Re: [gmx-users] Question about documentation of -a switch in g_hbond
On 11/06/2012 12:41 AM, Justin A. Lemkul wrote: On 6/10/12 10:36 AM, Andrew DeYoung wrote: Greetings, This might end up being a silly/embarrassing question, and if so, I apologize. I feel like I may be making a conceptual mistake, but I'm not sure. Is it true that a hydrogen bond is of the following form? Donor---Hydrogen ... Acceptor Is this the correct order? I think so. For example, in my system, I have: Oxygen---Hydrogen ... Fluorine In the documentation, the -a option has this description: Cutoff angle (degrees, Acceptor - Donor - Hydrogen) Why is the order Acceptor - Donor - Hydrogen (or, equivalently, Hydrogen - Donor - Acceptor)? Why isn't Hydrogen instead between Donor and Acceptor? Which angle does -a specify? Because it's easy to define from an algorithmic standpoint. A hydrogen bond is stronger depending on how close to linearity it is. Measuring an acute angle given by -a says that if the A-D-H angle is less than 35 degrees, you can vary between 0 and 35 easily to show the same thing as being within a certain range of being 180 degrees in terms of D-H-A. The component of H-bond detection based on the cut-off angle is not implemented as a cut-off in angle space, but rather in the space of the cosine of the angle. Cosines are easily computed using the inner product of the vectors that form them. There's no real advantage to computing cos(A-D-H) vs cos(D-H-A) because in either case you just compare the value in the appropriate sense with the appropriate value of the (signed) cos(acutoff). Defining the H-bond in terms of A-D-H has the advantage that if you later want to consider the angle distribution, the relevant (signed) angle range is centered around zero degrees. D-H-A would have a cluster below 180 and a cluster above -180, which is less convenient to deal with. For a given r(D-H), you can define the set of legal H-bond positions equivalently from either A-D-H or D-H-A, of course. Since r(D-H) is often constant for MD simulations, the conceptual difference between the definitions becomes moot. In neither case do you want to compute the angle with acos later, because the numerical accuracy of acos is poor around 0 and +/-180 from its near-linearity. Unfortunately g_hbond does do this, so I think I'll patch it. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] LINCS warnings
Hi Gromacs Friends .. I am trying to simulate octa-peptide in water model spc using G96 53a6 force field. my aim is to study the self assembly nature of these octapetide. I did following type of arrangment. I make antiparrallel arrangment of four peptide with distance of 0.5 nm in y direction, Then I translate these layer in z direction, Such that separation in each layer is 0.5 , I arranged six layer in Z direction(total 24 peptide 6 * 4=24 ), I did Steepest Descent Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 100 Double precision normally gives you higher accuracy. writing lowest energy coordinates. Steepest Descents converged to machine precision in 108 steps, but did not reach the requested Fmax 100. Potential Energy = -9.2318734e+04 Maximum force = 6.8985820e+04 on atom 1359 Norm of force = 9.8921991e+02 For nvt run I got Lincs Error Step 772, time 1.544 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.001014, max 0.009497 (between atoms 1360 and 1358) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 1359 1358 61.40.1000 0.1004 0.1000 Step 773, time 1.546 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.003091, max 0.027499 (between atoms 1359 and 1358) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 1360 1358 32.10.0991 0.0985 0.1000 1359 1358 90.00.1004 0.1027 0.1000 --- Program mdrun, VERSION 4.5.4 Source code file: /build/buildd/gromacs-4.5.4/src/mdlib/constr.c, line: 176 Fatal error: Too many LINCS warnings (1001) If you know what you are doing you can adjust the lincs warning threshold in your mdp file or set the environment variable GMX_MAXCONSTRWARN to -1, but normally it is better to fix the problem For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Carry Me Away (Motors) When I check the website at http://www.gromacs.org/Documentation/Errors I come to know that system is unstable or not properly energy minimised (e+04) is the source for such type of errors. But Truly I dont Want to change the arrangment (distance 0.5 nm), Please Help me to solve the above problem, All suggestion are welcome With Best Wishes, Rama David -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: md.log i/o error in futil.c +459
On 10/06/2012 5:50 PM, Inon Sharony wrote: Hi Mark! Thanks for the response. Just to follow up, the problem was that another program was deleting md.log before it could be accessed. This is entirely not the fault of GROMACS, however a more descriptive error message could have saved us some time (e.g. md.log not found as opposed to md.log could not be opened instead of file i/o error). Also, I still don't understand under which directory futil.c is located. I would check whether this file outdated and change the error message accordingly if it is. Thanks for the thought. One problem is that there are a wide range of circumstances that can provoke the conditions that mdrun detected in your case, e.g. missing file, network file system unavailability, invalid file permissions. At least some of those can be transient, also, so any detective work mdrun might do subsequent to an I/O failure might be inaccurate, or depend on details of the OS and file system in use. Unfortunately, GROMACS developers don't have the time to write and test code that can deal with all possible such contingencies, so the burden of solving the problem is pushed to those who know the most about their local conditions. This lets the GROMACS devs spend more time doing what they do best :-) Free software will be imperfect - and software for which you paid money is rarely fully satisfactory either! Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] LINCS warnings
On 11/06/2012 4:38 PM, rama david wrote: Hi Gromacs Friends .. I am trying to simulate octa-peptide in water model spc using G96 53a6 force field. my aim is to study the self assembly nature of these octapetide. I did following type of arrangment. I make antiparrallel arrangment of four peptide with distance of 0.5 nm in y direction, Then I translate these layer in z direction, Such that separation in each layer is 0.5 , I arranged six layer in Z direction(total 24 peptide 6 * 4=24 ), I did Steepest Descent Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 100 Double precision normally gives you higher accuracy. writing lowest energy coordinates. Steepest Descents converged to machine precision in 108 steps, but did not reach the requested Fmax 100. Potential Energy = -9.2318734e+04 Maximum force = 6.8985820e+04 on atom 1359 Norm of force = 9.8921991e+02 For nvt run I got Lincs Error Step 772, time 1.544 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.001014, max 0.009497 (between atoms 1360 and 1358) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 1359 1358 61.40.1000 0.1004 0.1000 Step 773, time 1.546 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.003091, max 0.027499 (between atoms 1359 and 1358) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 1360 1358 32.10.0991 0.0985 0.1000 1359 1358 90.00.1004 0.1027 0.1000 --- Program mdrun, VERSION 4.5.4 Source code file: /build/buildd/gromacs-4.5.4/src/mdlib/constr.c, line: 176 Fatal error: Too many LINCS warnings (1001) If you know what you are doing you can adjust the lincs warning threshold in your mdp file or set the environment variable GMX_MAXCONSTRWARN to -1, but normally it is better to fix the problem For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Carry Me Away (Motors) When I check the website at http://www.gromacs.org/Documentation/Errors I come to know that system is unstable or not properly energy minimised (e+04) is the source for such type of errors. But Truly I dont Want to change the arrangment (distance 0.5 nm), That force is likely too large for comfort. Something is unhappy such that you're seeing http://www.gromacs.org/Documentation/Terminology/Blowing_Up, and there are diagnostic strategies on that page. In particular, you must ensure you can simulate a single peptide successfully before you worry about doing more than one. Mark http://www.gromacs.org/Documentation/Terminology/Blowing_Up -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Regarding minim.mdp file.
On 11/06/2012 4:58 PM, Seera Suryanarayana wrote: Dear all gromacs users, i am running md using gromacs software.I want to down load minim.mdp file for creating a em.tpr file.But i don't know where i can get this file and how to download this file. There is no magic source for these. You have to design the contents of these files just as carefully as an experimental scientist designs an experiment. You can get some general guidance from the .mdp files available in all the tutorials you have done, but there is no substitute for reading about the algorithms and .mdp options in the GROMACS manual. You should attempt to replicate some appropriate published methodology before making choices of your own. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] LINCS warnings
Hi MARK, Thank you to your Quick reply, Please accept my apology for incomplete information... I did simulationm of single, Double and four peptide.. I also tried following I make antiparrallel arrangment of four peptide with distance of 0.4 nm in y direction, Then I translate these layer in z direction, Such that separation in each layer is 0.4 , I arranged eight layer in Z direction(total 24 peptide 8 * 4=32 ), All things was right. Thank you in Advance With Best Wishes, Rama David -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Rhamnose on 53a6
Hello again fellow gromacs users. I am looking to model a glucose-rhamnose disaccharide using the 53a6 forcefield. I wanted to take a look at the naming conventions for carbohydrates but I'm battling to find anything in the pdb2gmx force field files. I downloaded a package of force fields from the GROMOS website to get an idea about naming conventions for carbohydrates and couldn't see any mention of rhamnose anywhere. (allose, altrose, glucose, mannose, gulose, idose, galactose and talose are mentioned but no rhamnose). Does anyone have any information on naming conventions for rhamnose or whether or not rhamnose was ever present in this force field? Regards Marc -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] LINCS warnings
On 11/06/2012 5:49 PM, rama david wrote: Hi MARK, Thank you to your Quick reply, Please accept my apology for incomplete information... I did simulationm of single, Double and four peptide.. I also tried following I make antiparrallel arrangment of four peptide with distance of 0.4 nm in y direction, Then I translate these layer in z direction, Such that separation in each layer is 0.4 , I arranged eight layer in Z direction(total 24 peptide 8 * 4=32 ), All things was right. Well you'll have to follow the kind of advice in the diagnostic section of the link I gave last time. Since your topology is apparently sound, the initial conditions are likely suspect. Be sure you have visualized them, and that the box around them is definitely big enough. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] parameters for bond types for GROMOS force field.
Justin 1) So if I understood correctly I can make parametrisation of my uncommon group by the atb for instance. Than I can change itp file to rtp form and integrate this new residue to the existing ff. Finally when I will run pdb2gmx on the protein with the same group (even with different atom order) I obtain proper topology.top file. Doest it correct ? 2) I've defined bond between both of my atoms as the gb_15 and define this atoms as the C in the topology.top. Than I've run minimisation and short 3ns MD_run. Unfortunatelly this atoms was in the sp3 form and were not in the planar form :( What else should I do ? Could some operations with the angle term in topology.top help me? I've modified 612 613 614 2 as thega_27 but it also could not help me. James 2012/6/10 Justin A. Lemkul jalem...@vt.edu On 6/10/12 8:03 AM, James Starlight wrote: Justin, thanks again for help. Finally is there any generall solution to parametrise hetero-groups covalently bonded with the protein ? Many proteins consist of such groups e.g chromophore in GFP, retinall in rhodopsin as well as some prostetic groups in the enzymes. Parameterization schemes differ across force fields. It's never easy. I've tried to make something like you've told me via inclusion of pre-parametrised residues in the existing gromacs ff but forced with some problems due to the atom order in new ITP and gro files provided by ATb or PRODRG are different from initial pdb file so pdb2gmx on the whole protein where het-group in the old order would not work properly :( The output .itp files of ATB or PRODRG are not what you should be using. You can't #include a covalently attached residue and expect the resulting dynamics to be relevant; it's not like a ligand. What you need to do in those cases is create an .rtp entry (and any other incidental bonded and nonbonded additions, as stated before) that specifies whatever parameters you believe to be reliable. At that point, when the .rtp file is read, the atom order is irrelevant - if pdb2gmx finds the atoms it needs, it builds the topology. -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Rhamnose on 53a6
On 11/06/2012 6:11 PM, Marc Gordon wrote: Hello again fellow gromacs users. I am looking to model a glucose-rhamnose disaccharide using the 53a6 forcefield. I wanted to take a look at the naming conventions for carbohydrates but I'm battling to find anything in the pdb2gmx force field files. Not all force fields support sugars and even if they do, their (full) conversion to GROMACS can be dependent on someone taking the time to do so. I downloaded a package of force fields from the GROMOS website to get an idea about naming conventions for carbohydrates and couldn't see any mention of rhamnose anywhere. (allose, altrose, glucose, mannose, gulose, idose, galactose and talose are mentioned but no rhamnose). Does anyone have any information on naming conventions for rhamnose or whether or not rhamnose was ever present in this force field? That sounds like a question you should answer by reading the GROMOS force field literature. If you'll have to make a topology yourself, you'll have to read those anyway. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding .mdp files.
Dear all gromacs users, While i am running the commond mdrun -v -deffnm em iam getting the following error. Fatal error: Domain decomposition does not support simple neighbor searching, use gridsearching or use particle decomposition. kindly tell me how to overcome. Suryanarayana Seera, JRF, India. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] parameters for bond types for GROMOS force field.
On 11/06/2012 6:12 PM, James Starlight wrote: Justin 1) So if I understood correctly I can make parametrisation of my uncommon group by the atb for instance. Than I can change itp file to rtp form and integrate this new residue to the existing ff. Finally when I will run pdb2gmx on the protein with the same group (even with different atom order) I obtain proper topology.top file. Doest it correct ? The change to which you refer will be non-trivial because of the covalent bond. Charge distribution and atom types will change. 2) I've defined bond between both of my atoms as the gb_15 and define this atoms as the C in the topology.top. Than I've run minimisation and short 3ns MD_run. Unfortunatelly this atoms was in the sp3 form and were not in the planar form :( What else should I do ? Could some operations with the angle term in topology.top help me? I've modified 612 613 614 2 as thega_27 but it also could not help me. It is possible to hack something that will work, but the transferability of charges from an isolated form to a form covalently bound to a peptide is (at best) doubtful. If your atomic arrangement is changing, the presence of single vs double bonds must be changing, and that should basically guarantee non-transferability. The most correct form of a solution is to parameterise the modified form of the residue along the same lines as the original force field parameterization. That may or may not be feasible for you. It's hard to be more specific without knowing exactly what modified residue you are seeking to create. Mark James 2012/6/10 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu On 6/10/12 8:03 AM, James Starlight wrote: Justin, thanks again for help. Finally is there any generall solution to parametrise hetero-groups covalently bonded with the protein ? Many proteins consist of such groups e.g chromophore in GFP, retinall in rhodopsin as well as some prostetic groups in the enzymes. Parameterization schemes differ across force fields. It's never easy. I've tried to make something like you've told me via inclusion of pre-parametrised residues in the existing gromacs ff but forced with some problems due to the atom order in new ITP and gro files provided by ATb or PRODRG are different from initial pdb file so pdb2gmx on the whole protein where het-group in the old order would not work properly :( The output .itp files of ATB or PRODRG are not what you should be using. You can't #include a covalently attached residue and expect the resulting dynamics to be relevant; it's not like a ligand. What you need to do in those cases is create an .rtp entry (and any other incidental bonded and nonbonded additions, as stated before) that specifies whatever parameters you believe to be reliable. At that point, when the .rtp file is read, the atom order is irrelevant - if pdb2gmx finds the atoms it needs, it builds the topology. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Regarding .mdp files.
On 11/06/2012 6:21 PM, Seera Suryanarayana wrote: Dear all gromacs users, While i am running the commond mdrun -v -deffnm em iam getting the following error. Fatal error: Domain decomposition does not support simple neighbor searching, use gridsearching or use particle decomposition. kindly tell me how to overcome. As I said last time, there is no substitute for reading about the algorithms and .mdp options in the GROMACS manual. The above is an easy issue to read about and resolve - if you can't or won't do that, then you will face insurmountable barriers later. More, you will have exhausted the patience of people who might help you, because they have seen you make dozens of posts that make it easy to suppose that you are not trying to do background reading in order to learn enough to be able to solve your own problems. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding error.
Dear Justin sir, I am simulating a protein 1AKI.pdb which is example of your tutorial.I am doing simulations as your tutorial.I didnt get any errors upto the commond grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top -o em.tpr.After this as your tutorial i used the commond mdrun -v -deffnm em, then i got the following error. Fatal error: Domain decomposition does not support simple neighbor searching, use grid searching or use particle decomposition Kindly tell me how to overcome this error. Suryanarayana Seera, JRF, India. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] radius of gyration
Dear Gromacs users I have a question abut radius of gyration in proteins. I want to calculate it via MD simulation for calcium pump protein. Following the same method as described in justin lezozyme tutorial, we have dissolved the protein in water. I want to know that is it wise to study this parameter for this protein out of membrane and only in the box of water??? Thanks regards D.M-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Coordinate file for lipid bilayer
Dear all! Recently I've forced with the opposite problem. I have pre-equilbrated bilayer of highter dimensions than I need. How I could reduce lipid number of such bilayer as well as reduce total dimensions of such system ? E.g I have preequilibrated bilayer consisted of 340 lipids. I want to reduce it to the 200 lipids by the symmetrical deletion of the unnecessary lipids from each side. Is there simplest way to do it ? James 2012/5/28 Jon Kapla jon.ka...@mmk.su.se Hi, The easiest solution is probably to write a script that reorders the structure file (gro for example, just swap the lines in each lipid, and use editconf -f file.gro -resnr 1 to renumber) the way it is written in the topology. Cheers Jon On 2012-05-28 08:03, James Starlight wrote: Peter, Thanks for advise. I've found already pre-equilibrated POPC bilayers with 200 lipids. I've examined that lipids and found that they are very similar to the berger's lipids (it consists of equal nymber of atoms ) but the atom order in each lipid is slightly different than in Tieleman's popc.itp file so during processing of that lipids I've got error of non-matching atoms. Is there any trivial way to make new popc.itp based on existing gro file with correct atom order ? James 2012/5/26 Peter C. Lai p...@uab.edu Either use genbox -cs popc128b.gro or genconf -f popc128b.gro -nbox x y 0 Tieleman's lipids require you to generate a dummy tpr for use with trjconv to unwrap the pbc (trjconv -s em.tpr -f popc128b.pdb -o popc128b-nopbc.gro -pbc mol -ur compact) first. Lots of people have their own bilayer but they may be for different FFs which means the atom naming would not be immediately be compatible with your FF; for example mine are built for charmm36 and would require atom renaming for another FF, even charmm27. On 2012-05-26 11:24:12AM +0400, James Starlight wrote: Dear Gromacs Users! I want to perform MD simulation of my membrane protein in POPC or POPE bilayer using Tieleman's parameters for lipids by means of gromos united atom force field. The main problem is that the pre-equilibrated bilayers wich I found on the Dr. Tieleman's site consist of no more that 128 lipids but I want to simulate my protein with bigger number of lipids ( for example starting from 200 lipids ). What should I do in that case ? Could you provide me with some tools for construction of such united-atoms bilayers with desired dimensions ? Finally is there any others pre-equilibrated bilayers aviable for downloading besides Dr. Tieleman's site ? thanks for your help, James S. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- _ Jon Kapla Division of Physical Chemistry Dpt. of Materials and Environmental Chemistry (MMK) Arrhenius Laboratory Stockholm University SE-106 91 Stockholm Pos:PhD Student Phone: +46 8 16 11 79 (office) Phone: +46 70 304 19 89 (cell) E-mail: jon.ka...@mmk.su.se _ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read
Re: [gmx-users] Rhamnose on 53a6
Have you tryed online servers as http://davapc1.bioch.dundee.ac.uk/prodrg/or the Acpype (with Amber)? 2012/6/11 Marc Gordon marcgrd...@gmail.com Hello again fellow gromacs users. I am looking to model a glucose-rhamnose disaccharide using the 53a6 forcefield. I wanted to take a look at the naming conventions for carbohydrates but I'm battling to find anything in the pdb2gmx force field files. I downloaded a package of force fields from the GROMOS website to get an idea about naming conventions for carbohydrates and couldn't see any mention of rhamnose anywhere. (allose, altrose, glucose, mannose, gulose, idose, galactose and talose are mentioned but no rhamnose). Does anyone have any information on naming conventions for rhamnose or whether or not rhamnose was ever present in this force field? Regards Marc -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Coordinate file for lipid bilayer
On 6/11/12 6:05 AM, James Starlight wrote: Dear all! Recently I've forced with the opposite problem. I have pre-equilbrated bilayer of highter dimensions than I need. How I could reduce lipid number of such bilayer as well as reduce total dimensions of such system ? E.g I have preequilibrated bilayer consisted of 340 lipids. I want to reduce it to the 200 lipids by the symmetrical deletion of the unnecessary lipids from each side. Is there simplest way to do it ? Try genbox with the -box option (with your bilayer as -cs) to set a smaller box size that will give a suitable number of lipids. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] radius of gyration
On 6/11/12 5:20 AM, delara aghaie wrote: Dear Gromacs users I have a question abut radius of gyration in proteins. I want to calculate it via MD simulation for calcium pump protein. Following the same method as described in justin lezozyme tutorial, we have dissolved the protein in water. I want to know that is it wise to study this parameter for this protein out of membrane and only in the box of water??? In my opinion, that's not appropriate. The structure of a membrane protein can be highly sensitive to the environment, so any conclusions you reach would be suspect in the mind of a skeptical reviewer. Why not embed the protein in a membrane? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Rhamnose on 53a6
On 6/11/12 6:06 AM, Thales Kronenberger wrote: Have you tryed online servers as http://davapc1.bioch.dundee.ac.uk/prodrg/ or the Acpype (with Amber)? For Gromos parameterization, ATB produces much better results than PRODRG. http://compbio.biosci.uq.edu.au/atb/ Validation is always required, though :) -Justin 2012/6/11 Marc Gordon marcgrd...@gmail.com mailto:marcgrd...@gmail.com Hello again fellow gromacs users. I am looking to model a glucose-rhamnose disaccharide using the 53a6 forcefield. I wanted to take a look at the naming conventions for carbohydrates but I'm battling to find anything in the pdb2gmx force field files. I downloaded a package of force fields from the GROMOS website to get an idea about naming conventions for carbohydrates and couldn't see any mention of rhamnose anywhere. (allose, altrose, glucose, mannose, gulose, idose, galactose and talose are mentioned but no rhamnose). Does anyone have any information on naming conventions for rhamnose or whether or not rhamnose was ever present in this force field? Regards Marc -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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 mailto: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 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] Total energy of a group of atoms
Dear All, Sorry to trouble you with the same question, but my question from last friday was probably badly formulated, so I'll try again. Assume our system consists of ten atoms (atom indexes 1-10). It has two groups, group A has atoms 1, 7, 9 group B has atoms 2-6, 8, 10 Is it possible (either during the run or by postprocessing) to get the total energies associated to groups A and B (thus E_tot = E_tot(A) + E_tot(B) )? If not, what would be easiest strategy to hack this out? Would it be g_energy or g_enemat or something else? terveisin, Markus -- --www=http://www.iki.fi/markus.kaukonen --markus.kauko...@iki.fi --office: 1st year student at Helsinki University --home: Viinirinne 3 F 12, 02630 Espoo, FIN --tel: h 045-1242068 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] LINCS warnings
Hi Mark, I did simulation of the same system in vacuum, and system behave the normally, So the instability in the system is due to the spc Water model??? As per the link http://www.gromacs.org/Documentation/Terminology/Blowing_Up I think the source is (Please tell me is it right..?? or any else reason ) last option : you have a single water molecule somewhere within the system that is isolated from the other water molecules. How to find such water molecule and solve the problem?? Thank you in Advance . With Best Wishes, Rama David -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] LINCS warnings
On 6/11/12 6:23 AM, rama david wrote: Hi Mark, I did simulation of the same system in vacuum, and system behave the normally, So the instability in the system is due to the spc Water model??? As per the link http://www.gromacs.org/Documentation/Terminology/Blowing_Up The water model is not the problem. Your solvated system has clashes that cause instability. In vacuo, your solute has greater freedom to shift around. I think the source is (Please tell me is it right..?? or any else reason ) last option : you have a single water molecule somewhere within the system that is isolated from the other water molecules. How to find such water molecule and solve the problem?? I think this is unlikely. If you have any isolated waters, they might be sandwiched somewhere in your protein layers and should be easy to spot. The best strategy is to use the output of EM to your advantage. Look at the atom that had the highest force on it. What is it near? What might it be clashing with? What if you run EM in vacuo, followed by solvation, and another round of EM? From your earlier description, it seems to me that the system has been constructed to replicate some known experimental spacing, but doing so does not guarantee that whatever peptide structure you are replicating will necessarily produce a sensible result, or one that is free from clashes. Hence, you need to refine the model before continuing. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] LINCS warnings
Hi Justin, thank you for quick reply. You are right I have practicle result, And I want to replicate them.. Thank you for your suggestion.. With Best Wishes, Rama David On Mon, Jun 11, 2012 at 3:58 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 6/11/12 6:23 AM, rama david wrote: Hi Mark, I did simulation of the same system in vacuum, and system behave the normally, So the instability in the system is due to the spc Water model??? As per the link http://www.gromacs.org/**Documentation/Terminology/** Blowing_Up http://www.gromacs.org/Documentation/Terminology/Blowing_Up The water model is not the problem. Your solvated system has clashes that cause instability. In vacuo, your solute has greater freedom to shift around. I think the source is (Please tell me is it right..?? or any else reason ) last option : you have a single water molecule somewhere within the system that is isolated from the other water molecules. How to find such water molecule and solve the problem?? I think this is unlikely. If you have any isolated waters, they might be sandwiched somewhere in your protein layers and should be easy to spot. The best strategy is to use the output of EM to your advantage. Look at the atom that had the highest force on it. What is it near? What might it be clashing with? What if you run EM in vacuo, followed by solvation, and another round of EM? From your earlier description, it seems to me that the system has been constructed to replicate some known experimental spacing, but doing so does not guarantee that whatever peptide structure you are replicating will necessarily produce a sensible result, or one that is free from clashes. Hence, you need to refine the model before continuing. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Positive Potential Energy after equilibration
Hi gmx users, I'm trying to create an equilibrated 2,3 dihydroxynaphthalene solvent box. I used PRODRG2 server to create an itp file from the downloaded pdb file. I used genbox to insert the solvent randomly into a 5 nm cubic box. Then I energy minimised it and did NVT and NPT equilibration on the box. Both ran successfully but my system potential energy averages to 2.01e+4 after NPT. The temperature I used was 450 K which is well beyond its melting point and pressure I used was 1 bar. The force field I used was GROMOS53a6. Similar results were obtained when the above procedure was applied on beta naphthol. Can someone help me find where exactly have I gone wrong? Thank you for your help in advance. Satish Kamath IISc Bangalore India -- View this message in context: http://gromacs.5086.n6.nabble.com/Positive-Potential-Energy-after-equilibration-tp4998327.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Positive Potential Energy after equilibration
On 6/11/12 6:42 AM, Satish Kamath wrote: Hi gmx users, I'm trying to create an equilibrated 2,3 dihydroxynaphthalene solvent box. I used PRODRG2 server to create an itp file from the downloaded pdb file. I used genbox to insert the solvent randomly into a 5 nm cubic box. Then I energy minimised it and did NVT and NPT equilibration on the box. Both ran successfully but my system potential energy averages to 2.01e+4 after NPT. The temperature I used was 450 K which is well beyond its melting point and pressure I used was 1 bar. The force field I used was GROMOS53a6. Similar results were obtained when the above procedure was applied on beta naphthol. Can someone help me find where exactly have I gone wrong? Thank you for your help in advance. Did you refine the PRODRG topologies by recalculating the charges suitably? If not, you can expect bad results. http://pubs.acs.org/doi/abs/10.1021/ci100335w A positive potential indicates net repulsion in the system, so whatever cohesive interactions your molecules should be feeling are going unsatisfied or being outweighed by stronger repulsive interactions. Both of these factors suggest an inadequate topology. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] radius of gyration
Dear Justin. Thanks for your explanation. In lyzozyme tutorial the radius of gyration has been plooted against simulation time (there 1000 ps). When I plot the same graph, the horizontal axis is up to 500 (The number of frames for data calculation). Although, the gyrate.xvg file has gyration data for these 500 frames, how can I tell gnuplot to plot gyration versus simulation time (1000 ps)? Thanks Regards D.M From: Justin A. Lemkul jalem...@vt.edu To: delara aghaie d_agh...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, 11 June 2012, 14:46 Subject: Re: [gmx-users] radius of gyration On 6/11/12 5:20 AM, delara aghaie wrote: Dear Gromacs users I have a question abut radius of gyration in proteins. I want to calculate it via MD simulation for calcium pump protein. Following the same method as described in justin lezozyme tutorial, we have dissolved the protein in water. I want to know that is it wise to study this parameter for this protein out of membrane and only in the box of water??? In my opinion, that's not appropriate. The structure of a membrane protein can be highly sensitive to the environment, so any conclusions you reach would be suspect in the mind of a skeptical reviewer. Why not embed the protein in a membrane? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] radius of gyration
On 6/11/12 8:40 AM, delara aghaie wrote: Dear Justin. Thanks for your explanation. In lyzozyme tutorial the radius of gyration has been plooted against simulation time (there 1000 ps). When I plot the same graph, the horizontal axis is up to 500 (The number of frames for data calculation). Although, the gyrate.xvg file has gyration data for these 500 frames, how can I tell gnuplot to plot gyration versus simulation time (1000 ps)? Are you talking about the tutorial or your own data? If you are talking about the tutorial, then the run should have been for 1 ns. If there are fewer frames, then either the .mdp file was changed to specify less time or the simulation stopped prematurely. If you're talking about your own data, I have no way to know what was expected. You can't plot more frames than are present. I don't use gnuplot so I can't offer you any advice as to how you can manipulate the way the data are displayed. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] radius of gyration
Dear Justin My question can be related to both. Ok let me talk about the tutorial. The simulation has finished compeletly and log file and other outputs show the completion of 1 ns simulation. this is part of gyrate.xvg file I see: - @ s0 legend Rg @ s1 legend RgX @ s2 legend RgY @ s3 legend RgZ 0 1.40391 1.20269 1.02309 1.20363 2 1.41596 1.21322 1.03459 1.21146 4 1.41283 1.21881 1.02271 1.20861 6 1.41882 1.21595 1.03424 1.2157 8 1.4139 1.20694 1.03791 1.21006 10 1.42295 1.21367 1.03899 1.22356 12 1.42184 1.20803 1.0391 1.22646 --- 518 1.41756 1.20547 1.04411 1.21475 520 1.42478 1.21366 1.04952 1.21882 522 1.41129 1.20451 1.04001 1.20458 524 1.42205 1.20918 1.04929 1.21711 526 1.41778 1.20381 1.04779 1.21375 528 1.41853 1.20465 1.06006 1.20398 530 1.42129 1.20401 1.05779 1.21307 288,8 Bot --- This was the start and end of data reported in gyrate.xvg file. all the outputs are written in files every 1000 steps (1000*0.002=2ps). I expect to see in gyrate.xvg file, the last line for 500 which corresponds to the (500*2=1000ps) can you please explain the result for having lines till 530? --- About plotting the graph if I know use the two first coloumns, I will not have graph for Rg versus simulation time which I am interested in? Thanks for your time Regards D.M From: Justin A. Lemkul jalem...@vt.edu To: delara aghaie d_agh...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, 11 June 2012, 17:21 Subject: Re: [gmx-users] radius of gyration On 6/11/12 8:40 AM, delara aghaie wrote: Dear Justin. Thanks for your explanation. In lyzozyme tutorial the radius of gyration has been plooted against simulation time (there 1000 ps). When I plot the same graph, the horizontal axis is up to 500 (The number of frames for data calculation). Although, the gyrate.xvg file has gyration data for these 500 frames, how can I tell gnuplot to plot gyration versus simulation time (1000 ps)? Are you talking about the tutorial or your own data? If you are talking about the tutorial, then the run should have been for 1 ns. If there are fewer frames, then either the .mdp file was changed to specify less time or the simulation stopped prematurely. If you're talking about your own data, I have no way to know what was expected. You can't plot more frames than are present. I don't use gnuplot so I can't offer you any advice as to how you can manipulate the way the data are displayed. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] radius of gyration
On 6/11/12 9:09 AM, delara aghaie wrote: Dear Justin My question can be related to both. Ok let me talk about the tutorial. The simulation has finished compeletly and log file and other outputs show the completion of 1 ns simulation. this is part of gyrate.xvg file I see: - @ s0 legend Rg @ s1 legend RgX @ s2 legend RgY @ s3 legend RgZ 0 1.40391 1.20269 1.02309 1.20363 2 1.41596 1.21322 1.03459 1.21146 4 1.41283 1.21881 1.02271 1.20861 6 1.41882 1.21595 1.03424 1.2157 8 1.4139 1.20694 1.03791 1.21006 10 1.42295 1.21367 1.03899 1.22356 12 1.42184 1.20803 1.0391 1.22646 --- 518 1.41756 1.20547 1.04411 1.21475 520 1.42478 1.21366 1.04952 1.21882 522 1.41129 1.20451 1.04001 1.20458 524 1.42205 1.20918 1.04929 1.21711 526 1.41778 1.20381 1.04779 1.21375 528 1.41853 1.20465 1.06006 1.20398 530 1.42129 1.20401 1.05779 1.21307 288,8 Bot --- This was the start and end of data reported in gyrate.xvg file. all the outputs are written in files every 1000 steps (1000*0.002=2ps). I expect to see in gyrate.xvg file, the last line for 500 which corresponds to the (500*2=1000ps) can you please explain the result for having lines till 530? Your output file is not labeled according to frame number, it is labeled according to time and thus 530 corresponds to the time of 530 ps. If the file does indeed end there then either there is a corruption in the .xtc file, your simulation did not go to 1 ns, or g_gyrate exited prematurely. It's up to you to figure out what may have gone wrong. No one else can possibly know that. --- About plotting the graph if I know use the two first coloumns, I will not have graph for Rg versus simulation time which I am interested in? That's precisely what you will have. Look at the data labels in the .xvg file and you will see what each data set 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 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] radius of gyration
Dear Justin Thanks again. Ok I got it. Only there remains a question: you mean it is possible that the simulation has finished for 1 ns but the .xtc file does not have the information for whole frames or even it is possible for g_gyrate program to crash and give the non-compelete .xvg file? Regards D.M From: Justin A. Lemkul jalem...@vt.edu To: delara aghaie d_agh...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, 11 June 2012, 17:46 Subject: Re: [gmx-users] radius of gyration On 6/11/12 9:09 AM, delara aghaie wrote: Dear Justin My question can be related to both. Ok let me talk about the tutorial. The simulation has finished compeletly and log file and other outputs show the completion of 1 ns simulation. this is part of gyrate.xvg file I see: - @ s0 legend Rg @ s1 legend RgX @ s2 legend RgY @ s3 legend RgZ 0 1.40391 1.20269 1.02309 1.20363 2 1.41596 1.21322 1.03459 1.21146 4 1.41283 1.21881 1.02271 1.20861 6 1.41882 1.21595 1.03424 1.2157 8 1.4139 1.20694 1.03791 1.21006 10 1.42295 1.21367 1.03899 1.22356 12 1.42184 1.20803 1.0391 1.22646 --- 518 1.41756 1.20547 1.04411 1.21475 520 1.42478 1.21366 1.04952 1.21882 522 1.41129 1.20451 1.04001 1.20458 524 1.42205 1.20918 1.04929 1.21711 526 1.41778 1.20381 1.04779 1.21375 528 1.41853 1.20465 1.06006 1.20398 530 1.42129 1.20401 1.05779 1.21307 288,8 Bot --- This was the start and end of data reported in gyrate.xvg file. all the outputs are written in files every 1000 steps (1000*0.002=2ps). I expect to see in gyrate.xvg file, the last line for 500 which corresponds to the (500*2=1000ps) can you please explain the result for having lines till 530? Your output file is not labeled according to frame number, it is labeled according to time and thus 530 corresponds to the time of 530 ps. If the file does indeed end there then either there is a corruption in the .xtc file, your simulation did not go to 1 ns, or g_gyrate exited prematurely. It's up to you to figure out what may have gone wrong. No one else can possibly know that. --- About plotting the graph if I know use the two first coloumns, I will not have graph for Rg versus simulation time which I am interested in? That's precisely what you will have. Look at the data labels in the .xvg file and you will see what each data set 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 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] radius of gyration
On 6/11/12 9:28 AM, delara aghaie wrote: Dear Justin Thanks again. Ok I got it. Only there remains a question: you mean it is possible that the simulation has finished for 1 ns but the .xtc file does not have the information for whole frames or even it is possible for g_gyrate program to crash and give the non-compelete .xvg file? A large number of things are possible. You can use gmxcheck to verify the integrity of the .xtc file, and inspect the .log file to make sure the simulation was conducted as you expect it to. If g_gyrate had crashed, it would have been fairly obvious in the terminal. -Justin Regards D.M *From:* Justin A. Lemkul jalem...@vt.edu *To:* delara aghaie d_agh...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Monday, 11 June 2012, 17:46 *Subject:* Re: [gmx-users] radius of gyration On 6/11/12 9:09 AM, delara aghaie wrote: Dear Justin My question can be related to both. Ok let me talk about the tutorial. The simulation has finished compeletly and log file and other outputs show the completion of 1 ns simulation. this is part of gyrate.xvg file I see: - @ s0 legend Rg @ s1 legend RgX @ s2 legend RgY @ s3 legend RgZ 01.403911.202691.023091.20363 21.415961.213221.034591.21146 4 1.412831.218811.022711.20861 61.418821.215951.03424 1.2157 8 1.41391.206941.037911.21006 101.422951.213671.038991.22356 121.421841.20803 1.03911.22646 --- 5181.41756 1.205471.044111.21475 5201.42478 1.213661.049521.21882 5221.411291.204511.040011.20458 5241.422051.209181.049291.21711 5261.417781.203811.047791.21375 5281.418531.204651.06006 1.20398 5301.421291.204011.057791.21307 288,8 Bot --- This was the start and end of data reported in gyrate.xvg file. all the outputs are written in files every 1000 steps (1000*0.002=2ps). I expect to see in gyrate.xvg file, the last line for 500 which corresponds to the (500*2=1000ps) can you please explain the result for having lines till 530? Your output file is not labeled according to frame number, it is labeled according to time and thus 530 corresponds to the time of 530 ps. If the file does indeed end there then either there is a corruption in the .xtc file, your simulation did not go to 1 ns, or g_gyrate exited prematurely. It's up to you to figure out what may have gone wrong. No one else can possibly know that. --- About plotting the graph if I know use the two first coloumns, I will not have graph for Rg versus simulation time which I am interested in? That's precisely what you will have. Look at the data labels in the .xvg file and you will see what each data set 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 -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Fatal error: Atomtype O2 not found
hi sorry 4 not doing it before, right now am doing Solvate the Box step in molecular modelling am using Gromacs 4.5.5 ver during the first step i.e creating the topology file ,i tried to create the topology file by using the command pdb2gmx –ignh –ff G43a1 –f 1OMB.pdb –o fws.pdb –p fws.top for which gromacs showed me an error saying atomtypeXX not found in the residue type database i resolved this issue by going through gromacs manual by adding the missing atoms to the dna.rtp file and new atoms to atomtypes.atp file after which it produced the topology file int he next step i setup an box with the command editconf -bt cubic –f fws.pdb –o fws.pdb -c –d 0.9 in the third step i.e Solvate the Box i used the command genbox –cp fws.pdb –cs spc216.gro –o fws_b4em.pdb –p fws.top in the fourth step i.e Setup the energy minimization. i used the command grompp –f em.mdp –c fws_ion.pdb –p fws.top –o fws_em.tpr where its givving me an errror which says Fatal error: Unknown bond_atomtype O2 based on your replies i tried by adding the atom to ffbonded.itp file but it dint work. am attachning my dna.rtp ,atomtypes.atp,ffbonded .itp files please help -ram http://gromacs.5086.n6.nabble.com/file/n4998335/dna.rtp dna.rtp http://gromacs.5086.n6.nabble.com/file/n4998335/ffbonded.itp ffbonded.itp http://gromacs.5086.n6.nabble.com/file/n4998335/atomtypes.atp atomtypes.atp -- View this message in context: http://gromacs.5086.n6.nabble.com/Fatal-error-Atomtype-O2-not-found-tp4998254p4998335.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Fatal error: Atomtype O2 not found
On 6/11/12 9:54 AM, ramaraju801 wrote: hi sorry 4 not doing it before, right now am doing Solvate the Box step in molecular modelling am using Gromacs 4.5.5 ver during the first step i.e creating the topology file ,i tried to create the topology file by using the command pdb2gmx –ignh –ff G43a1 –f 1OMB.pdb –o fws.pdb –p fws.top for which gromacs showed me an error saying atomtypeXX not found in the residue type database i resolved this issue by going through gromacs manual by adding the missing atoms to the dna.rtp file and new atoms to atomtypes.atp file after which it produced the topology file int he next step i setup an box with the command editconf -bt cubic –f fws.pdb –o fws.pdb -c –d 0.9 in the third step i.e Solvate the Box i used the command genbox –cp fws.pdb –cs spc216.gro –o fws_b4em.pdb –p fws.top in the fourth step i.e Setup the energy minimization. i used the command grompp –f em.mdp –c fws_ion.pdb –p fws.top –o fws_em.tpr where its givving me an errror which says Fatal error: Unknown bond_atomtype O2 These are presumably commands from a tutorial, which is not what you're working on. The 1OMB.pdb file contains only protein, and the Gromos96 43a1 force field does not have DNA parameters, so this workflow is irrelevant. What you should provide is precisely what you are typing for your system, not the tutorial. We know the tutorial works; it's your system that doesn't work. based on your replies i tried by adding the atom to ffbonded.itp file but it dint work. am attachning my dna.rtp ,atomtypes.atp,ffbonded .itp files please help -ram http://gromacs.5086.n6.nabble.com/file/n4998335/dna.rtp dna.rtp I don't know what you changed here. Please tell us the change(s) you made. http://gromacs.5086.n6.nabble.com/file/n4998335/ffbonded.itp ffbonded.itp The O2-N3 bond parameters you added are nonsense. They specify a 1-nm bond with a 1-kJ/(mol nm^2) force constant. If you're just hacking away at these files hoping that the workflow will complete without error, then you're wasting your time because the dynamics will be nonsense. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Positive Potential Energy after equilibration
Dear Sir, Thank you for your response. I've read the paper and will look into the charge distribution. Thank you once again. Satish Kamath IISc Bangalore India -- View this message in context: http://gromacs.5086.n6.nabble.com/Positive-Potential-Energy-after-equilibration-tp4998327p4998337.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Question about documentation of -a switch in g_hbond
Justin and Mark, Thank you SO much for your help! Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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] 4. QM/MM Calculation with Orca (Minos Matsoukas)
Thank you very much for your answer, After setting up some qm/mm runs, I clearly understand what you mean. Wow, the qm calculations are some cpu eating monsters... M. On Fri, Jun 8, 2012 at 3:46 PM, Gerrit Groenhof ggro...@gwdg.de wrote: YOucan only use one thread in mdrun, but more than one in ORCA. Try to estimate the ratio of computation time spent between the QM and MM calculation to get an idea of why we never bothered to parallellize the MM part. Hope this helps, Gerrit 4. QM/MM Calculation with Orca (Minos Matsoukas) Dear GROMACS Users, I am using Gromacs with ORCA for a qm calculation, but I can only use 1 processor for mdrun. If I place the line !PAL4 in the topol.ORCAINFO and run mdrun -nt 1, it works, and ORCA parallelizes correctly for 4 processors, although mdrun only runs one thread. If I place the line !PAL4 in the topol.ORCAINFO and run mdrun -nt 4, it doesn‚t work. mdrun crashes with a segmentation fault error : Back Off! I just backed up md.log to ./#md.log.35# Reading file topol.tpr, VERSION 4.5.5 (single precision) Starting 4 threads QM/MM calculation requested. QM/MM calculation requested. QM/MM calculation requested. QM/MM calculation requested. there we go! there we go! there we go! there we go! Layer 0 nr of QM atoms 73 QMlevel: B3LYP/STO-3G /opt/soft/orca_2_9_1_linux_x86-64/opt/soft/orca_2_9_1_linux_x86-64... orca initialised... Segmentation fault (core dumped) Is this because mdrun can only run with 1 thread when used with ORCA ? Here‚s some information : OS: CentOS 6.2 x86_64 kernel 2.6.32-220 GROMACS: 4.5.5 compiled with options : --with-qmmm-orca --without-qmmm-gaussian ORCA: 2.9.1 for x86_64 OPENMPI: 1.4.3 My minimization mdp file is: ; ; Input file ; title = Yo ; a string cpp = /lib/cpp ; c-preprocessor integrator = cg ; ;integrator = l-bfgs rlist = 1.0 ; cut-off for ns rvdw = 1.0 ; cut-off for vdw rcoulomb = 1.5 ; cut-off for coulomb ; Energy minimizing stuff ; nsteps = 200 emtol = 10 emstep = 0.1 ;define = -DPOSRES constraints = none QMMM = yes QMMM-grps = MOL QMMMscheme = normal QMbasis = STO-3g QMmethod = b3lyp QMcharge = 1 QMmult = 1 - Thanks in advance -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Bonds and atom-pairs in g_hbond
Hi, I am analyzing hydrogen bonds using g_hbond. I have selected two non-overlapping groups; one is hydroxyl groups (OH, where O is the donor and H is the hydrogen), and the other is oxygens on PO4^3- (where F is the acceptor). I am using the switch -noda, which tells the program to take the -r value as the Hydrogen-Acceptor distance (here, H-O), rather than the Donor-Acceptor distance (here, O-O). My trajectory is 10 ns long. In the output after the calculation, I see the following: Found 233 different hydrogen bonds in trajectory Found 224 different atom-pairs within hydrogen bonding distance Can you please help me to understand the terms hydrogen bond and atom-pair within hydrogen bonding distance conceptually? I think that in order for a hydrogen and an acceptor to be considered hydrogen bonded, two criteria must be satisfied: (1) the distance (in this case, the distance between the hydrogen and the acceptor, since I am using -noda) must be less than the cutoff distance -r, and (2) the Acceptor-Donor-Hydrogen angle must be less than the cutoff angle -a. So distance and angle are the two criteria that must be met, according to g_hbond and most definitions of hydrogen bonding. So, apparently, g_hbond found 233 hydrogen bonds satisfying both the distance and angle criteria. But, g_hbond found 224 different atom-pairs within hydrogen bonding distance. My guess is that this means that there are 224 atom pairs satisfying the distance criterion (i.e., Hydrogen-Acceptor pairs within the cutoff distance, -r). But if my interpretation of the term atom-pair within hydrogen bonding distance is correct, how can there be 9 _fewer_ atom pairs that satisfy only the distance criterion (and not the angle criterion), than those that satisfy _both_ the distance criterion _and_ the angle criterion? Probably, I have the wrong pictures of the terms hydrogen bond and atom-pair within hydrogen bonding distance in my head. Thank you for your time! Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] RE: Bonds and atom-pairs in g_hbond
Hi again, I just realized that the output from g_hbond using the -num flag (by default, the file name is hbnum.xvg) also seems to make a distinction between hydrogen bonds and pairs within the distance. For example, here are the first few lines of this output file: @ s0 legend Hydrogen bonds @ s1 legend Pairs within 0.227905 nm 0 39 1 0.05 40 2 0.1 40 2 0.15 40 1 0.2 41 0 0.25 38 3 0.3 39 2 where 0.227905 nm is the value that I give to -r. Why are there so many more hydrogen bonds than pairs within -r, if the latter seems to be a necessary but not sufficient condition for the former? Best wishes! Andrew DeYoung Carnegie Mellon University -Original Message- From: Andrew DeYoung Sent: Monday, June 11, 2012 5:31 PM To: gmx-users@gromacs.org Subject: Bonds and atom-pairs in g_hbond Hi, I am analyzing hydrogen bonds using g_hbond. I have selected two non-overlapping groups; one is hydroxyl groups (OH, where O is the donor and H is the hydrogen), and the other is oxygens on PO4^3- (where F is the acceptor). I am using the switch -noda, which tells the program to take the -r value as the Hydrogen-Acceptor distance (here, H-O), rather than the Donor-Acceptor distance (here, O-O). My trajectory is 10 ns long. In the output after the calculation, I see the following: Found 233 different hydrogen bonds in trajectory Found 224 different atom-pairs within hydrogen bonding distance Can you please help me to understand the terms hydrogen bond and atom-pair within hydrogen bonding distance conceptually? I think that in order for a hydrogen and an acceptor to be considered hydrogen bonded, two criteria must be satisfied: (1) the distance (in this case, the distance between the hydrogen and the acceptor, since I am using -noda) must be less than the cutoff distance -r, and (2) the Acceptor-Donor-Hydrogen angle must be less than the cutoff angle -a. So distance and angle are the two criteria that must be met, according to g_hbond and most definitions of hydrogen bonding. So, apparently, g_hbond found 233 hydrogen bonds satisfying both the distance and angle criteria. But, g_hbond found 224 different atom-pairs within hydrogen bonding distance. My guess is that this means that there are 224 atom pairs satisfying the distance criterion (i.e., Hydrogen-Acceptor pairs within the cutoff distance, -r). But if my interpretation of the term atom-pair within hydrogen bonding distance is correct, how can there be 9 _fewer_ atom pairs that satisfy only the distance criterion (and not the angle criterion), than those that satisfy _both_ the distance criterion _and_ the angle criterion? Probably, I have the wrong pictures of the terms hydrogen bond and atom-pair within hydrogen bonding distance in my head. Thank you for your time! Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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: Bonds and atom-pairs in g_hbond
On 6/11/12 5:41 PM, Andrew DeYoung wrote: Hi again, I just realized that the output from g_hbond using the -num flag (by default, the file name is hbnum.xvg) also seems to make a distinction between hydrogen bonds and pairs within the distance. For example, here are the first few lines of this output file: @ s0 legend Hydrogen bonds @ s1 legend Pairs within 0.227905 nm 0 39 1 0.05 40 2 0.1 40 2 0.15 40 1 0.2 41 0 0.25 38 3 0.3 39 2 where 0.227905 nm is the value that I give to -r. Why are there so many more hydrogen bonds than pairs within -r, if the latter seems to be a necessary but not sufficient condition for the former? They are separate quantities. Either an atom pair is a hydrogen bond, or it is not. You have lots of hydrogen bonds (satisfying both distance and angle criteria), and a few atom pairs that satisfy distance only. By playing with the value passed to -a you can change how many are in each column (just an exercise, not necessarily useful). -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Total energy of a group of atoms
On 11/06/2012 8:22 PM, Markus Kaukonen wrote: Dear All, Sorry to trouble you with the same question, but my question from last friday was probably badly formulated, so I'll try again. Assume our system consists of ten atoms (atom indexes 1-10). It has two groups, group A has atoms 1, 7, 9 group B has atoms 2-6, 8, 10 Is it possible (either during the run or by postprocessing) to get the total energies associated to groups A and B (thus E_tot = E_tot(A) + E_tot(B) )? If not, what would be easiest strategy to hack this out? Would it be g_energy or g_enemat or something else? This is straightforward to do as far as non-bonded quantities go, but requires planning when you construct your .mdp for either the original run, or an mdrun -rerun. Look for energy groups in the manual. Decomposing the bonded quantities will require you do some more tedious work, e.g. zeroing parameters or removing molecules in the .top and doing a rerun. As Justin said, you will not be able to easily decompose the reciprocal-space term for PME, and whether these sums mean anything is doubtful. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] (no subject)
Dear All , I am facing problem in matching the coordinates number in this two files, em.gro and toplogy.top. I have tried with changing the number of solvents, adding ions (Na+) but in vain *Note :: My system has ' -1.00 ' charge ...so I have added one Sodium ion* So can anyone please get me out of this trouble ??? Fatal error: number of coordinates in coordinate file (em.gro, 64506) does not match topology (toplogy.top, 64504) -- *Tarak Karmakar Molecular Simulation Lab. Chemistry and Physics of Materials Unit Jawaharlal Nehru Centre for Advanced Scientific Research Jakkur P. O. Bangalore - 560 064 Karnataka, INDIA Ph. (lab) : +91-80-22082809 * -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] (no subject)
Could you paste your .top file and the command your add ions? Maybe the Cl- ion was also added when you added Na+ ion? On Tue, Jun 12, 2012 at 1:18 PM, tarak karmakar tarak20...@gmail.comwrote: Dear All , I am facing problem in matching the coordinates number in this two files, em.gro and toplogy.top. I have tried with changing the number of solvents, adding ions (Na+) but in vain *Note :: My system has ' -1.00 ' charge ...so I have added one Sodium ion* So can anyone please get me out of this trouble ??? Fatal error: number of coordinates in coordinate file (em.gro, 64506) does not match topology (toplogy.top, 64504) -- *Tarak Karmakar Molecular Simulation Lab. Chemistry and Physics of Materials Unit Jawaharlal Nehru Centre for Advanced Scientific Research Jakkur P. O. Bangalore - 560 064 Karnataka, INDIA Ph. (lab) : +91-80-22082809 * -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
