 1000 1000 1000 49431 1000 1000 1000 49441 1000 1000 1000 49451 1000 1000 1000 What is wrong? Atom numbering is done per [moleculetype] and has nothing to do with the atom numbers in the coordinate file. If you have a one-atom dummy [moleculetype], then the only valid content of posre_memb.itp is: [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 -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 * 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] top file
On 7/8/12 3:12 AM, Shima Arasteh wrote: Dear gmx users, I have gotten 2 topology files from a unique simulation ( a protein in water) with gmx and CHARMM36. I know the charges of atoms derived by PRODRG and CGENFF are different, but I'm wondering if the total charge which is visible in top file, is supposed to be the same? What items are expected to be the same? or be in agreement? The total charge is given in the qtot column of the .top file. In theory, at a given protonation state, any protein should have the same net charge under any force field. -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 * 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] define a new residue
On 7/8/12 7:10 AM, Shima Arasteh wrote: Because I saw that residues defined in aminoacids.rtp file don't have H in their carboxyl and atom N. So I decided to remove H ! Chemically, there is never an H atom on the C-terminal carbonyl of a group involved in a peptide bond. If you parameterized a molecule that was protonated in such a way, it will give an erroneous output. You can't just delete atoms, and shifting the charge by adding it back somewhere else is also very suspect, because you're changing the electronic nature of the compound. I would say you need a better parameterization protocol using a more suitable model compound. -Justin Sincerely, Shima From: francesco oteri To: Shima Arasteh Cc: Discussion list for GROMACS users Sent: Sunday, July 8, 2012 3:28 PM Subject: Re: [gmx-users] define a new residue Why have you removed the hydrogen? 2012/7/8 Shima Arasteh Dear Francesco, Thanks. Honestly I thought about this, but I don't know how much charges I need to increase or decrease of other atoms? Is it possible to add the FVAL with the H atom( which I removed before)? I mean that I apply the complete formyl-valine and don't remove the H atom. Thanks for your suggestions. Cheers, Shima From: francesco oteri To: Shima Arasteh ; Discussion list for GROMACS users Sent: Sunday, July 8, 2012 3:04 PM Subject: Re: [gmx-users] define a new residue Hi Shima, usually charge calculation are carried out on the system that is supposed to be used in the MD. So in my opinion you shouldn't remove the hydrogen. Anyway, if you wanna remove the hydrogen, either you increase the charge of some other atom or calculate the charges on the new residue without hydrogen. Francesco 2012/7/8 Shima Arasteh Hi dear gmx friends, I got the parameters of formyl-valine through the CHARMM website. Now I need to define it as a new residue FVAL( as Justin suggested me earlier) in .rtp file. To set the correct charges for atoms, I used the CHARMM output. In order to define FVAL to rtp file, I added these lines as below: CNC0.3490 ONO-0.4941 H1HC0.1002 NNH1-0.4233 HNH0.094 CACT10.1445 HAHB0.096 CBCT1-0.0977 HBHA0.098 CG1CT3-0.2689 HG11HA0.0910 HG12HA0.0911 HG13HA0.0912 CG2CT3-0.26813 HG21HA0.0914 HG22HA0.0915 HG23HA0.0916 CC0.20917 OO-0.39518 As you see I omitted the H connected to Carboxyl. Now the total charge of the new-defined residue is not zero (-0.333) . How can I correct it? I would appreciate you for your suggestions. Thanks in advance. Sincerely, Shima -- 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 -- Cordiali saluti, Dr.Oteri Francesco -- ============ 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 * 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] Crashes during protein-ligand simulation
On 7/7/12 11:08 AM, James Starlight wrote: justin, It seems that problem was in the big charge groups in the ligand.itp file. In particularly I've devided largest group into several smaller and there haven't any crashes been occured yet. With my last system with the the default COM group I've obtained crash on the 25ns with the error about ligand's big cngr exactly. By the way could you tell me how I could analyse stability of the protein-ligand system as well as contributions of the individual non-covalent contacts with the .EDR file? In my mdp file I've defined energygrps= Protein Ligand as the separate energy terms. During analysis of the edr file I've observed some options like LJ-SR:Protein-ADN ( this value was slightly negative (-100) during my trr ) Coul-14:Protein-ADN ( this value was constantly zero ) Coul-SR:ADN-rest ( this value was equal to the LJ-SR:Protein-ADN -100 ) What conclusions in general could I do based on that values ? How I could measure stability of the ligand ( beside dirrect RMSD measurement) from such energy terms? In isolation, these values are not indicative of anything. Their absolute values are completely dependent upon the parameters set in the topology. Force field parameterization methodology does not require that any topology reproduce protein-ligand energetics; only true free energy calculations might tell you this. In conjunction with other metrics (hydrogen bonding, contacts, RMSD, SASA, etc) you may be able to make some meaningful observations about ligand stability in the protein binding site. -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 * 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] error in grompp
On 7/7/12 8:20 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I want do to an energy minimization and simulation with position restraints. Additionally to the protein I have a membrane around my protein which I also ant to fix. If I won't fix it, it is in the whole box after the minimization and simulation but not around my protein. Since I only want the hydrogen atoms to be flexible I use the second option "protein-h" when I was asked by genrestr. This makes that the whole protein including the membrane of dummy atoms is fix. But when I want to use grompp I get the error: Atom index (4942) in position_restraints out of bounds (1-4941). This probably means that you have inserted topology section "position_restraints" in a part belonging to a different molecule than you intended to. In that case move the "position_restraints" section to the right molecule. The first 4941 atoms are of the "real" protein without the membrane and after this the membrane starts: 313LEUOC1 4940 3.429 4.330 3.090 313LEUOC2 4941 3.337 4.305 3.259 314DUMDUM 4942 1.996 2.371 6.171 315DUMDUM 4943 1.996 2.371 6.271 316DUMDUM 4944 1.996 2.471 6.171 When I remove the restriction of the DUM atoms I don't get the error but that is not what I want. Can you please tell me how I can fix the membrane? You need a separate position restraint .itp file. As the error message states, position restraints are only applicable per [moleculetype]. http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds -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 * 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] Re: specifying the direction of Pull in US
On 7/7/12 12:15 AM, Raj wrote: Thanks for ur suggestion Justin, I'm facing trouble in setting that vector, actually I cant figure out how can i set up a vector. Is there any easier way with which i can set up a vector. Thanks It can be set simply to the difference in the (x,y,z) coordinates of the COMs of the two groups. You can calculate the COM position of each group with g_traj -ox -com -x -y -z. Alternatively, if you use "pull_geometry = distance" and set "pull_dim = Y Y Y" then the pulling direction is the vector between the two groups in all dimensions. -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 * 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] Crashes during protein-ligand simulation
On 7/6/12 3:56 PM, James Starlight wrote: Justin, I've experimented with 2 dirrerent COM groups comm-grps = SOL_NA_CL XW Protein_CCl4_ADN ; 3 groups comm-grps = SOL_NA_CL_XW Protein_CCl4_ADN; 2 groups but the crashes were in both cases after 12- 15ns of simulation this time I've changed to the comm-grps = System and there have not been any crashes yet (to this time I've already calculated addition 20ns after privious crhased simulation using checkpoint file for the last simulation ). But it's posible that it was lucky coincidence :) Could you tell me how I could devide largest group in the above axample into several smaller sub-groups ? Should I do that separation randomly or there are most correct way for that ? (e.g within third cgnr separate all nitrogens and oxygens with corresponded hydrogens in the separate cgrp's from carbons) Look at existing examples in the force field .rtp file. In general, a charge group consists of a functional group (amine, carboxylate, etc) or small CHn units. Generally there are 2-4 atoms per charge group. There is some discussion on these topics in the manual. -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 * 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] Crashes during protein-ligand simulation
On 7/6/12 2:05 PM, James Starlight wrote: Justin, I've done all steps in accordance to your tutorial. I've already done the same systems with another ligands but had no problem. This time I've made topology of the ligand via ATB server. I've only noticed that some cgnr are too big in that topology . This is the example ADN 3 [ atoms ] ; nr type resnr resid atom cgnr chargemasstotal_charge 1NT1ADN N61 -0.844 14.0067 2 H1ADNH1110.422 1.0080 3 H1ADNH1210.422 1.0080 ; 0.000 4 C1ADN C820.097 12.0110 5HC1ADNH0120.177 1.0080 6NR1ADN N32 -0.642 14.0067 7 C1ADN C420.175 12.0110 8 C1ADN C520.092 12.0110 9NR1ADN N72 -0.556 14.0067 10 C1ADN C620.657 12.0110 ; 0.000 11 C1ADNC5'3 -0.677 12.0110 12 C1ADNC4'30.834 12.0110 13OE1ADNO4'3 -0.248 15.9994 14 C1ADNC1'3 -0.558 12.0110 15 C1ADNC2'30.603 12.0110 16 C1ADNC3'3 -0.212 12.0110 17NR1ADN N930.415 14.0067 18OA1ADNO2'3 -0.606 15.9994 19 H1ADNH0830.482 1.0080 20OA1ADNO3'3 -0.606 15.9994 21 H1ADNH0630.482 1.0080 22OA1ADNO5'3 -0.246 15.9994 23 H1ADNH0330.337 1.0080 ; -0.000 24 C1ADN C240.502 12.0110 25HC1ADNH1040.106 1.0080 26NR1ADN N14 -0.608 14.0067 ; 0.000 ; total charge of the molecule: -0.000 Large charge groups could account for errors in neighbor searching, leading to clashes that cause the simulation to collapse. 2) To the binding pocket I've inserted this ligand manually by means of superimposition with the reference x-ray structure wich include the same protein in the same conformation with the same ligand. I've done some systems already and that aproach was good :) OK, just be ready for reviewers to ask why you didn't do docking ;) 3) It's strange that the simulation crashes without any reasons ( the system is very stable during calculated 10-15ns trajectory) There's always a reason, you just haven't found it yet. The charge group size could indeed be the problem; neighbor searching can fail at any time when some atoms run into one another. Also I suppose that such problems could be with the COM groups this is the example from my mdp comm-grps = SOL_NA_CL XW Protein_CCl4_ADN here XW is the water wich were coppied from X-ray structure . Also in that system Ccl4 is the membrane mimicking layer so I've merged it with protein and ligand in the same group. I see no reason to add such complexity to the system. Breaking the crystal waters into their own COM removal group does not make sense to me. Physically, they are basically part of the protein. On the current stage I've tried to make changes in the mdp on comm-grps = System to check if the problem was with that COM motion And what was the outcome? I see no reason that two COM motion removal groups wouldn't be appropriate (as layers can slide with respect to one another, like a membrane) but three groups does not sound appropriate. -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 * 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] Boundary
On 7/6/12 3:06 PM, dariush wrote: Hi all, Why does GROMACS just provide PBC for boundary condition? However, LAMPPS as an example provides four kind of boundary: periodic, non-periodic and fixed, non-periodic and shrink-wrapped and non-periodic and shrink-wrapped with a minimum value. Gromacs can also do non-periodic systems by setting "pbc = no" in the .mdp file. A variety of options exist for walls, as well. If there are particular features that users want, they are welcome to implement them and submit them for review in the development code. Otherwise, if no one files a feature request on redmine, the developers aren't going to invest time in the feature unless they need it themselves. I would hazard a guess that 3-D periodic boundary conditions are the most commonly used in simulations of biomolecules. PBC makes problem when you want to make movie in VMD, even you add some mirror-wise molecule in each direction. Is there anyway to figure out this problem? Any trajectory can be "fixed" for visualization purposes with trjconv. You may need several iterations to achieve the desired effect. http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow -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 * 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] Re: bilayers move apart by nanometers upon implementing dihedral restraints on lipid tails
On 7/6/12 10:40 AM, khandelia wrote: Justin, Vitaly The topology is fine, I double-checked The simulation runs perfectly fine without the restraints. It is not a PBC effect, since the box size along z is > 50 nm after a ns or so. Does one need yet another restraint to hold the bilayer together? I have never had a need for any restraints to keep a bilayer intact. There has been some discussion about problems with dihedral restrains in the list earlier, but nothing like this. The problem you're observing seems to indicate that your manipulation of the lipid chain causes physical instability. How extensive are the restraints? How many atoms do they involve? You provided an "etc" in your previous message, so I'm trying to clarify what's going on. Is it even physically possible to orient the lipid chain in such a way? You've got basically all the consecutive dihedrals in a very specific orientation - is that compatible with your system? Can you run a simulation of a single lipid in vacuo using these restraints? -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 * 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] Error in Membrane simulations with POPC bilayer
On 7/6/12 10:48 AM, J Peterson wrote: Hi Justin and Anirban, I started a membrane simulation with POPC bilayer after a training with the given KALP peptide and DPPC bilayer. I am following both of your tutorials (mainly the Justin's). I have problem at where I generate a .tpr file for a DPPC (POPC here)-only system using grompp. I see another warning on non-matching number of atoms along with the error that you recommended a safe one. My error is Warning: atom name 3340 in topol_popc.top and popc_128b_H.pdb does not match (C12 - H2) Warning: atom name 3341 in topol_popc.top and popc_128b_H.pdb does not match (C13 - O) Warning: atom name 3342 in topol_popc.top and popc_128b_H.pdb does not match (O14 - H1) Warning: atom name 3343 in topol_popc.top and popc_128b_H.pdb does not match (C15 - H2) Warning: atom name 3344 in topol_popc.top and popc_128b_H.pdb does not match (O16 - O) Warning: atom name 3345 in topol_popc.top and popc_128b_H.pdb does not match (C17 - H1) Warning: atom name 3346 in topol_popc.top and popc_128b_H.pdb does not match (C18 - H2) Warning: atom name 3347 in topol_popc.top and popc_128b_H.pdb does not match (C19 - O) Warning: atom name 3348 in topol_popc.top and popc_128b_H.pdb does not match (C20 - H1) (more than 20 non-matching atom names) WARNING 1 [file topol_popc.top, line 26]: 10708 non-matching atom names atom names from topol_popc.top will be used atom names from popc_128b_H.pdb will be ignored Analysing residue names: There are: 128 Other residues There are: 2460 Water residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Number of degrees of freedom in T-Coupling group rest is 42105.00 Largest charge group radii for Van der Waals: 6.115, 5.932 nm Largest charge group radii for Coulomb: 6.546, 6.115 nm WARNING 2 [file em_st.mdp]: The sum of the two largest charge group radii (12.661407) is larger than rlist (0.90) Calculating fourier grid dimensions for X Y Z Using a fourier grid of 54x56x48, spacing 0.117 0.117 0.119 Estimate for the relative computational load of the PME mesh part: 0.45 This run will generate roughly 34 Mb of data There were 2 warnings --- Program grompp, VERSION 4.5.3 Source code file: grompp.c, line: 1563 Fatal error: Too many warnings (2), grompp terminated. If you are sure all warnings are harmless, use the -maxwarn option. Can any one of you help me move from here? The order of your [molecules] directive does not agree with the contents of the coordinate file. What you're seeing is a mismatch between lipid atom names and water (O, H1, and H2). The second warning may or may not be problematic. If your charge groups are split across periodic boundaries, they will be reconstructed properly. If your molecules are already whole, then you have a separate issue. -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 * 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] Re: specifying the direction of Pull in US
On 7/6/12 9:52 AM, Raj wrote: hi , When i applied distance I cant have control over the direction of the pull. The ligand is not exactly pulled along the direction i meant to pull You can specify the pull vector using the difference between the COM positions of the pull group and its reference. Set those (x,y,z) values to pull_vec1. -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 * 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] Crashes during protein-ligand simulation
On 7/6/12 1:12 AM, James Starlight wrote: Dear Gromacs users! I have some problems with the simulation of protein-ligand complex embedded in the ccl4-water environment. In addition there are some crystallography waters (xw) embedded in the protein interiour of the protein. I've done equilibration and minimisation of my system and run it in NVT ensemble. Finally I've already simulated this system in the apo form as well as without XW and there were no any problems. In the current case my system always crashed after 10-15 ns of simulation with the errors like Step 6651310, time 13302.6 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.060675, max 1.520945 (between atoms 3132 and 3130) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3148 3147 90.00.1281 0.1483 0.1000 3150 3149 90.00.1084 0.1444 0.1000 3131 3130 90.00.1321 0.1325 0.1000 3132 3130 90.00.1067 0.2521 0.1000 --- Program mdrun_mpi.openmpi, VERSION 4.5.5 Source code file: /tmp/build/gromacs-4.5.5/src/mdlib/constr.c, line: 189 here both atoms 3132 and 3130 are from LIGAND. During data analysing I didnt observed any serious artifacts in that system. In addition RMSD both of protein and ligand were very stable. Finally there are no fluctuations in energy or temperature. So I could understand why this crasshes could occur. If I try to continue this simulation from the crasshed checkpoint my simulation always goon but within next 5-10ns I've always obtain second crash etc. This is the last step from log file DD step 664 vol min/aver 0.758 load imb.: force 1.0% pme mesh/force 0.708 Step Time Lambda 66513300.00.0 Energies (kJ/mol) Angle G96AngleProper Dih. Improper Dih. LJ-14 5.78299e+011.24988e+042.10966e+031.81619e+038.94229e+01 Coulomb-14LJ (SR)LJ (LR) Disper. corr. Coulomb (SR) 4.65481e+048.27301e+04 -6.89535e+03 -2.15286e+03 -7.16722e+05 Coul. recip. PotentialKinetic En. Total Energy Conserved En. -1.72813e+05 -7.52733e+051.46708e+05 -6.06025e+05 -1.37045e+06 Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 3.10968e+02 -9.74796e+012.52993e+021.55693e-05 Could you explain me what could be wrong with that system and what addition data should I provide to help sheld light on that problem ? If the addition of a ligand causes the simulation to crash (and the simulation runs normally in the apo form with and without crystal waters), then that sounds like a problem with the ligand topology or its initial placement. What is the ligand? How did you generate and validate its topology? How did you place it? -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 * 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] Re: Problem with minimizing the energy of the solvated system
On 7/5/12 5:51 PM, jonas87 wrote: Protein-water.pdb has the following line: CRYST1 75.324 75.324 75.324 60.00 60.00 90.00 P 1 1 But after adding the NA/CL ions with genion the CRYST1 line is missing entirely from the output file protein-solvated.pdb Could this be because of the bug u mentioned? Sounds about right. I'm using the latest version of gromacs, that means this bug was reintroduced? Likely it was not fully fixed; I recall a change to editconf, but maybe genion needs a look as well. So it is ok to always output to .gro instead of .pdb? Always. -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 * 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] Re: Problem with minimizing the energy of the solvated system
On 7/5/12 5:05 PM, jonas87 wrote: I'm following the tutorial exactly. Even have my files named the same way. The contents of my minil.mdp (pcb is changed from no to xyz right before running the energy minimazation of the solvated system): title = Energy Minimization ; Title of run cpp = /lib/cpp ; Preprocessor define = -DFLEXIBLE integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1.0 ; Stop minimization when the maximum force < 1.0 kJ/mol nsteps = 500 ; Maximum number of (minimization) steps to perform nstenergy = 1 ; Write energies to disk every nstenergy steps energygrps = System; Which energy group(s) to write to disk ns_type = simple; Method to determine neighbor list (simple, grid) coulombtype = cut-off ; Treatment of long range electrostatic interactions rcoulomb= 1.0 ; long range electrostatic cut-off rvdw= 1.0 ; long range Van der Waals cut-off constraints = none ; Bond types to replace by constraints pbc = no; Periodic Boundary Conditions (yes/no) You're probably losing the box information somewhere along the line while switching back and forth between .gro and .pdb. The CRYST1 line in protein-solvated.pdb should agree with the previous settings. If it doesn't, something has gone wrong. I recall some previous version of Gromacs had issues reading and writing correct box vectors in .pdb files; I don't know which one. It's always safe to use .gro files for everything, though in principle, .pdb files should work as well. -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 * 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] Problem with minimizing the energy of the solvated system
On 7/5/12 3:15 PM, jonas87 wrote: Chopping out a bunch of unnecessary stuff... *editconf -f protein-EM-vacuum.pdb -o protein-PBC.gro -bt dodecahedron -d 1.0 * Read 1202 atoms No velocities found system size : 5.245 4.320 2.507 (nm) diameter: 5.532 (nm) center : 0.010 0.047 -0.011 (nm) box vectors : 0.000 0.000 0.000 (nm) box angles : 0.00 0.00 0.00 (degrees) box volume : 0.00 (nm^3) shift : 5.640 5.602 2.674 (nm) new center : 5.649 5.649 2.663 (nm) new box vectors : 7.532 7.532 7.532 (nm) Here, you're setting the box. The dimensions look sensible. (Chopping out more extraneous stuff) Here's where something is going wrong. Without seeing the contents of minim.mdp, it's hard to say exactly what, aside from a generic comment that the settings in the .mdp file are incompatible with the size of the box. Typically tutorials work quite well, so you should ensure that you're following everything exactly and keeping track of all your files so nothing has gotten switched up. grompp -v -f minim.mdp -c protein-solvated.pdb -p protein.top -o protein-EM-solvated.tpr * Ignoring obsolete mdp entry 'title' Ignoring obsolete mdp entry 'cpp' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3# checking input for internal consistency... processing topology... Generated 141 of the 1176 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_A' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 1 bonded neighbours molecule type 'NA' Excluding 1 bonded neighbours molecule type 'CL' processing coordinates... double-checking input for internal consistency... ERROR 1 [file protein.top, line 7583]: ERROR: One of the box lengths is smaller than twice the cut-off length. Increase the box size or decrease rlist. --- Program grompp, VERSION 4.5.5 Source code file: /build/buildd/gromacs-4.5.5/src/kernel/grompp.c, line: 1372 Fatal error: There was 1 error in input file(s) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Did you follow the link? It's where you can find an answer to almost every error you'll encounter. For instance: http://www.gromacs.org/Documentation/Errors#The_cut-off_length_is_longer_than_half_the_shortest_box_vector_or_longer_than_the_smallest_box_diagonal_element._Increase_the_box_size_or_decrease_rlist -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 * 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] question about energy minimization
On 7/5/12 10:52 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I want to minimize the energy of my structure. I use the following mdp file: define = -DPOSRES integrator = steep emtol = 10 nsteps = 5000 nstenergy = 1 energygrps = System coulombtype = PME rcoulomb= 0.9 rvdw= 0.9 rlist = 0.9 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 pbc = xyz But it nevers runs till the end. It allways stops before the end and I get no pdb file. When I use nsteps = 2000 there is no problem and I receive a pdb file but it says that there were not enough steps to get under a specific force value. My question is: is there a possibility to make the minimization run longer? Can I set a parameter that makes it run longer? Set nsteps to either a very high value or to -1 (which says run infinitely long). Note that several factors are working against you here, including the use of position restraints. These disfavor the motion of whatever the restrained atoms are, which can impede energy minimization. Also, assuming you're using single-precision Gromacs, an emtol of 10 is very low and unlikely to be achievable, especially using a single run of steepest descent EM. -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 * 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] bilayers move apart by nanometers upon implementing dihedral restraints on lipid tails
On 7/5/12 10:25 AM, himanshu khandelia wrote: I am trying to implement dihedral restraints for lipids in a bilayer using what is suggested here: http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints However, although the dihedral angles seem to be restrained fine, the leaflets move apart by 10s of nanometers along +z over a nanosecond or so, after which of course, the simulation crashes. Can anyone suggest what I might be doing wrong? Are the simulations stable in the absence of these restraints? Are you sure this isn't just a matter of periodicity creating the illusion of large-scale diffusion? -Justin version 4.5.4 In the mdp file: ;dihedral restraints dihre = yes dihre_fc = 100 In the topology: [ dihedral_restraints ] 17 18 19 20 11100012 18 19 20 21 11100012 19 20 21 22 11100012 20 21 22 23 11100012 21 22 23 24 11100012 ... etc. Himanshu -- ==== 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 * 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] COM RDF
On 7/4/12 1:31 PM, Dr. Vitaly V. G. Chaban wrote: Dear GROMACS people - I am calculating radial distribution function between the centers of mass of two large particles in a periodic box. My command is -- g_rdf_455 -n 2drops.ndx -rdf mol_com -s topol.tpr -f conf.gro My index file contains two groups of atoms standing for the first and the second supraparticles whose centers-of-mass I am interested in. Since here I provide the "conf.gro" file rather than a trajectory, I expect to get just one peak in my RDF, but instead I get multiple peaks at different separation distances (please, see http://i47.tinypic.com/24m826v.jpg). The groups of atoms in the index file are separated spatially, if this may matter. Would anyone kindly explain how the COM RDF function works? My ultimate purpose is to depict how the distance between those two centers-of-mass evolves in time. You also need to use the -com flag to use the COM of the reference group. -Justin The -com flag changed the output (please, see http://i48.tinypic.com/29uuo7b.jpg) but there is still a number of embarassing peaks after 7nm. Given the positions of these supraparticles, I would expect maximum about 10nm whereas the box side is 26nm. From the g_rdf help message -- The option -rdf sets the type of RDF to be computed. Default is for atoms or particles, but one can also select center of mass or geometry of molecules or residues. In all cases, only the atoms in the index groups are taken into account. I understand this in the following way. The centers-of-mass of the groups in the index file are computed and further the calculation proceeds as if these COMs were regular atoms. If I have only two groups, I should get one maximum. Am I not correct? In theory, yes. I have no idea how effective g_rdf is for this purpose. From your initial description, if you're just trying to track COM distance over time, why not use g_dist? That's precisely what it 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 * 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] COM RDF
On 7/4/12 1:07 PM, Dr. Vitaly V. G. Chaban wrote: Dear GROMACS people - I am calculating radial distribution function between the centers of mass of two large particles in a periodic box. My command is -- g_rdf_455 -n 2drops.ndx -rdf mol_com -s topol.tpr -f conf.gro My index file contains two groups of atoms standing for the first and the second supraparticles whose centers-of-mass I am interested in. Since here I provide the "conf.gro" file rather than a trajectory, I expect to get just one peak in my RDF, but instead I get multiple peaks at different separation distances (please, see http://i47.tinypic.com/24m826v.jpg). The groups of atoms in the index file are separated spatially, if this may matter. Would anyone kindly explain how the COM RDF function works? My ultimate purpose is to depict how the distance between those two centers-of-mass evolves in time. You also need to use the -com flag to use the COM of the reference group. -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 * 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] Nucleic acid simulation
On 7/4/12 6:45 AM, Ravi Raja Merugu wrote: Hello every one, Im interesting in performing a MD for Protein - RNA complex , Can any one suggest a good tutorial. Such systems do not differ significantly from simulations of simple proteins in water, since pdb2gmx can produce topologies for both proteins and nucleic acids. The remaining workflow is basically the same. -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 * 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] Regarding parameters for pull_groups in mdp file for the pull code
On 7/4/12 2:31 AM, neeru sharma wrote: Dear Gromacs Users, I have some queries about the parameters in the .mdp file for the pull code. If I want to pull my ligand, towards specific atom/group of atoms from the protein, how am I supposed to mentioned these in the mdp file? * pull = umbrella pull_geometry = distance pull_start = yes pull_ngroups= 1 pull_group0 = Ligand pull_group1 = Atom/group of atoms from the protein * Here, I want to specify the pull_group0 as "Ligand" and pull_group1 as "Atoms of the protein". My query is regarding these groups. Shall I just write the name of the Ligand and Atoms (specifying the atom no) or am I supposed to create a separate index file for each of them (one for ligand and other for group of atoms) ? All groups specified in the .mdp file must be either valid default groups or custom groups provided in an index file. -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 * 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] PMF trails off to infinity.
On 7/3/12 2:50 PM, Thomas Schlesier wrote: think you encounter the problem, that you construct your pmf from a 3d simulation and project it onto 1d, but do no correction. For TI (if you constrain the distance in all three directions) the pmf is given by V_pmf(r) = - \int [ F_c + 2/(beta*r) ] dr with F_c the constraint force and \beta = 1/(k_B*T). for umbrella sampling one should need the same factor -2/beta \int 1/r dr if one restraints the system in 3 directions. Since 'g_wham' uses no *.tpr it can not know the value of 'pull_dim' one should introduce the factor afterwards. The input to g_wham (at least in modern Gromacs versions) is a list of .tpr files (passed to the -it flag) and a list of pullx or pullf files (with -ix or -if). How is g_wham ignorant of these pull settings? -Justin There could also the problem that the dummy-atom interacts with the ligand, or other clashes, but i don't think so, because the force looks too fine. If the ligand would crash into something one should see a greatly increasing force. like around 1000-2500 in your force-profile, when the protein still helds the ligand in the binding pocket. Additional comment: 'pull_geometry = distance' is a really bad idea for pmf generation if one has an actual distance of 0 and the system is not isotropic, since distance only knows distances and has no ideas about directrions: place a reference particle at the origin of a box put a second particle on top of it pull along x pull along -x in both cases you get the distance r=|x|=|-x| if the system is isotropic, everything is fine if system is anisotropic you get problems on the nice side, this problem should affect simulations where one pulls a ligand away from a binding pocket, only for the windows which is centered the nearest to 0. for mapping an ion-channel with a reference group in the middle of the channel it's (/ it should be) far more worse, (if the system is not isotropic). Somewhere in the archive is a longer explainition, i discussed the topic with 2-3 different people... Am 03.07.2012 11:34, schrieb gmx-users-requ...@gromacs.org: Basically what I'm doing is pulling a ligand out of a protein towards a dummy atom, which has a mass of 1 and no charge. I've attached the a portion .mdp files for both the smd portion and the umbrella sampling. I know that the ligand gets very close possibly crashing into the dummy atom. So from what you're saying, I'm thinking this might be the source of the problem. - Laura ## smd.mdp## ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 123456 ;COM PULLING ; Pull type: no, umbrella, constraint or constant_force pull = umbrella ; Pull geometry: distance, direction, cylinder or position pull_geometry = distance ; Select components for the pull vector. default: Y Y Y pull_dim = Y Y Y ; Cylinder radius for dynamic reaction force groups (nm) pull_r1 = 1 ; Switch from r1 to r0 in case of dynamic reaction force pull_r0 = 1.5 pull_constr_tol = 1e-06 pull_start = yes pull_nstxout = 10 pull_nstfout = 1 ; Number of pull groups pull_ngroups = 1 ; Group name, weight (default all 1), vector, init, rate (nm/ps), kJ/(mol*nm^2) pull_group0 =JJJ pull_weights0 = pull_pbcatom0 = 0 pull_group1 = CPZ pull_weights1 = pull_pbcatom1 = 0 pull_vec1 = pull_init1 = pull_rate1 = -0.0006 pull_k1 = 800 pull_kB1 = ### um.mdp ## ;COM PULLING ; Pull type: no, umbrella, constraint or constant_force pull = umbrella ; Pull geometry: distance, direction, cylinder or position pull_geometry = distance ; Select components for the pull vector. default: Y Y Y pull_dim = Y Y Y ; Cylinder radius for dynamic reaction force groups (nm) pull_r1 = 1 ; Switch from r1 to r0 in case of dynamic reaction force pull_r0 = 1.5 pull_constr_tol = 1e-06 pull_start = yes pull_nstxout = 100 pull_nstfout = 100 ; Number of pull groups pull_ngroups = 1 ; Group name, weight (default all 1), vector, init, rate (nm/ps), kJ/(mol*nm^2) pull_group0 =JJJ pull_weights0 = pull_pbcatom0 = 0 pull_group1 = CPZ pull_weights1 = pull_pbcatom1 = 0 pull_vec1 = pull_init1 = 0 pull_rate1 = 0 pull_k1 = 1000 pull_kB1 = On 07/02/2012 04:38 PM, Justin A. Lemkul wrote: > > On 7/2/12 4:30 PM, Laura Kingsley wrote: >> Just for clarification, the PMF is read from right to left and the force profile >> is read from left to right. >> > The dramatic change in the magnitude and sign of the force, coupled with the > steady increase in PMF, indicates to me that some elements of your system are > crashing into one another. In the absence of an accompanying explanation of > what you're doing (description of system, procedure with .mdp parameters, etc) > that's the best I can offer. > > -Justin > >> On 07/02/2012 04:27 PM, Kingsley, Laura J wrote: >>> Here is a link to both the PMF profile and the force profil
Re: [gmx-users] inquiry about SAS
On 7/3/12 10:49 AM, Turgay Cakmak wrote: Hi all, I am calculating SAS using g_sas of my system (several peptides in water and ions, Na and Cl). I choose: for calculation group: non-water for output group: protein (400 out of 750 atoms were classified as hydrophobic) When I plot the Area vs time graphs, both the hydrophobic-SAS and hydrophilic-SAS decrease over the time. I think, the reason of the hydrophobic-SAS decrease from 65 nm2 to 30nm2 is due to aggregation of the peptides. But, I couldn't understant why hydrophilic-SAS is decreasing from 40 nm2 to 20nm2 over time. Do the results make sense? Sure, you've got both hydrophobic and hydrophilic contacts happening. May be I mis-understand the meanings of the hydrophobic and hydrophilic SAS. Please, someone could explain it to me, I would be so glad. These are merely subdivisions of total SASA. Atoms are either polar (hydrophilic) or nonpolar (hydrophobic) and thus contribute to the total SASA based on their characteristics. -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 * 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] question to mdp file
On 7/3/12 8:25 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Ah okey. Yes sorry that was a typo...I ment nsteps. So but is there a possibility to define a minimal step size so that the minimization ends when the energy does not changes much any more? Just set emtol to some unreasonably low value, and mdrun will end with this message (which is not really an error): http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision You can set emstep to whatever size you like to reach this point. -Justin On 7/3/12 8:11 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, is it correct when I set the nstep = -1 and emtol = $number that the minimization goes as long as the energy difference between the previous step and this step is not lower as $number. And that there is no maximal stepsize? No. The value of emtol is the target for the maximum force to define convergence, not the difference between previous and current steps, and it's not an energy term, it's force. The maximum step size is always set in emstep. What's more, "nstep" is not a correct keyword, but "nsteps" is. -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 * 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 -- ============ 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 * 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] Umbrella - Force constant
On 7/3/12 8:41 AM, Steven Neumann wrote: Dear Gmx Users, Do you know or can you suggest some results based on the comparison of the force constant in Umbrell Sampling? Any literature? That would be lovely, but I've never seen such a thing. One could probably write a book with all the test cases that would be required. My gut tells me that you can't generalize too much in terms of pulling simulations - the approach depends on what is being pulled (small molecule, peptide, large protein), what the medium is (water, membrane, etc), and what the interacting partner is (protein surface, ion channel, binding pocket). As far as I understand when you use the same staring coordinates (from the same pulling simulation) for windows but you just change the force constant (e.g. from 500 to 2000 kJ/mol nm2) you should increase number of windows (for f=2000) as smaller force constant will cover wider neigboruring distances - that makes sense. I am curious whether the final result will be the same? I guess with stronger force it will converge faster but more windows are required. is it the only one difference? Without a systematic comparison, it's hard to say, but in theory if one samples sufficiently and has good overlap between neighboring windows, the results should converge to the same answer. If someone knows of some applicable literature that has done such comparisons, please post a reference. I'd love to see it. Most SMD and US methodology is written with hand-waving explanations as to what the authors did and why it worked, and I have a suspicion that most reviewers don't have a better idea so they can't refute such claims. -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 * 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] Implicit solvent setup for large protein
On 7/3/12 8:57 AM, Ramon Crehuet Simon wrote: Dear all, I know several questions about implict solvent have already been asked in this list. I think and hope the question I have has not been raised. Forgive me if I am wrong. I have read that all-to-all kernels are the best option when doing implicit solvent. Otherwise one should use large cutoffs. I wanto to simulate a tetramer which has more than 1200 residues. I'm afraid all-to-all interactions are much too expensive in this case. So I should use largecutoffs. My question is, how large? Or, to be more precise, what should I monitor to check the the cutoffs are large enough? As an extra questions, if I don't use all-to-all kernels, is it still worth using the GPU to accelerate the calculation? In my experience, using long cutoffs leads to unstable trajectories and very poor energy conservation. The all-vs-all kernels are the only ones I use for implicit calculations. -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 * 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] question to mdp file
On 7/3/12 8:11 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, is it correct when I set the nstep = -1 and emtol = $number that the minimization goes as long as the energy difference between the previous step and this step is not lower as $number. And that there is no maximal stepsize? No. The value of emtol is the target for the maximum force to define convergence, not the difference between previous and current steps, and it's not an energy term, it's force. The maximum step size is always set in emstep. What's more, "nstep" is not a correct keyword, but "nsteps" is. -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 * 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] mdrun no structural output
On 7/3/12 5:40 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I wanted to do a minimization with mdrun but the only output I get is: 3m71_minim.edr 3m71_minim.log 3m71_minim.trr But no structure file like .pdb i.e. There was no error in the step before where I prepared the input file with grompp. My .mdp file looks like this: define = -DPOSRES integrator = steep emtol = 10 nsteps = 5000 nstenergy = 1 energygrps = System coulombtype = PME rcoulomb= 0.9 rvdw= 0.9 rlist = 0.9 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 pbc = xyz And also in this step there was no error. The end of the 3m71_minim.log looks like this: Step Time Lambda 2647 2647.00.0 Energies (kJ/mol) Bond AngleProper Dih. Improper Dih. LJ-14 5.35530e+022.26340e+031.17875e+041.31106e+024.73257e+03 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip. Position Rest. 6.58188e+049.41710e+04 -7.10195e+05 -1.62296e+059.89235e+02 Potential Pressure (bar) -6.92062e+05 -3.32594e+03 And the stdout looks like this: Step= 2646, Dmax= 3.6e-03 nm, Epot= -6.92039e+05 Fmax= 5.12625e+03, atom= 1022 Step= 2647, Dmax= 4.3e-03 nm, Epot= -6.92098e+05 Fmax= 3.72457e+03, atom= 1022 Step= 2647, Dmax= 4.3e-03 nm, Epot= -6.92062e+05 Fmax= 1.51933e+03, atom= 1022 Step= 2648, Dmax= 5.2e-03 nm, Epot= -6.92099e+05 Fmax= 4.25221e+03, atom= 1022 Step= 2648, Dmax= 5.2e-03 nm, Epot= -6.92041e+05 Fmax= 6.45781e+03, atom= 1022 The command for the mdrun was: mpirun -n 2 $gromacsPath/mdrun_mpi -c $path/3m71_minim.pdb -compact -deffnm $path/3m71_minim -s $path/3m71_minim_ion.tpr -v 2>>$path/minLogErr 1>>$path/minLogOut Can you please tell me whats wrong? When EM is done, mdrun prints very clear messages indicating convergence (or lack thereof) with information about maximum force and potential energy. If you're not seeing this information, mdrun isn't done or somehow got killed or hung up. -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 * 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] bindng energy & H bond energy calculation
On 7/3/12 2:24 AM, Ravi Raja Merugu wrote: Dear all, Can any one help e regarding 1.) I want to find the binding energy of ligand with the protein , and Umbrella sampling or free energy calculations can determine binding energies. 2.) Hydrogen Bond energy of the protein ligand interactions (for H-bond ).. and This term will probably be related to electrostatic interactions, but I don't know of any way to directly extract a "hydrogen bonding energy" in a literal sense. Most force fields don't include such a term. 3 ) if possible H bond distances along the time scale(say 10ns). Is there any way g_dist and/or g_hbond 4 ) to measure the contribution of hydrophobic / philic interactions of the protein active site with ligands binding energy.. Free energy calculations, decoupling van der Waals and Coulombic terms separately, will tell you this information. 5) to calculate the distance between the residues(let say Tyr and Arg) in my protein. (Actually I want to check a key interaction between them) g_dist -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 * 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] problems with editconf
On 7/3/12 5:10 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I want to put my protein in the box with editconf but when I look at it it is always at the border of the box and not at the center. I tried it with those two commands: editconf -f 3m71.gro -o 3m71_box.gro -center 4.59340 4.59470 5.17330 -c -bt dodecahedron -d 1.0 2>>logErr 1>>logOut editconf -f 3m71.gro -o 3m71_box.gro -c -bt dodecahedron -d 1.0 2>>logErr 1>>logOut With the first command it is at the upper border and with the second command it is at the right border. The coordinates of the firs command are from the 3m71.gro file. Can you please tell me what is wrong? Nothing. When visualizing the unit cell, it will appear as a triclinic box with the protein in a seemingly random location. You can re-wrap the unit cell with trjconv -pbc mol -ur compact (which requires a .tpr file) to see the dodecahedral unit cell with everything placed as you would expect. -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 * 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] PMF trails off to infinity.
On 7/2/12 4:51 PM, Laura Kingsley wrote: Basically what I'm doing is pulling a ligand out of a protein towards a dummy atom, which has a mass of 1 and no charge. I've attached the a portion .mdp files for both the smd portion and the umbrella sampling. I know that the ligand gets very close possibly crashing into the dummy atom. So from what you're saying, I'm thinking this might be the source of the problem. Sounds like it to me. -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 * 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] PMF trails off to infinity.
On 7/2/12 4:30 PM, Laura Kingsley wrote: Just for clarification, the PMF is read from right to left and the force profile is read from left to right. The dramatic change in the magnitude and sign of the force, coupled with the steady increase in PMF, indicates to me that some elements of your system are crashing into one another. In the absence of an accompanying explanation of what you're doing (description of system, procedure with .mdp parameters, etc) that's the best I can offer. -Justin On 07/02/2012 04:27 PM, Kingsley, Laura J wrote: Here is a link to both the PMF profile and the force profile: http://s1064.photobucket.com/albums/u370/laurakingsley/?action=view¤t=pull_fig.jpg -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Monday, July 02, 2012 3:56 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] PMF trails off to infinity. On 7/2/12 3:53 PM, Laura Kingsley wrote: Basically what I'm doing is pulling a ligand toward a dummy atom. I pull the ligand until its COM is very close (a few angstroms) from the dummy atom. Could this be causing this behavior? What information would help? I'm having a tough Collisions between any elements of your system would explain the problem, if it looks like what I'm picturing in my head :) time getting the figures attached but may be I could email them directly to you? Let me know. Bullet point #4 here provides a suggestion: http://www.gromacs.org/Support/Mailing_Lists#Mailing_List_Etiquette -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 * 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] PMF trails off to infinity.
On 7/2/12 3:53 PM, Laura Kingsley wrote: Basically what I'm doing is pulling a ligand toward a dummy atom. I pull the ligand until its COM is very close (a few angstroms) from the dummy atom. Could this be causing this behavior? What information would help? I'm having a tough Collisions between any elements of your system would explain the problem, if it looks like what I'm picturing in my head :) time getting the figures attached but may be I could email them directly to you? Let me know. Bullet point #4 here provides a suggestion: http://www.gromacs.org/Support/Mailing_Lists#Mailing_List_Etiquette -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 * 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] PMF trails off to infinity.
On 7/2/12 9:54 AM, Laura Kingsley wrote: Hello, I am using steered MD and umbrella sampling to generate a PMF profile for pulling a small ligand 3 nm. As I pull the ligand from 3A toward 0 A, the PMF starts a dramatic uphill climb. This does not agree with the force profile which seems to level out. Any ideas about what might be going wrong here? I am thinking this probably isn't correct, but I don't know where I've messed up. Thanks! I can attach the graphs if necessary. We'll probably need a better description of what you're doing, along with any applicable figures. It sounds to me like your ligand is crashing into something in your system, but that's just a guess based on incomplete information. -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 * 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] charmm36 parameters
HBL 1 1.0080000.10A 0.235197261589 0.092048 ; Not in C27 CCL 6 12.011000.34A 0.356359487256 0.29288 ; Not in C27 CL 6 12.011000.90A 0.356359487256 0.29288 CTL16 12.011000.14A 0.405358916754 0.08368 CTL26 12.01100-0.18 A 0.358141284692 0.234304 CTL36 12.01100-0.27 A 0.363486677001 0.326352 CTL56 12.01100-0.35 A 0.367050271874 0.33472 CEL16 12.01100-0.15 A 0.372395664183 0.284512 CEL26 12.011000.000 A 0.370613866746 0.267776 ; partial charge def not found OBL 8 15.999400 -0.52 A 0.302905564168 0.50208 OCL 8 15.999400 -0.76 A 0.302905564168 0.50208 O2L 8 15.999400 -0.78 A 0.302905564168 0.50208 OHL 8 15.999400 -0.66 A 0.315378146222 0.6363864 OSL 8 15.999400 -0.49 A 0.293996576986 0.4184 ; Different to C27 OSLP8 15.999400 -0.57 A 0.293996576986 0.4184 ; Not in C27 NH3L7 14.00700-0.30 A 0.329632525712 0.8368 NTL 7 14.00700-0.60 A 0.329632525712 0.8368 SL 16 32.06 1.33A 0.374177461619 1.96648 PL 15 30.974000 1.50A 0.38308644882.44764 ; The following atom types are NOT part of the CHARMM distribution ; atomtypes for additional water models #ifdef HEAVY_H OWT38 9.951400-0.834 A 3.15058e-01 6.36386e-01 ; TIP3p O HWT31 4.0320000.417 A 0.0 0.0 ; TIP3p H OWT48 9.9514000.0 A 3.15365e-01 6.48520e-01 ; TIP4p O HWT41 4.0320000.52A 0.0 0.0 ; TIP4p H MWT40 0.00-1.04 A 0.0 0.0 ; TIP4p vsite OWT58 9.9514000.0 A 3.12000e-01 6.69440e-01 ; TIP5p O HWT51 4.0320000.241 A 0.0 0.0 ; TIP5p H MWT50 0.00-0.241 A 0.0 0.0 ; TIP5p vsite OW 8 9.951400-0.82 A 3.16557e-01 6.50194e-01 ; SPC 0 HW 1 4.0320000.41A 0.0 0.0; SPC H #else OWT38 15.999400 -0.834 A 3.15058e-01 6.36386e-01 ; TIP3p O HWT31 1.0080000.417 A 0.0 0.0 ; TIP3p H OWT48 15.999400 0.0 A 3.15365e-01 6.48520e-01 ; TIP4p O HWT41 1.0080000.52A 0.0 0.0 ; TIP4p H MWT40 0.00-1.04 A 0.0 0.0 ; TIP4p vsite OWT58 15.999400 0.0 A 3.12000e-01 6.69440e-01 ; TIP5p O HWT51 1.0080000.241 A 0.0 0.0 ; TIP5p H MWT50 0.00-0.241 A 0.0 0.0 ; TIP5p vsite OW 8 15.999400 -0.82 A 3.16557e-01 6.50194e-01 ; SPC O HW 1 1.0080000.41A 0.0 0.0 ; SPC H #endif ; special dummy-type particles MNH30 0.000.00A 0.0 0.0 MNH20 0.000.00A 0.0 0.0 MCH30 0.000.00A 0.0 0.0 MCH3S 0 0.000.00A 0.0 0.0 ; Ions and noble gases (useful for tutorials) Cu2+29 63.546002.00A 2.08470e-01 4.76976e+00 Ar 18 39.948000.00A 3.41000e-01 2.74580e-02 ; Added by DvdS 05/2005 copied from GROMACS force field. SI 14 28.080000.00A 3.38550e-01 2.44704e+00 -- ==== 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 * 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] number of contact
On 7/2/12 8:18 AM, Turgay Cakmak wrote: Dear all, Does the "number of contact calculated by g_mindist" mean that interaction between two groups? If so, could you kindly check the reliability of the case I have written below. If the atoms are in contact within a given cutoff distance, then you can pretty safely assume they are interacting (provided the cutoff is not exorbitantly long, but 0.4 nm seems reasonable). -Justin I have 10 peptides (5 of them are X-peptide and 5 of them are Y-peptide) in a box filled with water. After MD simulation (production run), I saw all the peptides come together. Now, in order to understand whether hydrophobic forces are important for this aggregation or not, I calculated number of contacts between 2 index groups (First group consist of hydrophobic residues (FFAA) belong to X-peptide and second group again consist of hydrophobic residues (FFAA) belong to Y-peptide) using the following command; g_mindist -f .xtc -s .tpr -n .ndx -on -d 0.4 Then, when I looked the number of contact versus time graph, there is an increase in the number of contact over time. (I think this makes sense in the aggregation case.) Thanks in advance, Turgay -- ==== 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 * 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] Re: COM Pulling
On 7/1/12 12:02 AM, Raj wrote: Dear Justin, I've tried what you have suggested. I have used the pull code and gave 4 amino acid residues as a reference group. The location of the groups are one below the ligand (in the protein core) and 3 were on the above ( towards the active site gorge). When i used the code This sounds like a poor approach. If you have some residues that are internal and some that are external, mdrun won't do any productive pulling. Define one group in a concerted area as a reference group and pull with respect to it to move the ligand. -Justin pull = umbrella pull_geometry = distance ; simple distance increase pull_start = yes ; define initial COM distance > 0 pull_ngroups= 1 pull_group0 = DRG pull_group1 = reference groups pull_rate1 = 0.003 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 1000 ; kJ mol^-1 nm^-2 the ligand migrated more and more towards the protein , not coming out of the protein through the channel i defined by referring the amino acid groups when I tried with pull_geometry = position, the pull_vec i gave as 0 0 1 and pull_initial = 0.1 but the grompp ends up with an error saying pull_vec can not be zero. when i was trying to use pull_geometry = direction the system blowed up. but the pull_geometry = distance worked well. please give me a suggestion to resolve the issue -- View this message in context: http://gromacs.5086.n6.nabble.com/COM-Pulling-tp4998944p4998989.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- ======== 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 * 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] Berger lipid
On 6/30/12 11:03 AM, Shima Arasteh wrote: Thanks Justin. Yes, you are right. You wrote the tutorial for DPPC and I know that. ok, I saw the temperatures upper than 271 K is proper for POPC. It's acceptable that 310 mentioned in Peter's paper is correct. But I'm wondering how they chose "310" K? In his article, he explains that their study was done in mammalian cells. 310 K is physiological temperature for the human body. Peter, please correct me if this was not the intent of your study. -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 * 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] Berger lipid
On 6/30/12 10:33 AM, Shima Arasteh wrote: Dear Peter, Thanks for your link and the article. I'd like to know more about your paper. You've mentioned in it that the temperature of POPC equilibrated, is 310 K. As I saw in Justin's tutorial , 323 K is proper, however it was a I'll let Peter address the question directed to him, but I want to refute something stated here. One should not say that for membrane simulations "323 K is proper." I explain in the tutorial why this particular temperature is used in the context of DPPC only. I also provide a table of phase transition temperatures for several lipids to explain the reason why the elevated temperature was required in this case. -Justin different system simulated and also many parameters are not the same as your system . Would you telling me about the reason of 310 K? Thanks in advance Sincerely, Shima - Original Message - From: Peter C. Lai To: Shima Arasteh ; Discussion list for GROMACS users Cc: Sent: Friday, June 29, 2012 2:54 PM Subject: Re: [gmx-users] Berger lipid yes http://www.frontiersin.org/Bioinformatics_and_Computational_Biology/10.3389/fgene.2012.00061/abstract The files are here: http://uab.hyperfine.info/~pcl/files/popc36/ On 2012-06-28 09:58:26PM -0700, Shima Arasteh wrote: Yes, I remember now...you are right :) But I didn't know the linked you sent me, was your own output! However I wanted to know if it is necessary to produce the .itp file on my own or not. I still have this link, so will cite to you. It would be a good idea to see its package in lipidbook too. Thanks Peter Sincerely, Shima From: Peter Lai To: Discussion list for GROMACS users Sent: Friday, June 29, 2012 7:14 AM Subject: RE: [gmx-users] Berger lipid Uh didn't we go through all of this like more than a month ago? I published a paper using C36 POPC and even a linked to my popc.itp for it on this list... Of course Shima is welcome to pdb2gmx his own POPC, which I am fairly certain will result in an identical file... Lipidbook seems to only have C36 POPE. I guess maybe I will upload ours. From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Thursday, June 28, 2012 7:56 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Berger lipid On 6/28/12 8:54 PM, Shima Arasteh wrote: Yes, I know that as studied the Kalp15 tutorial. Sorry, the last question :) : DO I need to run pdb2gmx to get the top file of POPC in CHARMM36? Is it ok? Because I see that POPC.itp is also required for simulation of protein in bilayer. You need a topology of some sort. It depends on what parameters you have on hand. If you do not have popc.itp from anywhere, then you need to generate it somehow. If it is present in the .rtp file for CHARMM36 that you have, then you can run pdb2gmx on it. -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 * 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 mailing list gmx-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 mailing list gmx-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 -- 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
Re: [gmx-users] Re: .top file incoherent with the values in the ffbonded.itp file
On 6/29/12 6:10 PM, sreeta.g wrote: Hi Justin I have changed all the force field parameters as below, (I have already shown my ffbonded.itp file) ffnonbonded.itp ; name bond_typemasscharge ptype sigma epsilon opls_966 CA612.01100 0.240 A3.5000e-01 3.3600e-01 opls_967 CA612.01100 0.180 A3.5000e-01 3.3600e-01 opls_968 HB1 11.00800 0.060 A2.5700e-01 2.1000e-01 opls_969 HB2 11.00800 0.060 A2.5700e-01 2.1000e-01 opls_970 HB3 11.00800 0.060 A2.5700e-01 2.1000e-01 opls_971 HA1 11.00800 0.060 A2.5700e-01 2.1000e-01 opls_972 HA2 11.00800 0.060 A2.5700e-01 2.1000e-01 atomname2type.n2t Copls_136-0.120 12.011 4C 0.153 H 0.11H 0.110 H 0.110 Copls_966 0.240 12.011 4C 0.153 H 0.11H 0.110 O 0.143 Copls_135-0.180 12.011 4C 0.153 H 0.11H 0.110 H 0.110 Oopls_154-0.700 15.999 2C 0.143 H 0.097 aminoacid.rtp [ Pva ] [ atoms ] ; see atomtypes.atp for explainations CBopls_136 -0.120 1 HB1 opls_968 0.060 1 HB2 opls_969 0.060 1 CAopls_966 0.240 2 . (contd) so I have maintained consistency in my atom types in the ffbonded.itp files. When I am running Grompp, it gives 7988 errors and I have 9088 atoms in my polymer chain. All the errors mentioned are No default Ryckaert-Bell. types, which I explained to you in my first mail. So I am still unsure as to what my problem is and how I should deal with it. The only way to diagnose the problem is to check your self-consistency. Probably most of the errors are redundant. Choose one of them (it tells you the line where the error occurs), write down the atom numbers involved and then look up which atom types (not names) to which these numbers pertain. That is the missing interaction type that needs to be defined in ffbonded.itp. I can't tell what's wrong based on the snippets of files shown. You can, based on having a very careful look through all of your files. -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 * 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] error with grompp
On 6/29/12 5:38 PM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi Justin, yes I removed all the old resulting files and did everything again. So now there is the topology and coordinate file with only NA and CL and not NA+ or CL-. I also checked whether the molecules are listed in the same order as in the .gro file and it is the case. So that is also correct. What do you mean with: What does your [molecules] directive specify? My [molecules] part in the topology file looks like this: [ molecules ] ; Compound#mols Protein_chain_A 1 DUM 20088 SOL 13428 NA 29 CL 29 I see no reason this would not work. However, I just noticed from your previous message: ; Include water topology #include "amber03.ff/tip3p.itp" ; Include topology for ions #include "amber03.ff/ions.itp" #include "amber03.ff/spc.itp" #include "amber03.ff/dum.itp" You're using two different water models, so things are getting overridden there. With AMBER03, you should be using TIP3P, not SPC. The conflicting water models suggest you've made manual modifications to the topology. Perhaps there is some error as a result. -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 * 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] Re: .top file incoherent with the values in the ffbonded.itp file
On 6/29/12 4:44 PM, sreeta.g wrote: Hi Justin Thank you for your reply. However, when I am using the grompp command, the topol.tpr file is not being formed due to a fatal error. This fatal error is the cumulative of ' No default Ryckaert-Bell.' types for many atoms in the polymer chain. And as I suggested before, you should investigate which lines are causing complaints to diagnose why grompp is failing. Also, regarding the comment on the atom types and atom names, I have tried Google searching to find the difference, but in vain. An atom name is an arbitrary label. An atom type is a designator that supplies various nonbonded parameters (listed in the [atomtypes] directive of ffnonbonded.itp. The files you posted before seem to define your bonded parameters based on the names present in the coordinate file. This is an incorrect approach. Refer to existing force fields and the manual for examples. -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 * 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] .top file incoherent with the values in the ffbonded.itp file
On 6/29/12 3:55 PM, sreeta.g wrote: Hello My A.gro file is: 1PvB CB1 3.109 2.784 0.803 0. 0. 0. 1PvBHB12 3.156 2.880 0.843 0. 0. 0. 1PvBHB23 2.997 2.797 0.819 0. 0. 0. 1PvBHB34 3.129 2.765 0.693 0. 0. 0. 1PvB CA5 3.173 2.673 0.879 0. 0. 0. ... (contd.) My ffbonded.itp file has: [ bondtypes ] ; ij func b0(bond length) kb (force const) CBHB1 10.11 284512 CBHB2 10.11 284512 CBHB3 10.11 284512.0 ... (contd) [ angletypes ] ; i jk func th0cth HOOH CA1 105320 CACB CA1 109.45 482.3 CBCA CB1 109.45 482.3 OHCA CB1 107.8 460 ... (contd) [ dihedraltypes ] ; ijkl funcRB coefficients OH OH CA CB3 3.09.0 0.0 -12.0 0.0 0. ; CA CB CA CB3 5.75000 17.25000 0.0 -23.0 0.0 0. ; . (contd) However, my topol.top file looks like this: [ bonds ] ; aiaj functc0c1c2c3 1 2 1 1 3 1 1 4 1 1 5 1 112 1 (contd) [ angles ] ; aiajak functc0c1c2 c3 2 1 3 1 2 1 4 1 2 1 5 1 2 112 1 3 1 4 1 3 1 5 1 . (contd) [ dihedrals ] ; aiajakal functc0c1c2 c3c4c5 2 1 5 6 3 2 1 5 7 3 3 1 5 6 3 3 1 5 7 3 4 1 5 6 3 4 1 5 7 3 ... (contd) I have two issues: 1) I have mentioned the bond lengths and bond constants in the [bondtypes] and [angletypes ]directory of the ffbonded.itp file, however in the [bonds] [ angles ]directory in the topol.top file the Ryckaert-Bellemans coefficients are used, which are assigned as blanks. This is giving the error No default Ryckaert-Bell. types (multiple times). The "blanks" in the topology are totally normal. When assembling the .tpr file, grompp will look up the appropriate values in ffbonded.itp that match with the atom types it finds. If you are getting errors about missing parameters, you have failed to assign some interaction type. The error message should contain the offending lines. Note, too, that the parameters specified in ffbonded.itp are assigned by atom *type* and not atom *name* - perhaps this is the origin of your problem. 2) Also, the RB coefficients mentioned in the [dihedraltypes] of the ffbonded.itp are not used in the [dihedrals] directory of the topol.top file. This is again writing blanks for the RB coefficients. What is the issue and why is my topl.top file inconsistent with the inputs given in the ffbonded.itp file? The blanks are normal; see above comments. -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 * 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] pdb file of polymer
On 6/29/12 2:21 PM, Parvez khan wrote: Hi, I am trying to do polymer simulation with gromacs. I am new to gromacs and trying to construct topology for a system of polymer chains. My problem is that i am facing difficulties to creat pdb file for polymer chain containing 1000 monomers. I have used PRODRG server but it gives me a pdb and topology file up to maximum 41 monomers chain. I am not understanding what wrong with PRODRG server. Is there Nothing is wrong. It's just that PRODRG limits how many atoms are allowed in the input structure. any server or tool for generating db file. There are lots of ways to generate a coordinate file. Here are some suggestions: http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources -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 * 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] Structure optimization failure
On 6/29/12 11:10 AM, massimo sandal wrote: On 29 Jun 2012 15:09, "Justin A. Lemkul" mailto:jalem...@vt.edu>> wrote: > > > > On 6/29/12 9:04 AM, massimo sandal wrote: >> >> >> On 29 Jun 2012 14:08, "Justin A. Lemkul" mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> >> >> > >> > The settings in my tutorial are for use with OPLS-AA and are thus not >> suitable for a simulation with CHARMM. Cutoffs and other aspects will be different. >> >> This is interesting. In general, where can you find optimal mdp settings for >> each force field? >> > > By reading the primary literature for how each force field was derived. The parameters are only guaranteed to work within the context of correct cutoffs, electrostatic schemes, neighborlist update interval, water model used, etc. Some older force fields have been demonstrated to work well with PME even if originally derived with RF or some other method, but generally the other settings must adhere to the original parameterization. Some force fields can be very sensitive to these incorrect settings. > > Yes, I know, but I hoped someone could have put a table online or wrote a book chapter somewhere about this. Wouldn't it be nice to create a table of "standard settings" for each forcefield in the gmx documentation (with lit references of course)? Well, anyone is welcome to submit anything they feel would be useful... ;) I have considered this in the past, but have rejected the thought every time it comes to mind. It would be nice if there was a central repository of such parameters, but then likely a simulation becomes "do this, not that" with no required thought from the end user. If you make simulations a black box, everyone expects them to automatically work without fail. The other objection I have always had is the continual improvement of the field. If Gromacs puts out an "official" or "standard" list of what to do, it is always subject to change and then becomes incumbent upon a Gromacs contributor to verify its accuracy frequently. My personal fear is that this becomes an untenable task. Then in the case of an error, someone's whole Ph.D. could go out the window... In the end, I think it's always safe to ask the user to do a bit of legwork to understand the force field he or she wishes to use. The knowledge gained from an hour of reading will save a lot of potential headaches. I would reject any attempt to include such information in the manual (lest its settings become "official"), but if someone wants to put up a wiki page on the website with clear warnings and disclaimers, they are welcome to do so. Just my $0.02. -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 * 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] problem with git/4.6
On 6/29/12 11:08 AM, Michael Brunsteiner wrote: You should have it. In CMakeLists.txt, PROJECT_VERSION should be set to "4.6-dev" so you can check that. ithat what i looks like ... i now get: prompt> mdrun_d [...] :-) VERSION 4.6-dev-20120629-9c6be1c (-: [...] which gives me: g_bar_d -f mdv*.xvg -b 100 [...] total 0.000 - 1.000, DG -9.00 +/- 0.15 with vanilla 4.5.5 i get: g_bar_d -f mdv*.xvg -b 100 [...] total 0.000 - 1.000, DG -9.00 +/- 0.15 there's two points: 1) this value is fine, as, once combined with the coulomb part, it is very close to literature and exptl data. however, in both cases get this warning ... Second Law of Thermodynamics etc... and riduculously high s_B values at lambda=0. This indeed sounds like a bug worth fixing since it is present in the release-4-6 branch. 2) the reason i saw different DeltaG values earlier was that i had included (by mistake) the dhdl file from a single additional window at lambda=0 that was produced with exactly the same input apart from the value of 0.3 (instead of 0.5) for sc_sigma ... as far as i understand things (not very well perhaps) the resulting free energy difference should NOT depend on this parameter ... so neither should the result of g_bar ... but maybe it does when using foreign lambdas as i did here ? if this is so it might be a good idea making g_bar read tpr files to give a warning in such a case ... Whether or not sc_sigma has an effect depends on the topology. If you change the value, you can change the result of the calculation. g_bar has no need to read .tpr files, so I doubt it would be very useful to include them as an additional input. i guess for now i'll wait for a stable 4.6 - any ideas when this will be there? No clue. Maybe a few weeks, maybe not. There are several very large changes being put in place. But note that if you're getting the same error with the development version of the free energy code, you're likely to see the exact same thing in the 4.6 release. The free energy code merge is considered done and ready for production. If this is not the case, a bug report needs to be filed ASAP. Please submit a report at redmine.gromacs.org with a minimal test case. -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 * 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
