[gmx-users] LINCS warnings for bonds that do not exist
My simulation aborts rather quickly because it accumulates too many LINCS warning. I checked the various plots and everything seems to be stable (temperature, pressure, total energy, etc.). The stderr gives me warnings looking like this: Step 2304252, time 4608.5 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.043352, max 0.606635 (between atoms 150 and 151) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 150152 90.00.0985 0.1490 0.1000 150151 90.00.1314 0.1607 0.1000 The problem I see is that atom 150 and 151 do not even have a bond between them (they are the two hydrogens of one water molecule). I also get similar warning between 150 and 152, which are not even on the same water molecule. I have extensively equilibrated the system as I thought that it was the problem originally. Anyone here has an intuition as to why this may happen? Thanks, Christian -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] LINCS warnings for bonds that do not exist
On 8/2/12 9:57 AM, Christian Blouin wrote: My simulation aborts rather quickly because it accumulates too many LINCS warning. I checked the various plots and everything seems to be stable (temperature, pressure, total energy, etc.). The stderr gives me warnings looking like this: Step 2304252, time 4608.5 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.043352, max 0.606635 (between atoms 150 and 151) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 150152 90.00.0985 0.1490 0.1000 150151 90.00.1314 0.1607 0.1000 The problem I see is that atom 150 and 151 do not even have a bond between them (they are the two hydrogens of one water molecule). I also get similar warning between 150 and 152, which are not even on the same water molecule. I have extensively equilibrated the system as I thought that it was the problem originally. If that's true, then something is more fundamentally wrong. The constraint length of 0.1 nm indicates an O-H bond, which makes sense if atom 150 is actually an O, making 151 and 152 H atoms. H-H constraints are possible if using the SETTLE algorithm for rigid water, but in this case something seems inconsistent. Anyone here has an intuition as to why this may happen? LINCS warnings always indicate generic instability in the system. The only real advice is here: http://www.gromacs.org/Documentation/Terminology/Blowing_Up -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[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] 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] 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
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] 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
Re: [gmx-users] Lincs warnings
On 20/01/12, Ben Porebski b...@inoxx.net wrote: Hi all, I've been working on some structures between 2.5A and 3.4A in resolution and all of my structures suffer from lincs warnings. From reading the page about lincs warnings, I've performed a more lengthy equilibration: I'm using gromacs 4.0.7 single precision and the G53a6 force field with spc water model. - Genbox, add ions. - EM until converges - Positional restraints at 2,000 kJ/mol, 200, 20 and 2 for 100ps each at 100K - Followed by simulated annealing with the following parameters: ; Simulated annealing @ positional restraint of 2 kJ/mol annealing = single single annealing_npoints = 3 3 annealing_time = 0 50 2500 50 250 annealing_temp = 100 100 300 100 100 300 - This then undergoes 750ps of md at 300K. Once done. I continue the run in my production MD. Sometimes my structures will crash within 5 ns, sometimes it will run out for 60 ns before I start seeing any lincs warnings. An important trouble-shooting stage is to observe in a visualization program what happens in your simulation immediately before a crash, and look also at the variation in the energy terms. That might mean saving output more often. This could clue you in to a region of structure that is problematic, either atomic clashes that persist through EM+SA, or a malformed topology. See http://www.gromacs.org/Documentation/Terminology/Blowing_Up. Note also that restraining atoms to positions that are of low resolution can be problematic - you apparently don't want large rearrangements during equilibration, but it seems you need to permit more. Note what grompp -h has to say about position restraints. I've attempted to further refine the structures and they behave a little better, but still crash, just less often. To continue the simulation, I will not use the .trr output from the previous simulation. If this doesn't work, I'll run the simulation using shake for 2 ns, but this is significantly slower. I'm a little concerned that these crashes may be introducing some sort of error into the simulation and I'm not sure of the right way to get around this problem. I've played around with changing the lincs order and lincs iteration parameters, which appear to reduce the number of lincs warnings and slows down the simulation slightly. The constraint algorithms are normally not the problem, they're just the machinery most prone to breaking when something else goes wrong. As such, tweaking them is not productive. Another thing I've played with was the constraints. Changing this from all-bonds to hbonds. This stopped my crashes, but a co-worker thought that it may not be accurately modelling the system, or would introduce anomalies into the simulation. My impression was that changing from all-bonds to hbonds would improve the accuracy of the system... But I could be wrong. The accuracy of the numerical integration is strongly tied to the size of the time step and the kinds of constraints you are using. See manual section 6.5. One strategy in your case is a lengthy equilibration period with a short time step (say 0.5fs) and no constraints or restraints at all. Monitor the trends in the energy terms over this period to see if changes are occurring. Mark If anyone has experience with dealing with lincs warnings or simulating low resolution structures, help would be amazing. I've been stuck on this for quite some time now. Cheers, Ben -- 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] 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 a.mar...@cineca.it 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 http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please
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 Alessandroa.mar...@cineca.it 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
[gmx-users] LINCS Warnings in the middle of an MD run
Dear All, About the Lincs warnings in Christoph Meier’ problem, is there any improved method or a better way to deal with them? What we can do is to use shorter timesteps or re-start the simulation using a frame before the first lincs warning? [gmx-users] LINCS Warnings in the middle of an MD run K.A.Feenstra k.a.feenstra at chem.rug.nl mailto:gmx-users%40gromacs.org?Subject=%5Bgmx-users%5D%20LINCS%20Warnings%20in%20the%20middle%20of%20an%20MD%20runIn-Reply-To= Fri Dec 14 10:49:40 CET 2001 * Previous message: [gmx-users] LINCS Warnings in the middle of an MD run http://lists.gromacs.org/pipermail/gmx-users/2001-December/000337.html * Next message: [gmx-users] LINCS Warnings in the middle of an MD run http://lists.gromacs.org/pipermail/gmx-users/2001-December/000348.html * Messages sorted by: [ date ]http://lists.gromacs.org/pipermail/gmx-users/2001-December/date.html#346 [ thread ]http://lists.gromacs.org/pipermail/gmx-users/2001-December/thread.html#346 [ subject ]http://lists.gromacs.org/pipermail/gmx-users/2001-December/subject.html#346 [ author ]http://lists.gromacs.org/pipermail/gmx-users/2001-December/author.html#346 Christoph Meier wrote: Dear all, One of my GROMACS MD simulations crashed after running stably for almost 4ns (=several weeks on our system). The error message I get is this: ... LINCS WARNING relative constraint deviation after LINCS: max 0.000987 (between atoms 3286 and 3289) rms 0.26 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length ... I got almost 100 of these LINCS WARNINGs before the system eventually crashed. The atoms involved (3286 and 3289) belong to a protonated lysine residue, the topology of which was generated in the standard (pdb2gmx) way. Does anybody have suggestions as to what I could do to get round this problem ? Do you think there is anything wrong with the lysine residue or anything else ? I would be grateful for any advice you could give me. Thanks very much ! [.. after reading David's comment, I felt I could add something more...] This is a 'normal' error, in the sense that a rotatable group like your protonated NH3 group in the lysine sidechain, can build up a large rotational velocity. Since this motion couples only weakly with the rest of the system, once you have the high rot. velocity, it stays there for some time. If the velocity builds up too high, lincs will get problems re-setting the bond lengths that get elongeted due to centripetal forces. There is a finite chance to get this buil-up, which obviously increases with simulation length... In short, my view is that this is a more or less physical phenomenon (i.e. not a simulation artefact), but the problem is that eventually at very high velocities your timestep is actually too large. The workaround I usually take is to re-start the simulation using a frame a few 10's of ps before the first lincs warning, and introduce slight round-off errors by using only 6 decimal places (in stead of 7 which are the full precision). This works as follows: 1) use trjconv to write out one frame from your .trr as a .gro file, and set -ndec 6 for the number of decimal places, lile: trjconv -f traj.trr -dump 3890 -o frame.gro -ndec 6 2) use trjconv to convert the .gro file back to .trr: trjconv -f frame.gro -o frame.trr (this is because tpbconv will only read from a .trr file) 3) use tpbconv to generate a .tpr file with the coordinates/velocities from the selected frame: tpconv -s topol.tpr -f frame.trr -o tpxout.tpr you might want to tune the remaining run-time using the -extend option. 4) re-start mdrun using tpxout.tpr This trick works because the slight round-off you introduce (6 vs the 7 decimal places in a full precision .trr) will cause the simulation to 'veer' off its original path very slightly (not normally noticable), with a good chance of avoiding the problematic velocity build-up. -- Groetjes, Anton _ _ CONFIDENTIALITY: This email is intended solely for the person(s) named and may be confidential and/or privileged. If you are not the intended recipient, please delete it, notify us and do not copy, use, or disclose its content. Thank you. Towards A Sustainable Earth: Print Only When Necessary -- 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 with timestep of 5 fs (but not 4 fs)
Hello, I am recently experimenting with a 5 fs timestep using virtual hydrogens and LINCS. I am getting sporadic LINCS warnings, although the system appears stable and does not blow up during the 100ns in which I get such warnings. If I reduce the timestep to 4 fs from 5 fs (and increase nstlist to 5 from 4), then I do not get any such LINCS warnings. It occurs to me that in a larger timestep there could be a larger rotation and that this warning may be entirely benign. I am not sure about that, however, and would welcome any advice here, especially on the way that the 30 deg threshold for a warning message is derived. Thank you, Chris. Here is a snippit from my stderr output during a run: ... Step 1387503, time 6937.51 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000156, max 0.001672 (between atoms 17832 and 17831) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 17832 17831 30.90.0946 0.0947 0.0945 Step 1387503, time 6937.51 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000139, max 0.001582 (between atoms 17832 and 17828) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 17832 17831 31.10.0946 0.0946 0.0945 Step 3601434, time 18007.2 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.35, max 0.000308 (between atoms 18168 and 18165) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 18168 18167 30.10.0945 0.0945 0.0945 Step 4391822, time 21959.1 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000121, max 0.002041 (between atoms 14190 and 14189) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 14190 14189 30.50.0945 0.0947 0.0945 Step 4796357, time 23981.8 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000128, max 0.001443 (between atoms 15532 and 15531) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 15532 15531 31.50.0945 0.0946 0.0945 Step 4796357, time 23981.8 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000111, max 0.001185 (between atoms 15532 and 15531) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 15532 15531 31.80.0945 0.0946 0.0945 Step 4796358, time 23981.8 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000221, max 0.002694 (between atoms 15532 and 15531) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 15532 15531 34.00.0946 0.0948 0.0945 ... With a .mdp file that looks like this: integrator = sd nsteps = 2000 tinit = 0 dt = 0.005 comm_mode = linear nstcomm = 4 comm_grps = System nstxout = 2000 nstvout = 2000 nstfout = 2000 nstlog = 0 nstlist = 4 nstenergy = 2 nstxtcout = 2 ns_type = grid pbc = xyz coulombtype = PME rcoulomb= 0.9 fourierspacing = 0.12 pme_order = 4 vdwtype = cut-off rvdw_switch = 0 rvdw= 1.4 rlist = 0.9 DispCorr= no Pcoupl = Berendsen pcoupltype = semiisotropic compressibility = 4.5e-5 4.5e-5 ref_p = 1. 1. tau_p = 4.04.0 tcoupl = Berendsen tc_grps = System tau_t = 1.0 ref_t = 310. ld-seed = -1 annealing = no gen_vel = yes unconstrained-start = no gen_temp= 310. gen_seed= -1 constraints = all-bonds constraint_algorithm= lincs lincs-iter = 1 lincs-order = 6 ;;;EOF ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] LINCS warnings (6153)
Dear gmx-user, Im just making my first moves in protein dynamics simulation. Ive done some tutorials and peptide-water simulations. But now im intending to change the solvent to CCL4. Ive got the solvent parameters, made the topology file, and the .gro file with the solvent and peptide together. When I run mdrun commando an error message displays: Fatal error: Too many LINCS warnings (6153) 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 My .mdp file is: define = -DFLEXIBLE constraints = none integrator = steep dt = 0.002 ; ps ! nsteps = 400 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb= 1.0 vdwtype = cut-off rvdw= 1.4 fourierspacing = 0.12 fourier_nx= 0 fourier_ny= 0 fourier_nz= 0 pme_order = 4 ewald_rtol= 1e-5 optimize_fft= yes ; ; Energy minimizing stuff ; emtol = 1000.0 emstep = 0.01 Do you know what could be happening, and more important, how to solve it or where to look for the problem ? Thanks, Ernesto. _ More than messages–check out the rest of the Windows Live™. http://www.microsoft.com/windows/windowslive/___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] LINCS warnings (6153)
Ernesto Andres Román wrote: Dear gmx-user, Im just making my first moves in protein dynamics simulation. Ive done some tutorials and peptide-water simulations. But now im intending to change the solvent to CCL4. Ive got the solvent parameters, made the topology file, and the .gro file with the solvent and peptide together. When I run mdrun commando an error message displays: did you do a separate CCl4 simulation? you can probably also up the other lincs flags. Fatal error: Too many LINCS warnings (6153) 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 My .mdp file is: define = -DFLEXIBLE constraints = none integrator = steep dt = 0.002 ; ps ! nsteps = 400 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb= 1.0 vdwtype = cut-off rvdw= 1.4 fourierspacing = 0.12 fourier_nx= 0 fourier_ny= 0 fourier_nz= 0 pme_order = 4 ewald_rtol= 1e-5 optimize_fft= yes ; ; Energy minimizing stuff ; emtol = 1000.0 emstep = 0.01 Do you know what could be happening, and more important, how to solve it or where to look for the problem ? Thanks, Ernesto. check out the rest of the Windows Live™. More than mail–Windows Live™ goes way beyond your inbox. More than messages http://www.microsoft.com/windows/windowslive/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] LINCS warnings (6153)
Hi! I had the same problem and this is what worked for me: 1. You must do an equilibration run WITHOUT any constraints (replace constrained bonds with harmonic bonds (equilibrium bond length = constraint length and force constant suitably high) and increase weight of H atoms to 10.0. 2. Do an equilibration run ( 1ns if practical) with this system. 3. Use the confout.gro file it generates to start your run WITH constraints and the canonical H atom weights. This should work. Ashwin From: Ernesto Andres Román indi...@hotmail.com To: gmx-users@gromacs.org Sent: Thursday, 28 May, 2009 1:10:54 PM Subject: [gmx-users] LINCS warnings (6153) Dear gmx-user, Im just making my first moves in protein dynamics simulation. Ive done some tutorials and peptide-water simulations. But now im intending to change the solvent to CCL4. Ive got the solvent parameters, made the topology file, and the .gro file with the solvent and peptide together. When I run mdrun commando an error message displays: Fatal error: Too many LINCS warnings (6153) 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 My .mdp file is: define = -DFLEXIBLE constraints = none integrator = steep dt = 0.002 ; ps ! nsteps = 400 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb= 1.0 vdwtype = cut-off rvdw= 1.4 fourierspacing = 0.12 fourier_nx= 0 fourier_ny= 0 fourier_nz= 0 pme_order = 4 ewald_rtol= 1e-5 optimize_fft= yes ; ; Energy minimizing stuff ; emtol = 1000.0 emstep = 0.01 Do you know what could be happening, and more important, how to solve it or where to look for the problem ? Thanks, Ernesto. check out the rest of the Windows Live™. More than mail–Windows Live™ goes way beyond your inbox. More than messages Cricket on your mind? Visit the ultimate cricket website. Enter http://beta.cricket.yahoo.com___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] LINCS warnings generated in NPT ensemble and not in NVT
Lee Soin wrote: Hello! I'm using COM pulling with distance constraint between two domains of a protein. The energy minimization and a 100-ps equilibrating process in the NPT ensemble with position restraints on protein atoms all passed OK. Then I applied a distance constraint between COM of two domains and performed the simulaiton in the NPT ensemble. But after the first few steps I received such warnings: restraints and constraints are different phenomena in GROMACS, and it's not clear from this description you're aware of that. Perhaps you could describe better how you implemented your effects. :-) Step 7 Warning: pressure scaling more than 1%, mu: 1.03819 1.03819 1.03819 Step 8 Warning: pressure scaling more than 1%, mu: 0.98123 0.98123 0.98123 Step 9 Warning: pressure scaling more than 1%, mu: 0.746615 0.746615 0.746615 Step 10 Warning: pressure scaling more than 1%, mu: 1.34141 1.34141 1.34141 Step 10, time 0.02 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.017756, max 0.670789 (between atoms 3187 and 3188) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 4334 4336 41.30.0813 0.1101 0.1090 4334 4335 39.20.0813 0.1090 0.1090 4332 4334 32.10.1139 0.1548 0.1529 4325 4326 34.50.0813 0.1091 0.1090 4299 4301 31.10.1077 0.1468 0.1449 4293 4296 34.50.0814 0.1086 0.1090 4284 4285 30.60.0812 0.1093 0.1090 4225 4226 64.80.0812 0.1144 0.1090 4208 4210 31.00.1140 0.1522 0.1529 and then the program exited for too many LINCS warnings. The following two changes lead to no problem: (1) distance constraint between COM of two domains is applied, but the simulation is done in the NVT ensemble; (2) distance restraint using an umbrella potential instead of distance constraint is applied, and the simulation is done in NPT. So can anyone tell me what the problem is? Maybe, if they were confident of your nomenclature. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] LINCS warnings generated in NPT ensemble and not in NVT
The difference between restraints and constraints is indeed something I'm aware of :-) Even though distance restraint between COM of two domains worked just OK for me, I would prefer to use distance constraint since that will introduce fewer artifacts and can fix the distance between two domains exactly at the desired distance. So now everything I'm going to ask is under the assumption that I'm using distance constraint in COM pulling. The protein I'm using consists of two domains, and the problem is as follows: After energy minimization and a 100-ps equilibration in NPT, I applied a distance constraint between COM of two domains and performed COM pulling in the NPT ensemble. But after the first few steps I received such warnings: Step 7 Warning: pressure scaling more than 1%, mu: 1.03819 1.03819 1.03819 Step 8 Warning: pressure scaling more than 1%, mu: 0.98123 0.98123 0.98123 Step 9 Warning: pressure scaling more than 1%, mu: 0.746615 0.746615 0.746615 Step 10 Warning: pressure scaling more than 1%, mu: 1.34141 1.34141 1.34141 Step 10, time 0.02 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.017756, max 0.670789 (between atoms 3187 and 3188) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 4334 4336 41.30.0813 0.1101 0.1090 4334 4335 39.20.0813 0.1090 0.1090 4332 4334 32.10.1139 0.1548 0.1529 4325 4326 34.50.0813 0.1091 0.1090 4299 4301 31.10.1077 0.1468 0.1449 4293 4296 34.50.0814 0.1086 0.1090 4284 4285 30.60.0812 0.1093 0.1090 4225 4226 64.80.0812 0.1144 0.1090 4208 4210 31.00.1140 0.1522 0.1529 .. and then the program exited for too many LINCS warnings. If I change the ensemble to NVT, everything is OK. So I think I have made everything clear, haven't I? And thank you if you can help me again :-) -- SUN Li Department of Physics Nanjing University, China ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] LINCS warnings generated in NPT ensemble and not in NVT
Hello! I'm using COM pulling with distance constraint between two domains of a protein. The energy minimization and a 100-ps equilibrating process in the NPT ensemble with position restraints on protein atoms all passed OK. Then I applied a distance constraint between COM of two domains and performed the simulaiton in the NPT ensemble. But after the first few steps I received such warnings: Step 7 Warning: pressure scaling more than 1%, mu: 1.03819 1.03819 1.03819 Step 8 Warning: pressure scaling more than 1%, mu: 0.98123 0.98123 0.98123 Step 9 Warning: pressure scaling more than 1%, mu: 0.746615 0.746615 0.746615 Step 10 Warning: pressure scaling more than 1%, mu: 1.34141 1.34141 1.34141 Step 10, time 0.02 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.017756, max 0.670789 (between atoms 3187 and 3188) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 4334 4336 41.30.0813 0.1101 0.1090 4334 4335 39.20.0813 0.1090 0.1090 4332 4334 32.10.1139 0.1548 0.1529 4325 4326 34.50.0813 0.1091 0.1090 4299 4301 31.10.1077 0.1468 0.1449 4293 4296 34.50.0814 0.1086 0.1090 4284 4285 30.60.0812 0.1093 0.1090 4225 4226 64.80.0812 0.1144 0.1090 4208 4210 31.00.1140 0.1522 0.1529 and then the program exited for too many LINCS warnings. The following two changes lead to no problem: (1) distance constraint between COM of two domains is applied, but the simulation is done in the NVT ensemble; (2) distance restraint using an umbrella potential instead of distance constraint is applied, and the simulation is done in NPT. So can anyone tell me what the problem is? Thanks in advance. -- SUN Li Department of Physics Nanjing University, China ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
