[gmx-users] Persistence length of whole DNA molecule
Hi all, I want to calculate the persistence length of whole DNA molecule. I know that we can calculate it by using option g_polystat -f .trr -p p.xvg , but I am not able to figure out what set of of atoms I have to select while making the index, so that I could get persistence length of whole DNA molecule. I have tried by giving backbone atom index for calculation but not getting the correct values ? Please suggest me what atom index I should select which can include helical axis information while calculating the persistence length. Thanks regards, Mohan -- 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: Simulating a semi-membrane protein
On 7/22/13 10:21 PM, pavithrakb wrote: Dear Sir, Thank you. I understand it now. But, when apply the force field, should I select the membrane ff like gromos56 (like in your KALP tutorial) or will it be a complex process to select a ff? Choosing a force field is always complicated. There are numerous factors to consider and one must be knowledgeable about the different force fields, their applications to similar systems, and known defects or limitations. Choosing the same force field just because it is used as an example in a tutorial is a poor reason. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] how to remove some molecules
Dear gmx-users I would like to calculate the PMF in a system composed of nanotube+surfactants. for doing this I use the final configuration of previous surfactant adsorption simulation onto carbon nanotube. the problem is I want to remove some of non-adsorbed surfactant molecules. Would you please help me how I can do that? any help would be highly appreciated. -- 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] how to remove some molecules
On 7/23/13 5:40 AM, niaz poorgholami wrote: Dear gmx-users I would like to calculate the PMF in a system composed of nanotube+surfactants. for doing this I use the final configuration of previous surfactant adsorption simulation onto carbon nanotube. the problem is I want to remove some of non-adsorbed surfactant molecules. Would you please help me how I can do that? any help would be highly appreciated. Delete them from the .gro file with a text editor, adjust the number of atoms in the .gro file (second line), adjust the topology accordingly, and probably re-equilibrate for at least a short period of time. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] how to remove some molecules
Thank you Sir for your reply. but I do not know how to recognize the non-adsorbed molecules in a gro file? Is there any way to recognize them in a gro file( I have seen the in VMD)? -- 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] gpu cluster explanation
Hi Richard, Thank you for the help and sorry for the delay in my reply. I tried some test run changing some parameters (e.g. removing PME) and I was able to reach 20ns/day, so I think that 9-11 ns/day it's the max that I can obtain for my setting. thank your again for your help. cheers, Fra On Fri, 12 Jul 2013, at 03:41 PM, Richard Broadbent wrote: On 12/07/13 13:26, Francesco wrote: Hi all, I'm working with a 200K atoms system (protein + explicit water) and after a while using a cpu cluster I had to switch to a gpu cluster. I read both Acceleration and parallelization and Gromacs-gpu documentation pages (http://www.gromacs.org/Documentation/Acceleration_and_parallelization and http://www.gromacs.org/Documentation/Installation_Instructions_4.5/GROMACS-OpenMM) but it's a bit confusing and I need help to understand if I really have understood correctly. :) I have 2 type of nodes: 3gpu ( NVIDIA Tesla M2090) and 2 cpu 6cores each (Intel Xeon E5649 @ 2.53GHz) 8gpu and 2 cpu (6 cores each) 1) I can only have 1 MPI per gpu, meaning that with 3 gpu I can have 3 MPI max. 2) because I have 12 cores I can open 4 OPenMP threads x MPI, because 4x3= 12 now if I have a node with 8 gpu, I can use 4 gpu: 4 MPI and 3 OpenMP is it right? is it possible to use 8 gpu and 8 cores only? you could set -ntomp 0, however and setup mpi/thread mpi to use 8 cores. However, a system that unbalanced (huge amount of gpu power to comparatively little cpu power) is unlikely to get great performance. Using gromacs 4.6.2 and 144 cpu cores I reach 35 ns/day, while with 3 gpu and 12 cores I get 9-11 ns/day. That slowdown is in line with what I got when I tried a similar cpu-gpu setup. That said other's might have some advice that will improve your performance. the command that I use is: mdrun -dlb yes -s input_50.tpr -deffnm 306s_50 -v with n° gpu set via script : #BSUB -n 3 I also tried to set -npme / -nt / -ntmpi / -ntomp, but nothing changes. The mdp file and some statistics are following: START MDP title = G6PD wt molecular dynamics (2bhl.pdb) - NPT MD ; Run parameters integrator = md; Algorithm options nsteps = 2500 ; maximum number of steps to perform [50 ns] dt = 0.002 ; 2 fs = 0.002 ps ; Output control nstxout= 1 ; [steps] freq to write coordinates to trajectory, the last coordinates are always written nstvout= 1 ; [steps] freq to write velocities to trajectory, the last velocities are always written nstlog = 1 ; [steps] freq to write energies to log file, the last energies are always written nstenergy = 1 ; [steps] write energies to disk every nstenergy steps nstxtcout = 1 ; [steps] freq to write coordinates to xtc trajectory xtc_precision = 1000 ; precision to write to xtc trajectory (1000 = default) xtc_grps= system; which coordinate group(s) to write to disk energygrps = system; or System / which energy group(s) to writk ; Bond parameters continuation= yes ; restarting from npt constraints = all-bonds ; Bond types to replace by constraints constraint_algorithm= lincs ; holonomic constraints lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy lincs_warnangle = 30; [degrees] maximum angle that a bond can rotate before LINCS will complain That seems a little loose for constraints but setting that up and checking it's conserving energy and preserving bond lengths is something you'll have to do yourself Richard ; Neighborsearching ns_type = grid ; method of updating neighbor list cutoff-scheme = Verlet nstlist = 10; [steps] frequence to update neighbor list (10) rlist = 1.0 ; [nm] cut-off distance for the short-range neighbor list (1 default) rcoulomb = 1.0 ; [nm] long range electrostatic cut-off rvdw = 1.0 ; [nm] long range Van der Waals cut-off ; Electrostatics coulombtype= PME ; treatment of long range electrostatic interactions vdwtype = cut-off ; treatment of Van der Waals interactions ; Periodic boundary conditions pbc = xyz ; Dispersion correction DispCorr= EnerPres ; appling long range dispersion corrections ; Ewald fourierspacing= 0.12; grid spacing for FFT - controll the higest magnitude of wave vectors (0.12) pme_order = 4 ; interpolation order for PME,
[gmx-users] storage problem during a simulation
Hi all, This morning the gpu cluster that I'm using had some troubles with the network connection between nodes that deny access to the storage. Now, the simulations are still running and it seems that during the shut down mdrun wrote a lot of checkpoints and restarted the simulation once the communication was restored. Do you think that I will have distortions or errors in the final results? this is a portion of the log file: BEGIN LOG ... DD step 4680 vol min/aver 0.851 load imb.: force 18.2% Step Time Lambda 468193620.00.0 Energies (kJ/mol) AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 3.29220e+043.94888e+042.06055e+031.69577e+04 1.50705e+05 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential 3.28228e+05 -2.51293e+04 -3.04153e+068.44070e+03 -2.48786e+06 Kinetic En. Total EnergyTemperature Pres. DC (bar) Pressure (bar) 4.98840e+05 -1.98902e+063.10237e+02 -2.13738e+02 -4.80807e+01 Constr. rmsd 2.76295e-05 Writing checkpoint, step 46813920 at Tue Jul 23 02:45:44 2013 Writing checkpoint, step 46813960 at Tue Jul 23 09:48:22 2013 Writing checkpoint, step 46814000 at Tue Jul 23 09:48:23 2013 Writing checkpoint, step 46814040 at Tue Jul 23 09:48:24 2013 Writing checkpoint, step 46814080 at Tue Jul 23 09:48:25 2013 ... Writing checkpoint, step 46814960 at Tue Jul 23 09:48:44 2013 DD step 46814999 vol min/aver 0.865 load imb.: force 26.2% Step Time Lambda 4681500093630.00.0 Writing checkpoint, step 46815000 at Tue Jul 23 09:48:45 2013 Energies (kJ/mol) AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 3.28615e+043.93530e+041.99727e+031.70754e+04 1.51152e+05 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential 3.30108e+05 -2.51173e+04 -3.04119e+068.48412e+03 -2.48528e+06 Kinetic En. Total EnergyTemperature Pres. DC (bar) Pressure (bar) 4.97562e+05 -1.98772e+063.09443e+02 -2.13533e+02 3.68992e+01 Constr. rmsd 2.70999e-05 Writing checkpoint, step 46815040 at Tue Jul 23 09:48:46 2013 END LOG thank you for your help cheers, Fra -- Francesco Carbone PhD student Institute of Structural and Molecular Biology UCL, London fra.carbone...@ucl.ac.uk -- 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] Rotation Constraints - PMF
Dear user and expert, I'd like ask you a suggestion about a problem that I will try present you schematically. I have got a structure s and I have generated the topolgy file itp for it.A number of separate s in turn generate a complex structure A, that is characterized by a cylindrical shape. Now, I constructed a system with two cylindrical structures, A and B (in total made by 64 s structures), and I'd like make an Umbrella Sampling calculation in order to study the PMF varying the distance between A and B. My problem is that I'd like fix the orientation of the axis of each structure A and B long the z axis, during the dynamics. So I need to put a force into the system or a constrain, such that when the axis of A or B rotates respect to z axis, the force puts back the axis of the structure in the z direction. It this possible? If it is so, could you tell me how to do that? Than you very much, Anna -- 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] Persistence length of whole DNA molecule
Hi, I have not used g_polystat, and I cannot say about usage of this tool. I observed that you missed two oxygen atoms (O3' and O5') in the backbone atom index. There are several methods for the calculation of persistence length of a polymer, and you may look into literature for theories. For example, you can also use end-to-end distance distribution or radius of gyrations. But, these methods are based on the assumptions, so one should be careful. When DNA bends, helical axis is expected to bend simultaneously. Therefore, I suggested to use the helical axis in the last mail. You can calculate helical axis of the DNA using external tools such as 3DNA and Curves+ . If you will be able to calculate the length of axis over which correlations in the tangents are lost, that length will be persistence length. The persistence length of the DNA is ~40-50 nm. To calculate persistence length is difficult for very small DNA because bending in small DNA is rare in simulations. You may look into the literature for the methods applicable to sub-persistence length polymer. With best regards, Rajendra -- 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] Persistence length of whole DNA molecule
Thank you sir for a reply , I missed those atoms , I will try to replace it and then do it. The out put file contains not length but bonds, It says average persistence length is 4.3 bonds. I do not know how to calculate helical axis, I will try today using 3DNA and let you know. Thank you very much, Mohan Maruthi On Tue, Jul 23, 2013 at 3:59 PM, rajendra kumar rjd...@gmail.com wrote: Hi, I have not used g_polystat, and I cannot say about usage of this tool. I observed that you missed two oxygen atoms (O3' and O5') in the backbone atom index. There are several methods for the calculation of persistence length of a polymer, and you may look into literature for theories. For example, you can also use end-to-end distance distribution or radius of gyrations. But, these methods are based on the assumptions, so one should be careful. When DNA bends, helical axis is expected to bend simultaneously. Therefore, I suggested to use the helical axis in the last mail. You can calculate helical axis of the DNA using external tools such as 3DNA and Curves+ . If you will be able to calculate the length of axis over which correlations in the tangents are lost, that length will be persistence length. The persistence length of the DNA is ~40-50 nm. To calculate persistence length is difficult for very small DNA because bending in small DNA is rare in simulations. You may look into the literature for the methods applicable to sub-persistence length polymer. With best regards, Rajendra -- 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] how to remove some molecules
On 7/23/13 5:56 AM, niaz poorgholami wrote: Thank you Sir for your reply. but I do not know how to recognize the non-adsorbed molecules in a gro file? Is there any way to recognize them in a gro file( I have seen the in VMD)? Label them by name in VMD. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] Rotation Constraints - PMF
Hi Anna, please have a look at the Enforced Rotation Section in the Gromacs 4.6 manual. You can restrain the angle of rotation about an axis by setting the rotation rate to zero. There is also a 4.5 add-on available with rotational restraints in the Gromacs git repository (branch rotation). For more info you may want to look at this page: http://www.mpibpc.mpg.de/grubmueller/rotation Best, Carsten On Jul 23, 2013, at 12:18 PM, battis...@libero.it wrote: Dear user and expert, I'd like ask you a suggestion about a problem that I will try present you schematically. I have got a structure s and I have generated the topolgy file itp for it.A number of separate s in turn generate a complex structure A, that is characterized by a cylindrical shape. Now, I constructed a system with two cylindrical structures, A and B (in total made by 64 s structures), and I'd like make an Umbrella Sampling calculation in order to study the PMF varying the distance between A and B. My problem is that I'd like fix the orientation of the axis of each structure A and B long the z axis, during the dynamics. So I need to put a force into the system or a constrain, such that when the axis of A or B rotates respect to z axis, the force puts back the axis of the structure in the z direction. It this possible? If it is so, could you tell me how to do that? Than you very much, Anna -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- 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: Simulating a semi-membrane protein
Sir, I'm new to simulation. is there any papers or materials (book or website) to learn about the forcefields and their limitations. All the advice I get from people is to select a ff and membrane based on the previous works on that protein or protein family. I know its too much to ask but, can you please suggest some papers/materials on forcefields and selecting a membrane. I'm sure it will be useful to many beginners like me. Thankyou. -- View this message in context: http://gromacs.5086.x6.nabble.com/Simulating-a-semi-membrane-protein-tp5010032p5010050.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Simulating a semi-membrane protein
On 7/23/13 7:46 AM, pavithrakb wrote: Sir, I'm new to simulation. is there any papers or materials (book or website) to learn about the forcefields and their limitations. All the advice I get from people is to select a ff and membrane based on the previous works on that protein or protein family. I know its too much to ask but, can you please suggest some papers/materials on forcefields and selecting a membrane. I'm sure it will be useful to many beginners like me. You already have a good starting point - identify what others do. Precedent is important. Then ask yourself, why are others doing what they are doing? To answer that question requires quite a bit of reading. Several days spent reading about different force fields will save you months of wasted time if you blindly choose a poor one for your simulations. The primary literature for many force fields goes back over the course of decades, which will give you an appreciation for the underlying design, assumptions, and implementation of a force field. More recent articles certainly exist that have challenged these force fields under different conditions. Websites and textbooks would be convenient, but I have never seen anything comprehensive on this topic. Maybe someone else has and can suggest it. There is, however, a vast amount of literature that tests different force fields. Some names that come to mind include Bert de Groot and Robert Best, who I know have published several very nice force field comparisons, in addition to the publications of the labs from which the force fields originate. Expect to occupy a lot of time reading before doing any simulations - it is time well spent. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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: Simulating a semi-membrane protein
Dear Pavithrakb, First of all, your choice will depend on the available parameters for the lipid molecules that you want to simulate (check the Lipidbook repositoryhttp://lipidbook.bioch.ox.ac.uk/ ). Concerning the GROMOS force fields the most recent lipid parameters are the ones included in the G54A8 force field (Reif_2012_JCTC_8_3705, Reif_2013_JCTC_9_1247). However, Poger et al proposed an add-on to the standard G53A6 (Poger_2010_JCC_31_1117 and Poger_2010_JCTC_6_325), lately incorporated in the G54A7 (Schmidt_2011_EBJ_40_843), that is commonly used and yields good results for the analysed lipid parameters (i.e. in agreement with experimental measurements). Despite the aforementioned papers, you might want to go through the references listed bellow concerning several lipid parameters for GROMOS force fields or proposed modifications (e.g. cutoff schemes, charges, charge group distributions): - Berger lipids: Berger_1997_JB_72_2010 - Ash lipids: Tieleman_2006_JPCM_18_S1221 - G43A1-S3: Chiu_2009_JPCB_113_2748 - G45A3: Schuler_2001_JCC_22_1205, Chandrasekhar_2003_EBJ_32_67 - Modified Berger: Anezo_2003_JPCB_107_9424 - Modified ffG45A3: Anezo_2003_JPCB_107_9424 - Kukol lipids: Kukol_2009_JCTC_5_615 - G53A6L: Poger_2010_JCC_31_1117, Poger_2010_JCTC_6_325 - G54A7: Schmidt_2011_EBJ_40_843 - G54A8: Reif_2012_JCTC_8_3705, Reif_2013_JCTC_9_1247 -- Catarina Santos Research Student Molecular Simulation Group Instituto de Tecnologia Química e Biológica Universidade Nova de Lisboa Av.da República, Apartado 127 2781-901 Oeiras, Portugal -- 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] Calculate interaction energy dynamically
Thanks so much for the suggestion. By using the command: trjorder -f system.trr -s system.tpr -n system.ndx -da 3 -na 12 -r 2.0 -o system_ordered.trr the resulting system_ordered.trr indeed contained lipids 2,3,4... in the closest proximity to lipid 1 (within the specified cuttoff of 2.0 nm). Then by specifying new energy groups like lipid1, lipid2, etc the energy file was generated with the rerun flag: mdrun_-s system_ordered.tpr -rerun system_ordered.trr -o system_ordered_useless.trr -c system_ordered.gro -e system_ordered.edr many warnings were shown like: WARNING: there may be something wrong with energy file system_ordered.edr Found: step=-1, nre=68, nblock=0, time=31000. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file system_ordered.edr Found: step=-1, nre=68, nblock=0, time=32000. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file system_ordered.edr Found: step=-1, nre=68, nblock=0, time=33000. Trying to skip frame expect a crash though Do these warnings point to some error? From the generated energy file one optionally could select not only coulomb and vdw terms between the goups lipid1, lipid2 and lipid3 but also between lipid1 and lipid1. The coulomb output of lipid1-lipid1 is 0 while vdw is ~ -30-40 kJ/mol. Since the latter is the vdw energy of a lipid with itself should one understand this value as the interaction between different atoms of one lipid? The vdw interactions between lipid1-lipid2 is also ~ -30-40 kJ/mol. Apart from the feeling that these vdw numbers are ~ twice larger than they should does this procedure contain some obvious problems? Thanks very much for all the help. Date: Mon, 22 Jul 2013 08:39:27 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] Calculate interaction energy dynamically On 7/22/13 8:37 AM, Davit Hakobyan wrote: Thanks very much for all your suggestions! One way that you might approach it is to use mdrun -rerun. You could order the lipids with respect to the lipid of interest, such that the reference lipid is always molecule N and the nearest lipid is always written as N+1 in the ordered trajectory file. Then use normal index groups as your energygrps in the .mdp file and recalculate the energies with mdrun -rerun. Do I understand correctly that in the ordered trajectory each frame should have lipids ordered is such a way that in any two frames N and M the lipids with n and n + 1 indices should be neighbors but these need not necessarily be the same lipids in two frames ? Yes. Could you also please inform what command may one use to reorder lipids in a trajectory per frame? Start by reading trjorder -h. The exact approach depends on what you're dealing with. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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
[gmx-users] Getting a .tpr file for C-alpha atoms from an all atom .tpr file
Hello All, I there any way to get a .tpr for C-alpha atoms from an all atom .tpr file. -- *--- Thanks and Regards, Bipin Singh* -- 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] Getting a .tpr file for C-alpha atoms from an all atom .tpr file
On 7/23/13 11:58 AM, bipin singh wrote: Hello All, I there any way to get a .tpr for C-alpha atoms from an all atom .tpr file. tpbconv -h, particularly point 3. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] Calculate interaction energy dynamically
On 7/23/13 11:05 AM, Davit Hakobyan wrote: Thanks so much for the suggestion. By using the command: trjorder -f system.trr -s system.tpr -n system.ndx -da 3 -na 12 -r 2.0 -o system_ordered.trr the resulting system_ordered.trr indeed contained lipids 2,3,4... in the closest proximity to lipid 1 (within the specified cuttoff of 2.0 nm). Then by specifying new energy groups like lipid1, lipid2, etc the energy file was generated with the rerun flag: mdrun_-s system_ordered.tpr -rerun system_ordered.trr -o system_ordered_useless.trr -c system_ordered.gro -e system_ordered.edr many warnings were shown like: WARNING: there may be something wrong with energy file system_ordered.edr Found: step=-1, nre=68, nblock=0, time=31000. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file system_ordered.edr Found: step=-1, nre=68, nblock=0, time=32000. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file system_ordered.edr Found: step=-1, nre=68, nblock=0, time=33000. Trying to skip frame expect a crash though Do these warnings point to some error? Where do they come from - mdrun? g_energy? gmxcheck? If you haven't run gmxcheck on the .edr file, please do. From the generated energy file one optionally could select not only coulomb and vdw terms between the goups lipid1, lipid2 and lipid3 but also between lipid1 and lipid1. The coulomb output of lipid1-lipid1 is 0 while vdw is ~ -30-40 kJ/mol. Since the latter is the vdw energy of a lipid with itself should one understand this value as the interaction between different atoms of one lipid? Yes. There are several intramolecular terms that can come into play here. The vdw interactions between lipid1-lipid2 is also ~ -30-40 kJ/mol. Apart from the feeling that these vdw numbers are ~ twice larger than they should does this procedure contain some obvious problems? Upon what do you base your feeling? In principle, this is a very simple calculation to decompose the short-range nonbonded interactions in a pairwise fashion. Note that these are not free energies and there is no reason to believe that any given force field will be able to produce a physically meaningful value here as the force field almost certainly wasn't parameterized to reproduce such a value. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] Calculate interaction energy dynamically
Thank you very much for your continuous support. Date: Tue, 23 Jul 2013 12:06:57 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] Calculate interaction energy dynamically On 7/23/13 11:05 AM, Davit Hakobyan wrote: Thanks so much for the suggestion. By using the command: trjorder -f system.trr -s system.tpr -n system.ndx -da 3 -na 12 -r 2.0 -o system_ordered.trr the resulting system_ordered.trr indeed contained lipids 2,3,4... in the closest proximity to lipid 1 (within the specified cuttoff of 2.0 nm). Then by specifying new energy groups like lipid1, lipid2, etc the energy file was generated with the rerun flag: mdrun_-s system_ordered.tpr -rerun system_ordered.trr -o system_ordered_useless.trr -c system_ordered.gro -e system_ordered.edr many warnings were shown like: WARNING: there may be something wrong with energy file system_ordered.edr Found: step=-1, nre=68, nblock=0, time=31000. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file system_ordered.edr Found: step=-1, nre=68, nblock=0, time=32000. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file system_ordered.edr Found: step=-1, nre=68, nblock=0, time=33000. Trying to skip frame expect a crash though Do these warnings point to some error? Where do they come from - mdrun? g_energy? gmxcheck? If you haven't run gmxcheck on the .edr file, please do. The above warnings are issued by mdrun. The g_energy generates similar warnings like: WARNING: there may be something wrong with energy file system_ordered.edr Found: step=-1, nre=68, nblock=0, time=74000. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file system_ordered.edr Found: step=-1, nre=68, nblock=0, time=75000. Trying to skip frame expect a crash though Last energy frame read 75 time 75000.000 ... The gmxcheck command: gmxcheck -f system_ordered.trr -c system_ordered.tpr -n system_ordered.ndx -e system_ordered.edr does not give any warning/error. From the generated energy file one optionally could select not only coulomb and vdw terms between the goups lipid1, lipid2 and lipid3 but also between lipid1 and lipid1. The coulomb output of lipid1-lipid1 is 0 while vdw is ~ -30-40 kJ/mol. Since the latter is the vdw energy of a lipid with itself should one understand this value as the interaction between different atoms of one lipid? Yes. There are several intramolecular terms that can come into play here. The vdw interactions between lipid1-lipid2 is also ~ -30-40 kJ/mol. Apart from the feeling that these vdw numbers are ~ twice larger than they should does this procedure contain some obvious problems? Upon what do you base your feeling? In principle, this is a very simple calculation to decompose the short-range nonbonded interactions in a pairwise fashion. Note that these are not free energies and there is no reason to believe that any given force field will be able to produce a physically meaningful value here as the force field almost certainly wasn't parameterized to reproduce such a value. You should be right concerning the vdw values since my feeling was mistakenly based on resembling these absolute values with the difference of the interaction energies between the final and initial configuration (which is ~15-20 kJ/mol). Please let me know if you would have a suggestion about the above mdrun/g_energy warnings. Thanks very much again for your help and time. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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
[gmx-users] Re: gmx-users Digest, Vol 111, Issue 101
Dear Justin, Thank you for your suggestion... Best regards Collins On Mon, Jul 22, 2013 at 10:00 AM, gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Re: mdrun error (Justin Lemkul) 2. LAMBADA and InflateGRO2 (Atila Petrosian) 3. Persistence length calculation using g_polystat (Mohan maruthi sena) 4. Initial cell size is smaller than the cell size limit.. (Kavyashree M) 5. Re: Initial cell size is smaller than the cell size limit.. (Justin Lemkul) -- Message: 1 Date: Sun, 21 Jul 2013 07:14:30 -0400 From: Justin Lemkul jalem...@vt.edu Subject: Re: [gmx-users] mdrun error To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 51ebc296.1080...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 7/21/13 12:18 AM, Collins Nganou wrote: Dear Users, when trying to run the following command: mdrun -v -deffnm protein-EM-solvated -c protein-EM-solvated.pdb I have received the error below. Reading file dna-EM-solvated.tpr, VERSION 4.5.5 (single precision) Starting 2 threads --- Program mdrun, VERSION 4.5.5 Source code file: /build/buildd/gromacs-4.5.5/src/mdlib/domdec.c, line: 6005 Fatal error: Domain decomposition does not support simple neighbor searching, use grid searching or use particle decomposition For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I am looking any suggestion that can help me to overcome this error. Not all combinations of options are compatible, and mdrun already told you exactly what to do. If you want to use DD, you can't use nstype = simple, so you have to invoke mdrun -pd in this case or otherwise switch to nstype = grid. How you proceed depends on what you're trying to achieve with your .mdp settings. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- Message: 2 Date: Sun, 21 Jul 2013 16:43:16 +0430 From: Atila Petrosian atila.petros...@gmail.com Subject: [gmx-users] LAMBADA and InflateGRO2 To: gmx-users gmx-users@gromacs.org Message-ID: caon_0oxo2_zs9h5tifjsa6e7lt7r+8ajqroyfsdvhmp90r2...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Dear gromacs users I want to use LAMBADA and InflateGRO2 to create a system containing dopc lipid + cholesterol + drug. When I use ~/lib/lambada/lambada_rc1/lambada -f1 drug.gro -f2 lipid_chol.gro I encountered with Illegal division by zero at /home/karami/lib/lambada/ lambada_rc1/lambada line 677. How to resolve this issue? Please help me to do this step. Best wishes -- Message: 3 Date: Sun, 21 Jul 2013 23:27:26 +0530 From: Mohan maruthi sena maruthi.s...@gmail.com Subject: [gmx-users] Persistence length calculation using g_polystat To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: CAGbPF0V5mT5N4ZK4LVguaVZZ36PU= iuwpbdlumdgzwxfsub...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Dear gmx users, I would like to calculate persistence length of DNA using gromacs command g_polystat . The out put file of persists.xvg contains persistence length in number of bonds and it shows that the average persistence length = 4.3 bonds. How can we convert no of bonds in to length(nm)?. Please suggest me a way to solve this. Thanks for a reply in advance, With regards, Mohan -- Message: 4 Date: Mon, 22 Jul 2013 10:50:00 +0530 From: Kavyashree M hmkv...@gmail.com Subject: [gmx-users] Initial cell size is smaller than the cell size limit.. To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: caplgqjqw5f5yedmkw64ezgqmbms2fytykpx8njjst9wjfeo...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Dear users, While running a ligand bound MD using AMber03 force field. I got the following error
[gmx-users] GROMACS benchmarks (d.dppc, d.lzm, etc.) with V4.6.1
Hi Folks, I can't seem to get the GROMACS benchmarks to work with 4.6.1. They work fine with 4.5.5. Can anyone offer any suggestion? It dies in grompp first with the following: --- Program grompp_mpi, VERSION 4.6.1 Source code file: /lustre/tuccillo/lustre_backup/UT-NICS/gromacs-4.6.1/src/gmxlib/gmxcpp.c, line: 293 Fatal error: Topology include file spc.itp not found For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors -- View this message in context: http://gromacs.5086.x6.nabble.com/GROMACS-benchmarks-d-dppc-d-lzm-etc-with-V4-6-1-tp5010060.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] storage problem during a simulation
What does gmxcheck have to say about your output files? On Jul 23, 2013 12:17 PM, Francesco frac...@myopera.com wrote: Hi all, This morning the gpu cluster that I'm using had some troubles with the network connection between nodes that deny access to the storage. Now, the simulations are still running and it seems that during the shut down mdrun wrote a lot of checkpoints and restarted the simulation once the communication was restored. Do you think that I will have distortions or errors in the final results? this is a portion of the log file: BEGIN LOG ... DD step 4680 vol min/aver 0.851 load imb.: force 18.2% Step Time Lambda 468193620.00.0 Energies (kJ/mol) AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 3.29220e+043.94888e+042.06055e+031.69577e+04 1.50705e+05 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential 3.28228e+05 -2.51293e+04 -3.04153e+068.44070e+03 -2.48786e+06 Kinetic En. Total EnergyTemperature Pres. DC (bar) Pressure (bar) 4.98840e+05 -1.98902e+063.10237e+02 -2.13738e+02 -4.80807e+01 Constr. rmsd 2.76295e-05 Writing checkpoint, step 46813920 at Tue Jul 23 02:45:44 2013 Writing checkpoint, step 46813960 at Tue Jul 23 09:48:22 2013 Writing checkpoint, step 46814000 at Tue Jul 23 09:48:23 2013 Writing checkpoint, step 46814040 at Tue Jul 23 09:48:24 2013 Writing checkpoint, step 46814080 at Tue Jul 23 09:48:25 2013 ... Writing checkpoint, step 46814960 at Tue Jul 23 09:48:44 2013 DD step 46814999 vol min/aver 0.865 load imb.: force 26.2% Step Time Lambda 4681500093630.00.0 Writing checkpoint, step 46815000 at Tue Jul 23 09:48:45 2013 Energies (kJ/mol) AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 3.28615e+043.93530e+041.99727e+031.70754e+04 1.51152e+05 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential 3.30108e+05 -2.51173e+04 -3.04119e+068.48412e+03 -2.48528e+06 Kinetic En. Total EnergyTemperature Pres. DC (bar) Pressure (bar) 4.97562e+05 -1.98772e+063.09443e+02 -2.13533e+02 3.68992e+01 Constr. rmsd 2.70999e-05 Writing checkpoint, step 46815040 at Tue Jul 23 09:48:46 2013 END LOG thank you for your help cheers, Fra -- Francesco Carbone PhD student Institute of Structural and Molecular Biology UCL, London fra.carbone...@ucl.ac.uk -- 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] storage problem during a simulation
the simulations are still running, they should end tomorrow afternoon. Fra On Tue, 23 Jul 2013, at 06:26 PM, Mark Abraham wrote: What does gmxcheck have to say about your output files? On Jul 23, 2013 12:17 PM, Francesco frac...@myopera.com wrote: Hi all, This morning the gpu cluster that I'm using had some troubles with the network connection between nodes that deny access to the storage. Now, the simulations are still running and it seems that during the shut down mdrun wrote a lot of checkpoints and restarted the simulation once the communication was restored. Do you think that I will have distortions or errors in the final results? this is a portion of the log file: BEGIN LOG ... DD step 4680 vol min/aver 0.851 load imb.: force 18.2% Step Time Lambda 468193620.00.0 Energies (kJ/mol) AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 3.29220e+043.94888e+042.06055e+031.69577e+04 1.50705e+05 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential 3.28228e+05 -2.51293e+04 -3.04153e+068.44070e+03 -2.48786e+06 Kinetic En. Total EnergyTemperature Pres. DC (bar) Pressure (bar) 4.98840e+05 -1.98902e+063.10237e+02 -2.13738e+02 -4.80807e+01 Constr. rmsd 2.76295e-05 Writing checkpoint, step 46813920 at Tue Jul 23 02:45:44 2013 Writing checkpoint, step 46813960 at Tue Jul 23 09:48:22 2013 Writing checkpoint, step 46814000 at Tue Jul 23 09:48:23 2013 Writing checkpoint, step 46814040 at Tue Jul 23 09:48:24 2013 Writing checkpoint, step 46814080 at Tue Jul 23 09:48:25 2013 ... Writing checkpoint, step 46814960 at Tue Jul 23 09:48:44 2013 DD step 46814999 vol min/aver 0.865 load imb.: force 26.2% Step Time Lambda 4681500093630.00.0 Writing checkpoint, step 46815000 at Tue Jul 23 09:48:45 2013 Energies (kJ/mol) AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 3.28615e+043.93530e+041.99727e+031.70754e+04 1.51152e+05 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential 3.30108e+05 -2.51173e+04 -3.04119e+068.48412e+03 -2.48528e+06 Kinetic En. Total EnergyTemperature Pres. DC (bar) Pressure (bar) 4.97562e+05 -1.98772e+063.09443e+02 -2.13533e+02 3.68992e+01 Constr. rmsd 2.70999e-05 Writing checkpoint, step 46815040 at Tue Jul 23 09:48:46 2013 END LOG thank you for your help cheers, Fra -- Francesco Carbone PhD student Institute of Structural and Molecular Biology UCL, London fra.carbone...@ucl.ac.uk -- 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 -- Francesco Carbone PhD student Institute of Structural and Molecular Biology UCL, London fra.carbone...@ucl.ac.uk -- 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] storage problem during a simulation
gmxcheck can still read your output files safely. :-) On Tue, Jul 23, 2013 at 10:26 PM, Francesco frac...@myopera.com wrote: the simulations are still running, they should end tomorrow afternoon. Fra On Tue, 23 Jul 2013, at 06:26 PM, Mark Abraham wrote: What does gmxcheck have to say about your output files? On Jul 23, 2013 12:17 PM, Francesco frac...@myopera.com wrote: Hi all, This morning the gpu cluster that I'm using had some troubles with the network connection between nodes that deny access to the storage. Now, the simulations are still running and it seems that during the shut down mdrun wrote a lot of checkpoints and restarted the simulation once the communication was restored. Do you think that I will have distortions or errors in the final results? this is a portion of the log file: BEGIN LOG ... DD step 4680 vol min/aver 0.851 load imb.: force 18.2% Step Time Lambda 468193620.00.0 Energies (kJ/mol) AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 3.29220e+043.94888e+042.06055e+031.69577e+04 1.50705e+05 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential 3.28228e+05 -2.51293e+04 -3.04153e+068.44070e+03 -2.48786e+06 Kinetic En. Total EnergyTemperature Pres. DC (bar) Pressure (bar) 4.98840e+05 -1.98902e+063.10237e+02 -2.13738e+02 -4.80807e+01 Constr. rmsd 2.76295e-05 Writing checkpoint, step 46813920 at Tue Jul 23 02:45:44 2013 Writing checkpoint, step 46813960 at Tue Jul 23 09:48:22 2013 Writing checkpoint, step 46814000 at Tue Jul 23 09:48:23 2013 Writing checkpoint, step 46814040 at Tue Jul 23 09:48:24 2013 Writing checkpoint, step 46814080 at Tue Jul 23 09:48:25 2013 ... Writing checkpoint, step 46814960 at Tue Jul 23 09:48:44 2013 DD step 46814999 vol min/aver 0.865 load imb.: force 26.2% Step Time Lambda 4681500093630.00.0 Writing checkpoint, step 46815000 at Tue Jul 23 09:48:45 2013 Energies (kJ/mol) AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 3.28615e+043.93530e+041.99727e+031.70754e+04 1.51152e+05 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential 3.30108e+05 -2.51173e+04 -3.04119e+068.48412e+03 -2.48528e+06 Kinetic En. Total EnergyTemperature Pres. DC (bar) Pressure (bar) 4.97562e+05 -1.98772e+063.09443e+02 -2.13533e+02 3.68992e+01 Constr. rmsd 2.70999e-05 Writing checkpoint, step 46815040 at Tue Jul 23 09:48:46 2013 END LOG thank you for your help cheers, Fra -- Francesco Carbone PhD student Institute of Structural and Molecular Biology UCL, London fra.carbone...@ucl.ac.uk -- 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 -- Francesco Carbone PhD student Institute of Structural and Molecular Biology UCL, London fra.carbone...@ucl.ac.uk -- 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] Calculate interaction energy dynamically
On 7/23/13 1:54 PM, Davit Hakobyan wrote: Thank you very much for your continuous support. Date: Tue, 23 Jul 2013 12:06:57 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] Calculate interaction energy dynamically On 7/23/13 11:05 AM, Davit Hakobyan wrote: Thanks so much for the suggestion. By using the command: trjorder -f system.trr -s system.tpr -n system.ndx -da 3 -na 12 -r 2.0 -o system_ordered.trr the resulting system_ordered.trr indeed contained lipids 2,3,4... in the closest proximity to lipid 1 (within the specified cuttoff of 2.0 nm). Then by specifying new energy groups like lipid1, lipid2, etc the energy file was generated with the rerun flag: mdrun_-s system_ordered.tpr -rerun system_ordered.trr -o system_ordered_useless.trr -c system_ordered.gro -e system_ordered.edr many warnings were shown like: WARNING: there may be something wrong with energy file system_ordered.edr Found: step=-1, nre=68, nblock=0, time=31000. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file system_ordered.edr Found: step=-1, nre=68, nblock=0, time=32000. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file system_ordered.edr Found: step=-1, nre=68, nblock=0, time=33000. Trying to skip frame expect a crash though Do these warnings point to some error? Where do they come from - mdrun? g_energy? gmxcheck? If you haven't run gmxcheck on the .edr file, please do. The above warnings are issued by mdrun. The g_energy generates similar warnings like: WARNING: there may be something wrong with energy file system_ordered.edr Found: step=-1, nre=68, nblock=0, time=74000. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file system_ordered.edr Found: step=-1, nre=68, nblock=0, time=75000. Trying to skip frame expect a crash though Last energy frame read 75 time 75000.000 ... The gmxcheck command: gmxcheck -f system_ordered.trr -c system_ordered.tpr -n system_ordered.ndx -e system_ordered.edr does not give any warning/error. Can you please provide the actual gmxcheck output? -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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: Simulating a semi-membrane protein
Thank you both of you for taking time to help me.. This would be definitely useful. thank you so much. -- View this message in context: http://gromacs.5086.x6.nabble.com/Simulating-a-semi-membrane-protein-tp5010032p5010063.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] OpenSuse 12.1 + CUDA Installation Error
*Hi,* *I keep getting errors when I try to install gromacs in OpenSuse 12.1.* *I have installed cuda 5.0 and the nvidia cards. **I have tried with different parameters for cmake:* cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda *When I make, this error appears:* make [ 65%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_single/nb_kernel_ElecEwSh_VdwLJSh_GeomW3W3_avx_256_single.c.o make[2]: *** No hay ninguna regla para construir el objetivo `//home/cuda/Programas/gromacs-4.6.3/build/src/contrib/fftw/gmxfftw-prefix/lib/libfftw3f.a', necesario para `src/gmxlib/libgmx.so.8'. Alto. make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2 make: *** [all] Error 2 *So I decided to compile the fftw library myself with the command:* ./configure --enable-single --enable-shared --enable-sse2 --enable-avx * * *and I think that worked but then this error appears:* cmake .. -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda make [ 64%] Building NVCC (Device) object src/mdlib/nbnxn_cuda/./nbnxn_cuda_generated_nbnxn_cuda.cu.o /home/cuda3/Programas/gromacs-4.6.3/include/types/nbnxn_pairlist.h(216): error: identifier nbnxn_alloc_t is undefined /home/cuda3/Programas/gromacs-4.6.3/include/types/nbnxn_pairlist.h(217): error: identifier nbnxn_free_t is undefined 2 errors detected in the compilation of /tmp/tmpxft_76f4_-11_nbnxn_cuda.compute_20.cpp2.i. CMake Error at CMakeFiles/nbnxn_cuda_generated_nbnxn_cuda.cu.o.cmake:256 (message): Error generating file /home/cuda3/Programas/gromacs-4.6.3/build/src/mdlib/nbnxn_cuda/./nbnxn_cuda_generated_nbnxn_cuda.cu.o make[2]: *** [src/mdlib/nbnxn_cuda/./nbnxn_cuda_generated_nbnxn_cuda.cu.o] Error 1 make[1]: *** [src/mdlib/nbnxn_cuda/CMakeFiles/nbnxn_cuda.dir/all] Error 2 make: *** [all] Error 2 *I need to install with cuda, nevertheless I tried without to see if that would work:* cmake .. make Linking CXX shared library libgmx.so [ 65%] Built target gmx make: *** [all] Error 2 *And to see if I had not installed the library correctly I tried* cmake .. -DGMX_BUILD_OWN_FFTW=ON make [ 65%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_256_single/nb_kernel_ElecEwSh_VdwLJSh_GeomW3W3_avx_256_single.c.o make[2]: *** No hay ninguna regla para construir el objetivo `//home/cuda/Programas/gromacs-4.6.3/build/src/contrib/fftw/gmxfftw-prefix/lib/libfftw3f.a', necesario para `src/gmxlib/libgmx.so.8'. Alto. make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2 make: *** [all] Error 2 *I think the problem is related to the PC's (I have three clones) because I have installed Gromacs+CUDA in Ubuntu 12.04 without problems.* *Any suggestions would be very appreciated.* *Thanks* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] freez gropus
I am doing simulation of metal clusters with membranes by position restrain (with f=1000) the membrane. In this simulation the structure of metal cluster is collapsed after entering into membrane. I want to preserves its structure with out doing position restrain the metal cluster because it has to move. Can you please suggest me how can I solve this problem. -- regards M.SathishKumar -- 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: editconf: Invalid command line argument: –f
Yep, the pdf was not written or copy and pasted the - incorrectly. Thanks :) -Jonathan On Fri, Jul 12, 2013 at 3:03 PM, Jonathan Saboury jsab...@gmail.com wrote: I am following Tutorial 1 from https://extras.csc.fi/chem/courses/gmx2007/tutorial1/index.html I try the command editconf –f conf.gro –bt dodecahedron –d 0.5 –o box.gro but I get the error: Program editconf, VERSION 4.5.5 Source code file: /build/buildd/gromacs-4.5.5/src/gmxlib/statutil.c, line: 819 Invalid command line argument: –f Here are the files I am currently using: http://www.sendspace.com/file/a2twvx What is the problem? Thanks! -Jonathan -- 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] Limitations of simulations?
I just finished this tutorial and found it very informative: http://cinjweb.umdnj.edu/~kerrigje/pdf_files/trp_drug_tutor.pdf However, This was based on a complex from a pdb. I was wondering if it was possible to just simulate the protein without complex and put the ligand as a solute and actually have it complex with the protein. Obviously, if it could do this it would take a much longer time than just simulating a complex, but if given enough time, could it complex? I have no formal experience with simulations and currently have no one around me with enough knowledge on these topic to mentor me, so any help is very much appreciated! Thank you! :) -- 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] Limitations of simulations?
I would like to stop to receive this e-mail, how can i procide?Thanks Fábio Filippi MatioliGraduando em Física MédicaUNESP-BotucatuTel (19) 9291.6738 Date: Tue, 23 Jul 2013 22:57:29 -0700 From: jsab...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] Limitations of simulations? I just finished this tutorial and found it very informative: http://cinjweb.umdnj.edu/~kerrigje/pdf_files/trp_drug_tutor.pdf However, This was based on a complex from a pdb. I was wondering if it was possible to just simulate the protein without complex and put the ligand as a solute and actually have it complex with the protein. Obviously, if it could do this it would take a much longer time than just simulating a complex, but if given enough time, could it complex? I have no formal experience with simulations and currently have no one around me with enough knowledge on these topic to mentor me, so any help is very much appreciated! Thank you! :) -- 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
