[gmx-users] walls in martini
Dear Prof. I want to use walls (in z=0 and z=z_box) for my simulation with martini coarse-grained force field, but always it give me error! Do the martini force field support walls? Should I use just 12-6 for wall_type? May I ask your help about this, Please? Best regards Sara-- 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] Infrared
Hi, Hernan. You wrote 16 Jan 2012 ?., 19:23:27: > Dear gmx-user, > I am working in the dinamicas fo aluminophosphates material. I need to > calculated de IR spectrum from the trajectory. if is it possible to do > this with gromacs?, GROMACS is great! Couple years ago I calculated with gromacs IR spectra for water clusters: "Far-infrared radiation absorption cross section of clusterized water vapor", Technical Physics Letters, Volume 36, Number 2, 173-176, DOI: 10.1134/S1063785010020240 > if someone can help me with this (paper or reviews) it would be > great. see refs [5, 7-9] in our paper. > Best Wishes > Hernan -- Regards, Dmitri mailto:ddu...@ngs.ru-- 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] genbox
You can use the command genbox -cs with the option -maxsol number to specify the number of water molecules Good luck Cuong 2012/1/16 vidhya sankar > Hello Justin, > Thanks for your patient reply > > I would like to solvate my molecules with specific > number of water molecules > what option is a suitable to do that ? in editconf > with regards > S.Vidhya sankar > > -- > 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 > -- Nguyen Van Cuong PhD student - Curtin University of Technology Mobile: (+61) 452213981 -- 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] Is there a way to omit particles with q=0 from Coulomb-/PME-calculations?
On 17/01/2012 4:55 AM, Thomas Schlesier wrote: Dear all, Is there a way to omit particles with zero charge from calculations for Coulomb-interactions or PME? In my calculations i want to coarse-grain my solvent, but the solute should be still represented by atoms. In doing so the solvent-molecules have a zero charge. I noticed that for a simulation with only the CG-solvent significant time was spent for the PME-part of the simulation. If i would simulate the complete system (atomic solute + coarse-grained solvent), i would save only time for the reduced number of particles (compared to atomistic solvent). But if i could omit the zero-charge solvent from the Coulomb-/PME-part, it would save much additional time. Is there an easy way for the omission, or would one have to hack the code? If the latter is true, how hard would it be and where do i have to look? (First idea would be to create an index-file group with all non-zero-charged particles and then run in the loops needed for Coulomb/PME only over this subset of particles.) I have only experience with Fortran and not with C++. Only other solution which comes to my mind would be to use plain cut-offs for the Coulomb-part. This would save time required for doing PME but will in turn cost time for the calculations of zeros (Coulomb-interaction for the CG-solvent). But more importantly would introduce artifacts from the plain cut-off :( Particles with zero charge are not included in neighbour lists used for calculating Coulomb interactions. The statistics in the "M E G A - F L O P S A C C O U N T I N G" section of the .log file will show that there is significant use of loops that do not have "Coul" component. So already these have no effect on half of the PME calculation. I don't know whether the grid part is similarly optimized, but you can test this yourself by comparing timing of runs with and without charged solvent. 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)
-- 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] Coarse Grained Cytochrom C
Hi all, Has anybody used Coarse grained model for Cytochrome C? I could create a model using MARTINI forcefiels (using martinize.py script and 1HRC.pdb file), but it does not have HEM and HOH groups. Can anybody help me? Kind Regards, Dariush Mohammadyani Department of Structural Biology University of Pittsburgh School of Medicine Biomedical Science Tower 3 3501 Fifth Avenue Pittsburgh, PA 15261 USA -- 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] Problem with trjconv and centering bilayer.
Ioannis Beis wrote: Dear gromacs users, I am trying to center the trajectory of a bilayer in the rectangular simulation box in the frame of my effort to calculate the bilayer thickness with g_dist. According to the visualization, the upper layer of the membrane lies on the lowest part of the box and the lower part of the membrane on the highest part of the box, with the water in the middle. There should not be anything wrong with drifting along the z-axis, since the initial structure was at the very bottom of the box, so even a small drift downwards -due to the pbc- would place the lower part of the membrane on the top of the box. I tried issuing: trjconv -f my_trajectory.xtc -s my_initial_structure.gro -o my_trajectory_no_jump.xtc -pbc nojump with 0 (for system) and subsequently trjconv -f my_trajectory_no_jump.xtc -s DOPC_1DOG.tpr -o my_trajectory_no_jump_center.xtc -center -boxcenter tric -pbc mol with 1 (other) for centering and 0 (system) for output. I used this kind of commands some time ago and they worked fine. Now strangely the bilayer remains around the position that I described in the beginning. Is it possible that the program treats the bilayer separated as it looks in vmd and considers the geometrical center in the middle of the water instead of the middle of the bilayer? That's exactly what it does. I tried the -trans flag to translate the bilayer along z-axis near the center and repeated the steps, but the new trajectory wasn't even visible in vmd. In addition, the .gro files generated by trjconv are apparently trajectory files instead of structure files. I don't feel confident about using editconf for operations like translation of a single initial structure, because as far as I understand editconf is a tool meant mostly for setting up systems; thus I was sceptical about messing a structure with editconf that I would later on use together with an .xtc file as input for trjconv. However, trjconv doesn't seem to generate structure output files. I don't understand the meaning of a .gro file as trajectory file since there are already at least 3 file formats for trajectories. Generally speaking, a trajectory is just a series of coordinates, so you can output it into a number of formats, including .gro and .pdb, among others. You get a chain of coordinate files that may (or may not) end up being useful in some applications. So how can I bring my bilayer's trajectory in the center of the unit cell for reliable thickness calculation without drifts? Is it possible at the same time to have clear visualization without disturbances? trjconv with -pbc mol still gives rise to lines in the visualization, apparently as a result of atom jumps. Sadly trajectory files cannot be inspected and visualization is quite handy for certain types of feedback in various data analysis-related tasks, so it would be nice if the trajectories used for analysis also look proper in vmd. I can think of two approaches, the first of which I have used so it should work ;) 1. Provide a custom index group specifying only a single lipid atom from the end of a hydrocarbon chain and center on it. Therefore, its geometric center has to be the center of the box, and it should bring the rest of the membrane to the (visual) center of the unit cell. 2. Calculate the distance with the trajectory you have now, and subtract it from the z-length (assuming the membrane plane is x-y) of the box (stored in the .edr file). -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Chemical potential
Dear Gmx Users, Can you please suggest a method (and further reading) for calculation of a chemical potential in Gromacs. Is it possible e.g. to calculate the chemical potential of my ligand or water in systerm consisting protein and ligand? Thank you Steven -- 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] Is there a way to omit particles with q=0 from Coulomb-/PME-calculations?
Dear all, Is there a way to omit particles with zero charge from calculations for Coulomb-interactions or PME? In my calculations i want to coarse-grain my solvent, but the solute should be still represented by atoms. In doing so the solvent-molecules have a zero charge. I noticed that for a simulation with only the CG-solvent significant time was spent for the PME-part of the simulation. If i would simulate the complete system (atomic solute + coarse-grained solvent), i would save only time for the reduced number of particles (compared to atomistic solvent). But if i could omit the zero-charge solvent from the Coulomb-/PME-part, it would save much additional time. Is there an easy way for the omission, or would one have to hack the code? If the latter is true, how hard would it be and where do i have to look? (First idea would be to create an index-file group with all non-zero-charged particles and then run in the loops needed for Coulomb/PME only over this subset of particles.) I have only experience with Fortran and not with C++. Only other solution which comes to my mind would be to use plain cut-offs for the Coulomb-part. This would save time required for doing PME but will in turn cost time for the calculations of zeros (Coulomb-interaction for the CG-solvent). But more importantly would introduce artifacts from the plain cut-off :( Hope anyone could help. Greetings Thomas -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Problem with trjconv and centering bilayer.
Dear gromacs users, I am trying to center the trajectory of a bilayer in the rectangular simulation box in the frame of my effort to calculate the bilayer thickness with g_dist. According to the visualization, the upper layer of the membrane lies on the lowest part of the box and the lower part of the membrane on the highest part of the box, with the water in the middle. There should not be anything wrong with drifting along the z-axis, since the initial structure was at the very bottom of the box, so even a small drift downwards -due to the pbc- would place the lower part of the membrane on the top of the box. I tried issuing: trjconv -f my_trajectory.xtc -s my_initial_structure.gro -o my_trajectory_no_jump.xtc -pbc nojump with 0 (for system) and subsequently trjconv -f my_trajectory_no_jump.xtc -s DOPC_1DOG.tpr -o my_trajectory_no_jump_center.xtc -center -boxcenter tric -pbc mol with 1 (other) for centering and 0 (system) for output. I used this kind of commands some time ago and they worked fine. Now strangely the bilayer remains around the position that I described in the beginning. Is it possible that the program treats the bilayer separated as it looks in vmd and considers the geometrical center in the middle of the water instead of the middle of the bilayer? I tried the -trans flag to translate the bilayer along z-axis near the center and repeated the steps, but the new trajectory wasn't even visible in vmd. In addition, the .gro files generated by trjconv are apparently trajectory files instead of structure files. I don't feel confident about using editconf for operations like translation of a single initial structure, because as far as I understand editconf is a tool meant mostly for setting up systems; thus I was sceptical about messing a structure with editconf that I would later on use together with an .xtc file as input for trjconv. However, trjconv doesn't seem to generate structure output files. I don't understand the meaning of a .gro file as trajectory file since there are already at least 3 file formats for trajectories. So how can I bring my bilayer's trajectory in the center of the unit cell for reliable thickness calculation without drifts? Is it possible at the same time to have clear visualization without disturbances? trjconv with -pbc mol still gives rise to lines in the visualization, apparently as a result of atom jumps. Sadly trajectory files cannot be inspected and visualization is quite handy for certain types of feedback in various data analysis-related tasks, so it would be nice if the trajectories used for analysis also look proper in vmd. Thank you in advance. Best regards, Ioannis -- 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] About solvation
vidhya sankar wrote: Dear Mark Thank you for your reply. I did As u said But when I visualize the resulting .gro files in VMD .The solute molecules are centered (i used the center option in editconf) But solvent molecules are are away . but within the box i need Solute molecules to be closely surrounded by solvent molecules . Is there is Any way to do this ? If you're limiting the solvation to a finite number of solvent molecules, then your box needs to be of the correct size to accommodate those molecules. It sounds like your box is simply too large. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] About solvation
Dear Mark Thank you for your reply. I did As u said But when I visualize the resulting .gro files in VMD .The solute molecules are centered (i used the center option in editconf) But solvent molecules are are away . but within the box i need Solute molecules to be closely surrounded by solvent molecules . Is there is Any way to do this ? Thanks In Advance -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Announce: Project - Evolutionary Algorithm with Gromacs, Initial results
We would like to announce the first version of a mono-objective algorithm that use GROMACS for Protein Structure Prediction (PSP). Although it is initial version, it was compared with other methodologies. These results were sent to WCCI [1] congress. We would like to share them with who are interested. We are looking for ideas and suggestions to add to this project. The source-code of this algorithm is [2]. Now, we are developing NSGAII algorithm, a multi-objective concept, to work with PSP. All objectives are computed with GROMACS. [1] http://www.ieee-wcci2012.org/ [2] https://gitorious.org/protpred-gromacs Best Regards, -- Rodrigo Antonio Faccioli Ph.D Student in Electrical Engineering University of Sao Paulo - USP Engineering School of Sao Carlos - EESC Department of Electrical Engineering - SEL Intelligent System in Structure Bioinformatics http://laips.sel.eesc.usp.br Phone: 55 (16) 3373-9366 Ext 229 Curriculum Lattes - http://lattes.cnpq.br/1025157978990218 Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5 -- 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: LINCS warnings and number of cpus
I tried and it got even worse: every # of cpus configuration gave the LINCS WARNING message. Thanks anyway. Alessandro Il 16/01/2012 15.58, Dr. Vitaly V. Chaban ha scritto: Dear users, I would like to ask your help about understanding a problem i'm not able to recognize by myself. Basically, a user of our sistem (IBM SP6, power6 architecture) is trying to run a simulation of a very simple sistem, a polymer chain in a lot of water molecules. While the simulation works perfectly in serial on her local pc, when she tries to run it in SP6 using 2 cpus in parallel, the simulation doesn't even start due of these errors: /starting mdrun 'PVA head29tail in water' 250 steps, 5000.0 ps. Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 83427404711319.468750, max 431899260485632.00 (between atoms 59 and 60) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 37 38 89.60.1530 124222742528. 0.1530 38 41 89.1 0.1530 104382357504. 0.1530 Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 56829711484907.867188, max 212898492186624.00 (between atoms 3 and 4) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 61 62 89.00.1530 1380386603008. 0.1530 58 61 87.6 0.1530 669758914560. 0.1530 58 59 89.20.1430 1994809540608. 0.1430 59 60 90.00.1000 43189926887424. 0.1000 57 58 88.30.1530 1126801342464. 0.1530 54 57 85.90.1530 198269452288. 0.1530 54 55 89.60.1430 1261346488320. 0.1430 38 39 89.60.1430 156364750848. 0.1430 39 40 90.00.1000 3183089549312. 0.1000 // [...] 18 21 89.9 0.1530 215265542144. 0.1530 18 19 90.00.1430 872386920448. 0.1430 19 20 90.00.1000 6085561286656. 0.1000 95 96 90.00.1000 5006930477056. 0.1000 97 98 89.70.1530 215830478848. 0.1530 98101 90.50.1530 232671739904. 0.1530 98 99 90.00.1430 746076962816. 0.1430 99100 90.00.1000 6068662435840. 0.1000 step 0: Water molecule starting at atom 6014 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. step 0: Water molecule starting at atom 7355 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates step 0 Warning: 1-4 interaction between 37 and 40 at distance 3039839053625.364 which is larger than the 1-4 table size 2.200 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size Warning: 1-4 interaction between 61 and 64 at distance 15924520737123.646 which is larger than the 1-4 table size 2.200 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size ERROR: 0031-250 task 0: Segmentation fault ERROR: 0031-250 task 1: Segmentation fault /The same errors occur when trying the simulation up to 4 cpus, but (and that's the strange thing), everything works fine with 6+ cpus (actually, there are some numbers giving an incompatibility error, like /"There is no domain decomposition for 7 nodes that is compatible with the given box and a minimum cell size of 0.95625 nm"/, but for example 6 or 8 cpus give a successful run). Can anyone understand what is the reason of this strange behaviour? Thanks, Marani Alessandro (HPC User support, CINECA - Italy) Hmm... Try "mdrun -pd %NUMPROC" -- 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] table-potential, why table from r=0->r_c+1?
Thomas Schlesier wrote: Dear all, what is the reason, that the tabulated potential must go till r_c+1 (r_c = cut-off radius) and not only up to r_c? I think we only calculate the interactions till r_c and truncate the rest. So everything behind r_c would be redundant information (due to the truncation it would be set to 0). If this would be right, i could fill everything from r_c to r_c+1 with 0's, but this sounds to easy. Please see the explanation in section 7.3.12 of the manual, specifically the "table-extension" keyword. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] LINCS warnings and number of cpus
Thank for you answer. Meanwhile, our user told us that she found the ideal configuration for running her simulations; nevertheless, i linked her this discussion in case she can find some interesting suggestion. Cheers, Alessandro Il 16/01/2012 16.05, Matthew Zwier ha scritto: Ciao, I've seen this behavior (something running fine on one core but failing on multiple cores, or certain multiples of cores) frequently. It's almost always due to an unstable system. Have your user try equilibrating longer, or minimize with flexible water before trying equilibration. You can search the GROMACS web site for the phrase "blowing up" for more information. Cheers, Matt Z. On Mon, Jan 16, 2012 at 8:37 AM, Marani Alessandro wrote: Dear users, I would like to ask your help about understanding a problem i'm not able to recognize by myself. Basically, a user of our sistem (IBM SP6, power6 architecture) is trying to run a simulation of a very simple sistem, a polymer chain in a lot of water molecules. While the simulation works perfectly in serial on her local pc, when she tries to run it in SP6 using 2 cpus in parallel, the simulation doesn't even start due of these errors: starting mdrun 'PVA head29tail in water' 250 steps, 5000.0 ps. Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 83427404711319.468750, max 431899260485632.00 (between atoms 59 and 60) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 37 38 89.60.1530 124222742528. 0.1530 38 41 89.10.1530 104382357504. 0.1530 Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 56829711484907.867188, max 212898492186624.00 (between atoms 3 and 4) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 61 62 89.00.1530 1380386603008. 0.1530 58 61 87.60.1530 669758914560. 0.1530 58 59 89.20.1430 1994809540608. 0.1430 59 60 90.00.1000 43189926887424. 0.1000 57 58 88.30.1530 1126801342464. 0.1530 54 57 85.90.1530 198269452288. 0.1530 54 55 89.60.1430 1261346488320. 0.1430 38 39 89.60.1430 156364750848. 0.1430 39 40 90.00.1000 3183089549312. 0.1000 [...] 18 21 89.90.1530 215265542144. 0.1530 18 19 90.00.1430 872386920448. 0.1430 19 20 90.00.1000 6085561286656. 0.1000 95 96 90.00.1000 5006930477056. 0.1000 97 98 89.70.1530 215830478848. 0.1530 98101 90.50.1530 232671739904. 0.1530 98 99 90.00.1430 746076962816. 0.1430 99100 90.00.1000 6068662435840. 0.1000 step 0: Water molecule starting at atom 6014 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. step 0: Water molecule starting at atom 7355 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates step 0 Warning: 1-4 interaction between 37 and 40 at distance 3039839053625.364 which is larger than the 1-4 table size 2.200 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size Warning: 1-4 interaction between 61 and 64 at distance 15924520737123.646 which is larger than the 1-4 table size 2.200 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size ERROR: 0031-250 task 0: Segmentation fault ERROR: 0031-250 task 1: Segmentation fault The same errors occur when trying the simulation up to 4 cpus, but (and that's the strange thing), everything works fine with 6+ cpus (actually, there are some numbers giving an incompatibility error, like "There is no domain decomposition for 7 nodes that is compatible with the given box and a minimum cell size of 0.95625 nm", but for example 6 or 8 cpus give a successful run). Can anyone understand what is the reason of this strange behaviour? Thanks, Marani Alessandro (HPC User support, CINECA - Italy) -- 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_Lis
[gmx-users] table-potential, why table from r=0->r_c+1?
Dear all, what is the reason, that the tabulated potential must go till r_c+1 (r_c = cut-off radius) and not only up to r_c? I think we only calculate the interactions till r_c and truncate the rest. So everything behind r_c would be redundant information (due to the truncation it would be set to 0). If this would be right, i could fill everything from r_c to r_c+1 with 0's, but this sounds to easy. Greetings Thomas -- 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 and number of cpus
Ciao, I've seen this behavior (something running fine on one core but failing on multiple cores, or certain multiples of cores) frequently. It's almost always due to an unstable system. Have your user try equilibrating longer, or minimize with flexible water before trying equilibration. You can search the GROMACS web site for the phrase "blowing up" for more information. Cheers, Matt Z. On Mon, Jan 16, 2012 at 8:37 AM, Marani Alessandro wrote: > Dear users, > I would like to ask your help about understanding a problem i'm not able to > recognize by myself. > Basically, a user of our sistem (IBM SP6, power6 architecture) is trying to > run a simulation of a very simple sistem, a polymer chain in a lot of water > molecules. While the simulation works perfectly in serial on her local pc, > when she tries to run it in SP6 using 2 cpus in parallel, the simulation > doesn't even start due of these errors: > > starting mdrun 'PVA head29tail in water' > 250 steps, 5000.0 ps. > > Step 0, time 0 (ps) LINCS WARNING > relative constraint deviation after LINCS: > rms 83427404711319.468750, max 431899260485632.00 (between atoms 59 and > 60) > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > 37 38 89.6 0.1530 124222742528. 0.1530 > 38 41 89.1 0.1530 104382357504. 0.1530 > > Step 0, time 0 (ps) LINCS WARNING > relative constraint deviation after LINCS: > rms 56829711484907.867188, max 212898492186624.00 (between atoms 3 and > 4) > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > 61 62 89.0 0.1530 1380386603008. 0.1530 > 58 61 87.6 0.1530 669758914560. 0.1530 > 58 59 89.2 0.1430 1994809540608. 0.1430 > 59 60 90.0 0.1000 43189926887424. 0.1000 > 57 58 88.3 0.1530 1126801342464. 0.1530 > 54 57 85.9 0.1530 198269452288. 0.1530 > 54 55 89.6 0.1430 1261346488320. 0.1430 > 38 39 89.6 0.1430 156364750848. 0.1430 > 39 40 90.0 0.1000 3183089549312. 0.1000 > [...] > 18 21 89.9 0.1530 215265542144. 0.1530 > 18 19 90.0 0.1430 872386920448. 0.1430 > 19 20 90.0 0.1000 6085561286656. 0.1000 > 95 96 90.0 0.1000 5006930477056. 0.1000 > 97 98 89.7 0.1530 215830478848. 0.1530 > 98 101 90.5 0.1530 232671739904. 0.1530 > 98 99 90.0 0.1430 746076962816. 0.1430 > 99 100 90.0 0.1000 6068662435840. 0.1000 > step 0: Water molecule starting at atom 6014 can not be settled. > Check for bad contacts and/or reduce the timestep if appropriate. > > step 0: Water molecule starting at atom 7355 can not be settled. > Check for bad contacts and/or reduce the timestep if appropriate. > Wrote pdb files with previous and current coordinates > Wrote pdb files with previous and current coordinates > step 0 > Warning: 1-4 interaction between 37 and 40 at distance 3039839053625.364 > which is larger than the 1-4 table size 2.200 nm > These are ignored for the rest of the simulation > This usually means your system is exploding, > if not, you should increase table-extension in your mdp file > or with user tables increase the table size > Warning: 1-4 interaction between 61 and 64 at distance 15924520737123.646 > which is larger than the 1-4 table size 2.200 nm > These are ignored for the rest of the simulation > This usually means your system is exploding, > if not, you should increase table-extension in your mdp file > or with user tables increase the table size > ERROR: 0031-250 task 0: Segmentation fault > ERROR: 0031-250 task 1: Segmentation fault > > The same errors occur when trying the simulation up to 4 cpus, but (and > that's the strange thing), everything works fine with 6+ cpus (actually, > there are some numbers giving an incompatibility error, like "There is no > domain decomposition for 7 nodes that is compatible with the given box and a > minimum cell size of 0.95625 nm", but for example 6 or 8 cpus give a > successful run). > > Can anyone understand what is the reason of this strange behaviour? > Thanks, > Marani Alessandro (HPC User support, CINECA - Italy) > > -- > 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 htt
[gmx-users] Re: LINCS warnings and number of cpus
> > Dear users, > I would like to ask your help about understanding a problem i'm not able > to recognize by myself. > Basically, a user of our sistem (IBM SP6, power6 architecture) is trying > to run a simulation of a very simple sistem, a polymer chain in a lot of > water molecules. While the simulation works perfectly in serial on her > local pc, when she tries to run it in SP6 using 2 cpus in parallel, the > simulation doesn't even start due of these errors: > > /starting mdrun 'PVA head29tail in water' > 250 steps, 5000.0 ps. > > Step 0, time 0 (ps) LINCS WARNING > relative constraint deviation after LINCS: > rms 83427404711319.468750, max 431899260485632.00 (between atoms 59 > and 60) > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > 37 38 89.6 0.1530 124222742528. 0.1530 > 38 41 89.1 0.1530 104382357504. 0.1530 > > Step 0, time 0 (ps) LINCS WARNING > relative constraint deviation after LINCS: > rms 56829711484907.867188, max 212898492186624.00 (between atoms 3 > and 4) > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > 61 62 89.0 0.1530 1380386603008. 0.1530 > 58 61 87.6 0.1530 669758914560. 0.1530 > 58 59 89.2 0.1430 1994809540608. 0.1430 > 59 60 90.0 0.1000 43189926887424. 0.1000 > 57 58 88.3 0.1530 1126801342464. 0.1530 > 54 57 85.9 0.1530 198269452288. 0.1530 > 54 55 89.6 0.1430 1261346488320. 0.1430 > 38 39 89.6 0.1430 156364750848. 0.1430 > 39 40 90.0 0.1000 3183089549312. 0.1000 > // [...] > 18 21 89.9 0.1530 215265542144. 0.1530 > 18 19 90.0 0.1430 872386920448. 0.1430 > 19 20 90.0 0.1000 6085561286656. 0.1000 > 95 96 90.0 0.1000 5006930477056. 0.1000 > 97 98 89.7 0.1530 215830478848. 0.1530 > 98 101 90.5 0.1530 232671739904. 0.1530 > 98 99 90.0 0.1430 746076962816. 0.1430 > 99 100 90.0 0.1000 6068662435840. 0.1000 > step 0: Water molecule starting at atom 6014 can not be settled. > Check for bad contacts and/or reduce the timestep if appropriate. > > step 0: Water molecule starting at atom 7355 can not be settled. > Check for bad contacts and/or reduce the timestep if appropriate. > Wrote pdb files with previous and current coordinates > Wrote pdb files with previous and current coordinates > step 0 > Warning: 1-4 interaction between 37 and 40 at distance 3039839053625.364 > which is larger than the 1-4 table size 2.200 nm > These are ignored for the rest of the simulation > This usually means your system is exploding, > if not, you should increase table-extension in your mdp file > or with user tables increase the table size > Warning: 1-4 interaction between 61 and 64 at distance > 15924520737123.646 which is larger than the 1-4 table size 2.200 nm > These are ignored for the rest of the simulation > This usually means your system is exploding, > if not, you should increase table-extension in your mdp file > or with user tables increase the table size > ERROR: 0031-250 task 0: Segmentation fault > ERROR: 0031-250 task 1: Segmentation fault > > /The same errors occur when trying the simulation up to 4 cpus, but (and > that's the strange thing), everything works fine with 6+ cpus (actually, > there are some numbers giving an incompatibility error, like /"There is > no domain decomposition for 7 nodes that is compatible with the given > box and a minimum cell size of 0.95625 nm"/, but for example 6 or 8 cpus > give a successful run). > > Can anyone understand what is the reason of this strange behaviour? > Thanks, > Marani Alessandro (HPC User support, CINECA - Italy) Hmm... Try "mdrun -pd %NUMPROC" -- Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA -- 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)
-- 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 and number of cpus
Dear users, I would like to ask your help about understanding a problem i'm not able to recognize by myself. Basically, a user of our sistem (IBM SP6, power6 architecture) is trying to run a simulation of a very simple sistem, a polymer chain in a lot of water molecules. While the simulation works perfectly in serial on her local pc, when she tries to run it in SP6 using 2 cpus in parallel, the simulation doesn't even start due of these errors: /starting mdrun 'PVA head29tail in water' 250 steps, 5000.0 ps. Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 83427404711319.468750, max 431899260485632.00 (between atoms 59 and 60) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 37 38 89.60.1530 124222742528. 0.1530 38 41 89.10.1530 104382357504. 0.1530 Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 56829711484907.867188, max 212898492186624.00 (between atoms 3 and 4) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 61 62 89.00.1530 1380386603008. 0.1530 58 61 87.60.1530 669758914560. 0.1530 58 59 89.20.1430 1994809540608. 0.1430 59 60 90.00.1000 43189926887424. 0.1000 57 58 88.30.1530 1126801342464. 0.1530 54 57 85.90.1530 198269452288. 0.1530 54 55 89.60.1430 1261346488320. 0.1430 38 39 89.60.1430 156364750848. 0.1430 39 40 90.00.1000 3183089549312. 0.1000 // [...] 18 21 89.90.1530 215265542144. 0.1530 18 19 90.00.1430 872386920448. 0.1430 19 20 90.00.1000 6085561286656. 0.1000 95 96 90.00.1000 5006930477056. 0.1000 97 98 89.70.1530 215830478848. 0.1530 98101 90.50.1530 232671739904. 0.1530 98 99 90.00.1430 746076962816. 0.1430 99100 90.00.1000 6068662435840. 0.1000 step 0: Water molecule starting at atom 6014 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. step 0: Water molecule starting at atom 7355 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates step 0 Warning: 1-4 interaction between 37 and 40 at distance 3039839053625.364 which is larger than the 1-4 table size 2.200 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size Warning: 1-4 interaction between 61 and 64 at distance 15924520737123.646 which is larger than the 1-4 table size 2.200 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size ERROR: 0031-250 task 0: Segmentation fault ERROR: 0031-250 task 1: Segmentation fault /The same errors occur when trying the simulation up to 4 cpus, but (and that's the strange thing), everything works fine with 6+ cpus (actually, there are some numbers giving an incompatibility error, like /"There is no domain decomposition for 7 nodes that is compatible with the given box and a minimum cell size of 0.95625 nm"/, but for example 6 or 8 cpus give a successful run). Can anyone understand what is the reason of this strange behaviour? Thanks, Marani Alessandro (HPC User support, CINECA - Italy) -- 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] About g_traj, plotting displacement
Kiwoong Kim wrote: Hi, I'm trying to plot the displacements in z-coordinate of each particle belonging to some index group using g_traj. I typed below thing in prompt g_traj -f md_0_2_nvt.xtc -s md_0_2_nvt.tpr -n index_traj.ndx -nox -noy -b 0 -e 50 -ox traj -w -xvg xmgrace There are 6 atoms in the desired index group. Although I selected the desired index group (let assume it is 1, 2, 3, 4, 5, 6 labelled) atoms, the g_traj only plots the displacement of first atom in index group (i.e., the displacement of atom 1 but not 2, 3, 4, 5, 6). I want to plot the displacements of all atoms (1 - 6). How do I have to do??? What things is incorrect? Likely the manner in which the data sets were plotted. Use a text editor to confirm that there are 6 data sets in traj.xvg, then if you find what you expect: xmgrace -nxy traj.xvg Otherwise, there may be some problem such that only 1 data set is produced, but I have never seen that happen. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] About g_traj, plotting displacement
Hi, I'm trying to plot the displacements in z-coordinate of each particle belonging to some index group using g_traj. I typed below thing in prompt g_traj -f md_0_2_nvt.xtc -s md_0_2_nvt.tpr -n index_traj.ndx -nox -noy -b 0 -e 50 -ox traj -w -xvg xmgrace There are 6 atoms in the desired index group. Although I selected the desired index group (let assume it is 1, 2, 3, 4, 5, 6 labelled) atoms, the g_traj only plots the displacement of first atom in index group (i.e., the displacement of atom 1 but not 2, 3, 4, 5, 6). I want to plot the displacements of all atoms (1 - 6). How do I have to do??? What things is incorrect? Have a good day :) -- 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] Infrared
Dear gmx-user, I am working in the dinamicas fo aluminophosphates material. I need to calculated de IR spectrum from the trajectory. if is it possible to do this with gromacs?, if someone can help me with this (paper or reviews) it would be great. Best Wishes Hernan This message was sent using IMP, the Internet Messaging Program. -- 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: Need help regarding renumtop
On 14/01/12 08:30, Suman Nandy wrote: Respected Sir, According to suggestions, in gmxusers, I have used renumtop, although it renumbers the ligand topology, but gives a duplicate atom label. ; ERROR: duplicate atom label '4968' for atom #4968 (already used for atom #4968) I used the command "./renumtop topol_Protein_chain_A.itp topol_Chain_B.itp". Kindly help me to overcome this problem. I have also posted it in gmxusers (http://www.mail-archive.com/gmx-users@gromacs.org/msg47032.html) renumtop is intended to be used with a single molecule topology; so the way you use it will not work, as each of the .itp files will contain the topology for a molecule (protein chain). Also, renumtop will require *unique labels* for all atoms, even though they need not be consecutively numbered, and may even be non-numerical. If you want to create a combined molecule topology for both chains, you will first need to (manually) concatenate the corresponding sections (atoms, bonds, angles, etc.) of both topology files, and make sure all atom number/labels are unique. You might do that by appending 'b' to all atom numbers (in all sections) of topol_Chain_B.itp. P.s., I'm not regularly reading the gmx-users list anymore. If you want a response from me, please (also) reply to me directly. -- Groetjes, Anton _ ___ | | | | _ _ ___,| K. Anton Feenstra | | / \ / \'| | | IBIVU/Bioinformatics - Free University Amsterdam | |( | )| | | De Boelelaan 1083A - 1081 HV Amsterdam - Netherlands | | \_/ \_/ | | | Tel +31 20 59 87783 - Fax +31 20 59 87653 - Room P136 | | | feens...@few.vu.nl - www.few.vu.nl/~feenstra/ | | | "I Am Testing Your Grey Matter" (Red Hot Chili| | | Peppers) | |_|___| -- 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] On HBond definition
Hi everyone! On this page http://manual.gromacs.org/online/g_hbond.html there is an option -r2 when using g_hbond. What is this r2? I can't find it in the Gromacs manual. option -a is the angle H-O-O, option -r is the O-O distance which can be switched to H-A by using the "-da no". Need help on what is -r2 (could this be for specifying a third criterion for the for distance O-H in addition to the angle cut-off and O-O distance cut-off). Thanks! Bernard -- 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] pdb2gmx -ss option
Thank you for your response. I use 3.3.3 version because it's this one which is installed on the cluster, and that is difficult to change it without causing any bug and a reviewing is in process for the webservice. So change it now should be difficult. To be able to select cysteins with the -ss option, the distance criterion must be met? In fact, my purpose was to get closer cystein that not met this creterion. But it seems to be not the best solution. Thank you --- Pierre THEVENET On 16/01/12, pitheve...@free.fr wrote: Dear all, I'm using the old 3.3.3 version of gromacs and I try to use the -ss option of pdb2gmx to select interactively the ss bridge in my protein. But I don't remark any change between using -ss option and not using it. The -inter option give me some interactive options such as lys or arg but not ss interactive selection. Could you help me? -- There are various possible reasons, including that the distance criterion is not met, or that your cysteine residues are in different soon-to-be moleculetypes. Unfortunately you haven't provided enough detailed description of your system or your pdb2gmx command line or its output for anyone to work with. You should be sure to have a compelling scientific reason for wanting to use 3.3.3. Performance and useability are much higher with modern versions. 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 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] pdb2gmx -ss option
On 16/01/12, pitheve...@free.fr wrote: > > Dear all, > > I'm using the old 3.3.3 version of gromacs and I try to use the -ss option of > pdb2gmx to select interactively the ss bridge in my protein. > > But I don't remark any change between using -ss option and not using it. The > -inter option give me some interactive options such as lys or arg but not ss > interactive selection. > > Could you help me? > > There are various possible reasons, including that the distance criterion is not met, or that your cysteine residues are in different soon-to-be moleculetypes. Unfortunately you haven't provided enough detailed description of your system or your pdb2gmx command line or its output for anyone to work with. You should be sure to have a compelling scientific reason for wanting to use 3.3.3. Performance and useability are much higher with modern versions. 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] pdb2gmx -ss option
Dear all, I'm using the old 3.3.3 version of gromacs and I try to use the -ss option of pdb2gmx to select interactively the ss bridge in my protein. But I don't remark any change between using -ss option and not using it. The -inter option give me some interactive options such as lys or arg but not ss interactive selection. Could you help me? Thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] genbox
On 16/01/12, vidhya sankar wrote: > > > > > > > > > > > > > > Hello Justin, > > Thanks for your patient reply > > > I would like to solvate my molecules with specific number > of water molecules > what option is a suitable to do that ? in editconf > > with regards > > S.Vidhya sankar > > > > > > See genbox -h. There is an option to set an upper bound on the number of solvent molecules added. It's up to you to choose a suitable volume beforehand. 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] genbox
Hello Justin, Thanks for your patient reply I would like to solvate my molecules with specific number of water molecules what option is a suitable to do that ? in editconf with regards S.Vidhya sankar -- 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
