Re: [gmx-users] Validation of molecular dynamic simulation results
Well, I also would check which kind of movements I am looking for. It is a known fact that some domain (and, thereby, larger) movements occur in larger timescales and that might not be your case. E.g: you are expecting to see major movements in nanoseconds timescale. I hope this helps. Best regards, -- Marcelo Depólo Polêto Uppsala Universitet - Sweden -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Long trajectory split
But it is not quite happening simultaneously, Justin. It is producing one after another and, consequently, backing up the files. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Long trajectory split
Pretty sure. I ran other simulations in the same system and worked just fine. About the frames, each file contains different number of frames, apparently random numbers (one file contains 400ns of data and other contains 10ns) 2014-02-23 17:54 GMT+01:00 Dr. Vitaly Chaban vvcha...@gmail.com: are you sure that your binary is parallel? how many frames do those trajectory files contain? Dr. Vitaly V. Chaban On Sun, Feb 23, 2014 at 5:32 PM, Marcelo Depólo marcelodep...@gmail.com wrote: Maybe I should explain it better. I am using *mpirun -np 24 mdrun -s prt.tpr -e prt.edr -o prt.trr*, pretty much a standard line. This job in a batch creates the outputs and, after some (random) time, a back up is done and new files are written, but the job itself do not finish. 2014-02-23 17:12 GMT+01:00 Justin Lemkul jalem...@vt.edu: On 2/23/14, 11:00 AM, Marcelo Depólo wrote: But it is not quite happening simultaneously, Justin. It is producing one after another and, consequently, backing up the files. You'll have to provide the exact commands you're issuing. Likely you're leaving the output names to the default, which causes them to be backed up rather than overwritten. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Marcelo Depólo Polêto Uppsala Universitet - Sweden Science without Borders - CAPES Phone: +46 76 581 67 49 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Marcelo Depólo Polêto Uppsala Universitet - Sweden Science without Borders - CAPES Phone: +46 76 581 67 49 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Long trajectory split
Justin, as far as I realized, the next log file starts at 0ps what would mean that it is re-starting for some reason. At first, I imagined that it was only splitting the data among files due to some kind of size limit, as you said, but when I tried to concatenate the trajectories, it gives me a non-sense output, with a lot of 'beginnings'. I will check with the cluster experts if there is some kind of size limit.It seems to be the most logical source of the problem to me. Mark, the only difference this time is the time-scale set since the beginning. Apart from the protein itself, even the .mdp files were copied from a sucessful folder. But thank you both for the support. 2014-02-23 20:20 GMT+01:00 Mark Abraham mark.j.abra...@gmail.com: On Sun, Feb 23, 2014 at 6:48 PM, Marcelo Depólo marcelodep...@gmail.com wrote: Justin, the other runs with the very same binary do not produce the same problem. Mark, I just omitted the _mpi of the line here, but is was compiled as _mpi. OK, that rules that problem out, but please don't simplify and approximate. Computers are exact, and trouble shooting problems with them requires all the information. If we all understood perfectly we wouldn't be having problems ;-) Those files do get closed at checkpoint intervals, so they can be hashed for the hash value to be saved in the checkpoint. It is conceivable some file system would not close-and-re-open them properly. The .log files would comment about at least some such conditions. But the real question is what you are doing differently from the times when you have observed normal behaviour! Mark My log file top: *Gromacs version:VERSION 4.6.1Precision: singleMemory model: 64 bitMPI library:MPIOpenMP support: disabledGPU support:disabledinvsqrt routine:gmx_software_invsqrt(x)CPU acceleration: SSE4.1FFT library:fftw-3.3.2-sse2Large file support: enabledRDTSCP usage: enabledBuilt on: Sex Nov 29 16:08:45 BRST 2013Built by: root@jupiter [CMAKE]Build OS/arch: Linux 2.6.32.13-0.4-default x86_64Build CPU vendor: GenuineIntelBuild CPU brand:Intel(R) Xeon(R) CPU X5650 @ 2.67GHzBuild CPU family: 6 Model: 44 Stepping: 2Build CPU features: apic clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc pcid pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3(...)* *Initializing Domain Decomposition on 24 nodesDynamic load balancing: autoWill sort the charge groups at every domain (re)decompositionInitial maximum inter charge-group distances:two-body bonded interactions: 0.621 nm, LJ-14, atoms 3801 3812 multi-body bonded interactions: 0.621 nm, G96Angle, atoms 3802 3812Minimum cell size due to bonded interactions: 0.683 nmMaximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.820 nmEstimated maximum distance required for P-LINCS: 0.820 nmThis distance will limit the DD cell size, you can override this with -rconGuess for relative PME load: 0.26Will use 18 particle-particle and 6 PME only nodesThis is a guess, check the performance at the end of the log fileUsing 6 separate PME nodesScaling the initial minimum size with 1/0.8 (option -dds) = 1.25Optimizing the DD grid for 18 cells with a minimum initial size of 1.025 nmThe maximum allowed number of cells is: X 8 Y 8 Z 8Domain decomposition grid 3 x 2 x 3, separate PME nodes 6PME domain decomposition: 3 x 2 x 1Interleaving PP and PME nodesThis is a particle-particle only nodeDomain decomposition nodeid 0, coordinates 0 0 0* 2014-02-23 18:08 GMT+01:00 Justin Lemkul jalem...@vt.edu: On 2/23/14, 11:32 AM, Marcelo Depólo wrote: Maybe I should explain it better. I am using *mpirun -np 24 mdrun -s prt.tpr -e prt.edr -o prt.trr*, pretty much a standard line. This job in a batch creates the outputs and, after some (random) time, a back up is done and new files are written, but the job itself do not finish. It would help if you can post the .log file from one of the runs to see the information regarding mdrun's parallel capabilities. This still sounds like a case of an incorrectly compiled binary. Do other runs with the same binary produce the same problem? -Justin 2014-02-23 17:12 GMT+01:00 Justin Lemkul jalem...@vt.edu: On 2/23/14, 11:00 AM, Marcelo Depólo wrote: But it is not quite happening simultaneously, Justin. It is producing one after another and, consequently, backing up the files. You'll have to provide the exact commands you're issuing. Likely you're leaving the output names to the default, which causes them to be backed up rather than overwritten. -Justin -- == Justin
Re: [gmx-users] Long trajectory split
Dear Dr, Which details or files do you need? I would be very happy to solve this question by posting any kind of files that you request. 2014-02-23 22:21 GMT+01:00 Dr. Vitaly Chaban vvcha...@gmail.com: You do not provide all the details. As was pointed at the very beginning, most likely you have incorrect parallelism in this case. Can you post all the files you obtain for people to inspect? Dr. Vitaly V. Chaban On Sun, Feb 23, 2014 at 9:04 PM, Marcelo Depólo marcelodep...@gmail.com wrote: Justin, as far as I realized, the next log file starts at 0ps what would mean that it is re-starting for some reason. At first, I imagined that it was only splitting the data among files due to some kind of size limit, as you said, but when I tried to concatenate the trajectories, it gives me a non-sense output, with a lot of 'beginnings'. I will check with the cluster experts if there is some kind of size limit.It seems to be the most logical source of the problem to me. Mark, the only difference this time is the time-scale set since the beginning. Apart from the protein itself, even the .mdp files were copied from a sucessful folder. But thank you both for the support. 2014-02-23 20:20 GMT+01:00 Mark Abraham mark.j.abra...@gmail.com: On Sun, Feb 23, 2014 at 6:48 PM, Marcelo Depólo marcelodep...@gmail.com wrote: Justin, the other runs with the very same binary do not produce the same problem. Mark, I just omitted the _mpi of the line here, but is was compiled as _mpi. OK, that rules that problem out, but please don't simplify and approximate. Computers are exact, and trouble shooting problems with them requires all the information. If we all understood perfectly we wouldn't be having problems ;-) Those files do get closed at checkpoint intervals, so they can be hashed for the hash value to be saved in the checkpoint. It is conceivable some file system would not close-and-re-open them properly. The .log files would comment about at least some such conditions. But the real question is what you are doing differently from the times when you have observed normal behaviour! Mark My log file top: *Gromacs version:VERSION 4.6.1Precision: singleMemory model: 64 bitMPI library:MPIOpenMP support: disabledGPU support:disabledinvsqrt routine:gmx_software_invsqrt(x)CPU acceleration: SSE4.1FFT library:fftw-3.3.2-sse2Large file support: enabledRDTSCP usage: enabledBuilt on: Sex Nov 29 16:08:45 BRST 2013Built by: root@jupiter [CMAKE]Build OS/arch: Linux 2.6.32.13-0.4-default x86_64Build CPU vendor: GenuineIntelBuild CPU brand:Intel(R) Xeon(R) CPU X5650 @ 2.67GHzBuild CPU family: 6 Model: 44 Stepping: 2Build CPU features: apic clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc pcid pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3(...)* *Initializing Domain Decomposition on 24 nodesDynamic load balancing: autoWill sort the charge groups at every domain (re)decompositionInitial maximum inter charge-group distances:two-body bonded interactions: 0.621 nm, LJ-14, atoms 3801 3812 multi-body bonded interactions: 0.621 nm, G96Angle, atoms 3802 3812Minimum cell size due to bonded interactions: 0.683 nmMaximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.820 nmEstimated maximum distance required for P-LINCS: 0.820 nmThis distance will limit the DD cell size, you can override this with -rconGuess for relative PME load: 0.26Will use 18 particle-particle and 6 PME only nodesThis is a guess, check the performance at the end of the log fileUsing 6 separate PME nodesScaling the initial minimum size with 1/0.8 (option -dds) = 1.25Optimizing the DD grid for 18 cells with a minimum initial size of 1.025 nmThe maximum allowed number of cells is: X 8 Y 8 Z 8Domain decomposition grid 3 x 2 x 3, separate PME nodes 6PME domain decomposition: 3 x 2 x 1Interleaving PP and PME nodesThis is a particle-particle only nodeDomain decomposition nodeid 0, coordinates 0 0 0* 2014-02-23 18:08 GMT+01:00 Justin Lemkul jalem...@vt.edu: On 2/23/14, 11:32 AM, Marcelo Depólo wrote: Maybe I should explain it better. I am using *mpirun -np 24 mdrun -s prt.tpr -e prt.edr -o prt.trr*, pretty much a standard line. This job in a batch creates the outputs and, after some (random) time, a back up is done and new files are written, but the job itself do not finish. It would help if you can post the .log file from one of the runs to see the information regarding mdrun's parallel capabilities. This still sounds like a case
Re: [gmx-users] RDF analysis with respect to center of mass of otein
Carlos, You might want to try a PBC correction with -pbc nojump and another RDF calculation with the corrected trajectory. 2014-09-19 19:10 GMT-03:00 Justin Lemkul jalem...@vt.edu: On 9/19/14 6:07 PM, Carlos Navarro Retamal wrote: Hi Justin, Thanks again for all your help. If the problem is related to periodicity, why if i consider the whole protein i got ‘normal’ results? A normal (non-COM-based) RDF is an atom-based RDF, so periodicity doesn't affect the outcome. In any case i centered the protein with the following command: trjconv -f npt_production.xtc -s npt_production.tpr -center -pbc mol -o traj_center.xtc and then i measure the RDF with the following one: g_rdf -com -f traj_center.xtc -s npt_production.tpr -n index.ndx -o TEST-carbons.xvg But i’m still seeing these weirds peaks a short distance. Unlikely, but it could be related to nrexcl; that's what you should try next. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Marcelo Depólo Polêto Biochemicist University of Viçosa - Brazil -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Atom-barycenter distance
Hi guys! Consider the atoms 1, 2 and 3 forming a triangle: I was wondering how can I calculate the barycenter of this triangle using the atoms coordinates? I want to measure the distance through time but I am not sure if there is a simple way to do it. Cheers! -- Marcelo Biochemicist University of Viçosa - Brazil -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] RDF calculation.
Well, since you are not interested in the duplex stability, I would not use -COM. See, during the simulation, the center-of-mass of such a small helix part can drastically move, leading to a questionable result. Check your system and make sure that you will not face this situation. About the PMF, that depends on the ions you are using and the forcefields. It is already known that some of them are poorly described, so check that out too. Hope it can help! Cheers! 2014-12-27 7:17 GMT-02:00 soumadwip ghosh soumadwipgh...@gmail.com: Hi, I am studying the dynamics of a double stranded DNA in presence of small molecules. I want to study the preferential binding of these molecules in the grooves and backbones of the DNA and also calculate the feasibility of these binding in terms of calculating the free energy change.My question is- 1. while calculating radial distribution functions say between DNA minor groove and choline, should I consider the center-off-mass atom of the minor groove by using the -COM option of g_rdf? 2. Do you think calculation of PMF from g(r) for a specific ion binding with the DNA can provide reliable free energy change or do I have to switch to umbrella sampling? PS: I only want to investigate the small molecule binding, not the stability of the DNA duplex as a whole. Thanks for your time in advance. Soumadwip Ghosh Research Fellow Indian Institute of Technology Bombay India -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Marcelo Depólo Polêto Biochemicist University of Viçosa - Brazil -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] DNA-protein complex
2015-03-18 5:26 GMT-03:00 Urszula Uciechowska urszula.uciechow...@biotech.ug.edu.pl: The force field that I used was ambe99bsc0, and my input file was: ; 7.3.3 Run Control integrator = md; md integrator tinit = 0 ; [ps] starting time for run dt = 0.002 ; [ps] time step for integration nsteps = 500 ; maximum number of steps to integrate, 0.002 * 2,500,000 = 5,000 ps comm_mode = Linear; remove center of mass translation nstcomm = 1 ; [steps] frequency of mass motion removal comm_grps = Protein Non-Protein ; group(s) for center of mass motion removal ; 7.3.8 Output Control nstxout = 250 ; [steps] freq to write coordinates to trajectory nstvout = 250 ; [steps] freq to write velocities to trajectory nstfout = 250 ; [steps] freq to write forces to Why such a low output frequency? You are writing every 5ns.. this is too high for any kind of small system simulation. trajectory nstlog = 100 ; [steps] freq to write energies to log file nstenergy = 500 ; [steps] freq to write energies to energy file nstxtcout = 500 ; [steps] freq to write coordinates to xtc trajectory xtc_precision = 1000 ; [real] precision to write xtc trajectory xtc_grps= System; group(s) to write to xtc trajectory energygrps = System; group(s) to write to energy file ; 7.3.9 Neighbor Searching nstlist = 1 ; [steps] freq to update neighbor list ns_type = grid ; method of updating neighbor list pbc = xyz ; periodic boundary conditions in all directions rlist = 0.8 ; [nm] cut-off distance for the short-range neighbor list ; 7.3.10 Electrostatics coulombtype = PME ; Particle-Mesh Ewald electrostatics rcoulomb= 0.8 ; [nm] distance for Coulomb cut-off ; 7.3.11 VdW vdwtype = cut-off ; twin-range cut-off with rlist where rvdw = rlist rvdw= 0.8 ; [nm] distance for LJ cut-off DispCorr= EnerPres ; apply long range dispersion corrections for energy ; 7.3.13 Ewald fourierspacing = 0.12 ; [nm] grid spacing for FFT grid when using PME pme_order = 4 ; interpolation order for PME, 4 = cubic ewald_rtol = 1e-5 ; relative strength of Ewald-shifted potential at rcoulomb ; 7.3.14 Temperature Coupling tcoupl = v-rescale ; temperature coupling with Nose-Hoover ensemble tc_grps = ProteinNon-Protein; groups to couple seperately to temperature bath tau_t = 0.10.1; [ps] time constant for coupling ref_t = 310310; [K] reference temperature for coupling ; 7.3.15 Pressure Coupling pcoupl = parrinello-rahman ; pressure coupling where box vectors are variable pcoupltype = isotropic ; pressure coupling in x-y-z directions tau_p = 2.0 ; [ps] time constant for coupling compressibility = 4.5e-5; [bar^-1] compressibility ref_p = 1.0 ; [bar] reference pressure for coupling ; 7.3.17 Velocity Generation gen_vel = no; velocity generation turned off ; 7.3.18 Bonds constraints = all-bonds ; convert all bonds to constraints constraint_algorithm= LINCS ; LINear Constraint Solver continuation= yes ; apply constraints to the start configuration lincs_order = 4 ; highest order in the expansion of the contraint coupling matrix lincs_iter = 1 ; number of iterations to correct for rotational lengthening lincs_warnangle = 30; [degrees] maximum angle that a bond can rotate before LINCS will complain It remains difficult to foresee anything without the protocol that you have used. Just the production mdp file will not provide enough info to say anything. Please send your protocol and mdp files. Cheers! -- Marcelo Depólo Polêto Student of MSc Cell and Molecular Biology - UFRGS (Brazil) B.Sc. Biochemistry - University of Viçosa (Brazil) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] DNA-protein complex
2015-03-17 14:35 GMT-03:00 Urszula Uciechowska urszula.uciechow...@biotech.ug.edu.pl: Hi, I am running MD for dsDNA-protein complex. After 50ns I observed that the DNA is unwinding. What did go wrong? Should I have changed something in my input file? You might want to send your input files, so as your force field that you have choose. It is hard to say anything without more details. Also, what do you mean by 'unwinding'? Could you be more specific? Thank you in advance for your suggestions. best regards Urszula Cheers! -- Marcelo Depólo Polêto B.Sc. Biochemistry - University of Viçosa (Brazil) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Carbohydrate force fields in GROMACS
2015-03-20 14:21 GMT-03:00 Justin Lemkul jalem...@vt.edu: On 3/20/15 1:16 PM, Marcelo Depólo wrote: As my previous email said: there is a modified GROMOS forcefield for carbohydrated. Install it and check out which kind of modifications on topologies you should do. Install it, sure, but from where? You provided a DOI to the article, which makes no reference to the availability of the parameters. If the implication is that one needs to manually modify all of the force field files according to what the authors reported, that's one thing, but if you know of a site from which you can download the modified force field, that would be helpful. You can find the forcefield here: http://dqfnet.ufpe.br/biomat/Software.html, provided by one of leaders of the paper. I would be curious to see how well the parameters perform, as well. -Justin 2015-03-20 13:51 GMT-03:00 Justin Lemkul jalem...@vt.edu: On 3/20/15 12:46 PM, mish wrote: Many thanks. Is it possible that GROMOS parameters re also available in similar format like CHARMM? With GROMACS there is only aminoacids.rtp provided for recent GROMOS parameters. In general, I see only protein, dna, rna and lipid parameters are provided in code (included in /top directory) but not for carbohydrates. Do I need to get GROMOS one from literature ? They're included in aminoacids.rtp for every GROMOS force field, but those parameters likely aren't the latest (since they go back to 43A1), so you'll have to replace them or create your own force field directory with updated parameters. Check the user contributions page or the ATB server; they may have the latest files. -Justin On Fri, Mar 20, 2015 at 5:36 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/20/15 12:30 PM, mish wrote: Many thanks. I know parameters are available in literature but my question was how to use them in GROMACS. Now, I can see different residue names (e.g AMAN, BMAN, AGAL, BGAL etc for different monosaccharides in CHARMM). I think I will need to edit input pdb file accordingly. However, I am still Yes, .rtp and coordinate file residue names must match. not sure of methylated monosaccharides have to be constructed as modified monosaccharides, or there are CHARMM parameters for methy (as a separate residue) available and one should use 2 residues in such case. I will have a look in archive to find-out how to create modified monosaccharides. In CHARMM, there are patches that are applied to various residues. There is limited support for such modifications in GROMACS. You can define .tdb entries, but those only work for Protein, DNA, and RNA. So you should not define separate residues for, e.g. a monosaccharide and a methyl residue. Instead, a methylated sugar as a single .rtp entry is the foolproof approach. Chapter 5 of the manual is your friend (.rtp syntax is straightforward) as well as http://www.gromacs.org/ Documentation/How-tos/Adding_a_Residue_to_a_Force_Field -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu
Re: [gmx-users] Carbohydrate force fields in GROMACS
There is also a Modified GROMOS forcefield for glycans here: http://dx.doi.org/10.1021/ct300479h Cheers! -- Marcelo Depólo Polêto Student of MSc Cell and Molecular Biology - UFRGS (Brazil) B.Sc. Biochemistry - University of Viçosa (Brazil) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Carbohydrate force fields in GROMACS
As my previous email said: there is a modified GROMOS forcefield for carbohydrated. Install it and check out which kind of modifications on topologies you should do. 2015-03-20 13:51 GMT-03:00 Justin Lemkul jalem...@vt.edu: On 3/20/15 12:46 PM, mish wrote: Many thanks. Is it possible that GROMOS parameters re also available in similar format like CHARMM? With GROMACS there is only aminoacids.rtp provided for recent GROMOS parameters. In general, I see only protein, dna, rna and lipid parameters are provided in code (included in /top directory) but not for carbohydrates. Do I need to get GROMOS one from literature ? They're included in aminoacids.rtp for every GROMOS force field, but those parameters likely aren't the latest (since they go back to 43A1), so you'll have to replace them or create your own force field directory with updated parameters. Check the user contributions page or the ATB server; they may have the latest files. -Justin On Fri, Mar 20, 2015 at 5:36 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/20/15 12:30 PM, mish wrote: Many thanks. I know parameters are available in literature but my question was how to use them in GROMACS. Now, I can see different residue names (e.g AMAN, BMAN, AGAL, BGAL etc for different monosaccharides in CHARMM). I think I will need to edit input pdb file accordingly. However, I am still Yes, .rtp and coordinate file residue names must match. not sure of methylated monosaccharides have to be constructed as modified monosaccharides, or there are CHARMM parameters for methy (as a separate residue) available and one should use 2 residues in such case. I will have a look in archive to find-out how to create modified monosaccharides. In CHARMM, there are patches that are applied to various residues. There is limited support for such modifications in GROMACS. You can define .tdb entries, but those only work for Protein, DNA, and RNA. So you should not define separate residues for, e.g. a monosaccharide and a methyl residue. Instead, a methylated sugar as a single .rtp entry is the foolproof approach. Chapter 5 of the manual is your friend (.rtp syntax is straightforward) as well as http://www.gromacs.org/ Documentation/How-tos/Adding_a_Residue_to_a_Force_Field -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Marcelo Depólo Polêto Student of MSc Cell and Molecular Biology - UFRGS (Brazil) B.Sc. Biochemistry - University of Viçosa (Brazil) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] genbox + python bug?
Thanks for the insights, Mark. It was a 'aprun' issue. When I remove it from the command, everything worked out. -- Marcelo 2015-03-13 14:10 GMT-03:00 Mark Abraham mark.j.abra...@gmail.com: On Fri, Mar 13, 2015 at 5:46 PM, Marcelo Depólo marcelodep...@gmail.com wrote: Hey, I have a python script running gmx commands (version 4.6.7) until the following: *if systype == 'system_1' or systype == 'system_2':genboxcommand = aprun -n 1 genbox_mpi -cs spc216.gro -cp + prefix + .min0.gro -p + prefix + .top -o + prefix + .wat.gro -maxsol + str(water+ion) + os.system(genboxcommand)* And I get the following: *Invalid command line argument:--cp* As you can see, the -cp flag is correct at the command, but inside the script it is read as '--cp' for some reason. Also, other gmx commands run just fine before the crash. This might be a synergetic bug from python and genbox? Does anyone has a suggestion? I'd actually suspect aprun of over-stepping its bounds - I seem to recall some issue like this reported. Anyway, it is useless to run genbox with MPI (and generally useless to do so in a workflow that needs to run mdrun on a machine where aprun would be used, where your compute resources are lying idle while genbox and friends do string processing and file I/O...), so I'd either do my non-mdrun processing separately, or via a version of GROMACS that is not compiled to run with MPI. Perhaps you can get away with just running genbox_mpi on its own, YMMV. Mark -- Marcelo Depólo Polêto B.Sc. Biochemistry - University of Viçosa (Brazil) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Marcelo Depólo Polêto B.Sc. Biochemistry - University of Viçosa (Brazil) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] genbox + python bug?
Hey, I have a python script running gmx commands (version 4.6.7) until the following: *if systype == 'system_1' or systype == 'system_2':genboxcommand = aprun -n 1 genbox_mpi -cs spc216.gro -cp + prefix + .min0.gro -p + prefix + .top -o + prefix + .wat.gro -maxsol + str(water+ion) + os.system(genboxcommand)* And I get the following: *Invalid command line argument:--cp* As you can see, the -cp flag is correct at the command, but inside the script it is read as '--cp' for some reason. Also, other gmx commands run just fine before the crash. This might be a synergetic bug from python and genbox? Does anyone has a suggestion? -- Marcelo Depólo Polêto B.Sc. Biochemistry - University of Viçosa (Brazil) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Fluorine Gromos LJ parameters
Hi, I've done an extensively search out the web but I could not find LJ parameters for Fluoride (ionic). Gromos54A7 has only Fluorine parameters. Does anyone knows any new parameters for that? Best regards! -- Marcelo Depólo Polêto Student of MSc Cell and Molecular Biology - UFRGS (Brazil) B.Sc. Biochemistry - University of Viçosa (Brazil) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Maximum Force constant for Position Restraints
Hi guys! Is there a maximum value of Force Constant for Position restraints? Reading the Manual I could only find the default and the equation to describe it. Best, -- Marcelo Depólo Polêto Group of Structural Bioinformatics - Center of Biotechnology Student of MSc Cell and Molecular Biology - UFRGS (Brazil) B.Sc. Biochemistry - University of Viçosa (Brazil) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Maximum Force constant for Position Restraints
Thanks Alex. But then, theoretically, is there no limit? All depends on your system's content, right? 2015-04-21 16:16 GMT-03:00 Alex nedoma...@gmail.com: Correction: tau/pi on the left for the highest value and 5*tau/pi for the 10 x period suggestion above. On Tue, Apr 21, 2015 at 1:13 PM, Alex nedoma...@gmail.com wrote: I think this can be estimated from a general physical argument. The absolute max in my opinion should come from 4*pi*tau = sqrt(m/k), where m is the mass of the lightest restrained particle in the system, k is the constant you seek, and tau is the timestep. The coefficient is four because of the Nyquist theorem. I believe GMX tests for high vibrational frequencies according to 20*pi*tau on the left (ten times the period). Hope this helps. Alex On Tue, Apr 21, 2015 at 1:02 PM, Marcelo Depólo marcelodep...@gmail.com wrote: Hi guys! Is there a maximum value of Force Constant for Position restraints? Reading the Manual I could only find the default and the equation to describe it. Best, -- Marcelo Depólo Polêto Group of Structural Bioinformatics - Center of Biotechnology Student of MSc Cell and Molecular Biology - UFRGS (Brazil) B.Sc. Biochemistry - University of Viçosa (Brazil) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Marcelo Depólo Polêto Group of Structural Bioinformatics - Center of Biotechnology Student of MSc Cell and Molecular Biology - UFRGS (Brazil) B.Sc. Biochemistry - University of Viçosa (Brazil) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Position restraint for ions
Hi! I was wondering if there is any clear way to create position restraints for ions. I am using: *g_select -s rna_ions.gro -n index.ndx -on rna_ion.ndx -select 'group non-Water'* - to create an index for my RNA and Ions; and: *genrestr -f rna_ions.gro -n rna_ion.ndx -o rna_ion.itp -fc 800 800 800* - to create an .itp file for them. I am also including this new .itp file to the topology using the proper 'ifdef' statements, but I get this when I run grompp: *Fatal error:[ file rna_ion.itp, line 1753 ]:Atom index (90849) in position_restraints out of bounds (1-1748).This probably means that you have inserted topology section position_restraintsin a part belonging to a different molecule than you intended to.In that case move the position_restraints section to the right molecule.* It seems the ions are not included as the same moleculetype as the RNA and Gromacs see this as an error. Would someone knows a neat way to do this? Cheers! -- Marcelo Depólo Polêto Student of MSc Cell and Molecular Biology - UFRGS (Brazil) B.Sc. Biochemistry - University of Viçosa (Brazil) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] A query
Nope! They are just for our amusement. Maybe only one has to do it: Check your input! David van der Spoel Cheers! Marcelo Depólo Em 13/04/2015 07:05, Priya Das priyadas...@gmail.com escreveu: Dear All, *gcq#6: It's So Lonely When You Don't Even Know Yourself (Red Hot Chili Peppers)* Such messages pop up after running the gromacs commands on terminal. Do these messages have any meaning ? Have they anything to do with the programs we are running? -- *Let us all join hands to save our Mother Earth* Regards, Priya Das Research Scholar Dept. of Computational Biology and Bioinformatics, University of Kerala -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Position restraint for ions
*Fatal error:[ file rna_ion.itp, line 1753 ]:Atom index (90849) in position_restraints out of bounds (1-1748).This probably means that you have inserted topology section position_restraintsin a part belonging to a different molecule than you intended to.In that case move the position_restraints section to the right molecule.* It seems the ions are not included as the same moleculetype as the RNA and Gromacs see this as an error. Would someone knows a neat way to do this? The ions need to be merged into the RNA [moleculetype] definition in order for this to work. This isn't something that is done after the fact with index groups as you're trying above; the topologies need to be merged, e.g. with pdb2gmx -chainsep -merge, or by hand if the ions aren't part of the input coordinate file. Thanks, Justin. I have tried that by using '-merge all' but this created a .top without the ions. RNA and water only. grompp even warned me that my system now has non-zero charge. Any ideas? And surprisingly, if I remove the water with 'editconf', and only then I merge them using pdb2gmx, then the topology is written right (with the ions and zero net charge). Confusing, han? -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 -- Marcelo Depólo Polêto Student of MSc Cell and Molecular Biology - UFRGS (Brazil) B.Sc. Biochemistry - University of Viçosa (Brazil) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Position restraint for ions
2015-04-14 14:54 GMT-03:00 Justin Lemkul jalem...@vt.edu: On 4/14/15 1:48 PM, Marcelo Depólo wrote: Hi! I was wondering if there is any clear way to create position restraints for ions. I am using: *g_select -s rna_ions.gro -n index.ndx -on rna_ion.ndx -select 'group non-Water'* - to create an index for my RNA and Ions; and: *genrestr -f rna_ions.gro -n rna_ion.ndx -o rna_ion.itp -fc 800 800 800* - to create an .itp file for them. I am also including this new .itp file to the topology using the proper 'ifdef' statements, but I get this when I run grompp: *Fatal error:[ file rna_ion.itp, line 1753 ]:Atom index (90849) in position_restraints out of bounds (1-1748).This probably means that you have inserted topology section position_restraintsin a part belonging to a different molecule than you intended to.In that case move the position_restraints section to the right molecule.* It seems the ions are not included as the same moleculetype as the RNA and Gromacs see this as an error. Would someone knows a neat way to do this? The ions need to be merged into the RNA [moleculetype] definition in order for this to work. This isn't something that is done after the fact with index groups as you're trying above; the topologies need to be merged, e.g. with pdb2gmx -chainsep -merge, or by hand if the ions aren't part of the input coordinate file. Thanks, Justin. I have tried that by using '-merge all' but this created a .top without the ions. RNA and water only. grompp even warned me that my system now has non-zero charge. Any ideas? -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Marcelo Depólo Polêto Student of MSc Cell and Molecular Biology - UFRGS (Brazil) B.Sc. Biochemistry - University of Viçosa (Brazil) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Position restraint for ions
2015-04-14 17:26 GMT-03:00 Justin Lemkul jalem...@vt.edu On 4/14/15 3:25 PM, Marcelo Depólo wrote: *Fatal error:[ file rna_ion.itp, line 1753 ]:Atom index (90849) in position_restraints out of bounds (1-1748).This probably means that you have inserted topology section position_restraintsin a part belonging to a different molecule than you intended to.In that case move the position_restraints section to the right molecule.* It seems the ions are not included as the same moleculetype as the RNA and Gromacs see this as an error. Would someone knows a neat way to do this? The ions need to be merged into the RNA [moleculetype] definition in order for this to work. This isn't something that is done after the fact with index groups as you're trying above; the topologies need to be merged, e.g. with pdb2gmx -chainsep -merge, or by hand if the ions aren't part of the input coordinate file. Thanks, Justin. I have tried that by using '-merge all' but this created a .top without the ions. RNA and water only. grompp even warned me that my system now has non-zero charge. Any ideas? And surprisingly, if I remove the water with 'editconf', and only then I merge them using pdb2gmx, then the topology is written right (with the ions and zero net charge). Confusing, han? I can offer no rationalization without seeing your commands and perhaps getting access to your files. Merging RNA+ions is something I do routinely, but I always do that before adding any water or anything else. So how do you insert your ions without water to be exchanged for the ions? -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Marcelo Depólo Polêto Student of MSc Cell and Molecular Biology - UFRGS (Brazil) B.Sc. Biochemistry - University of Viçosa (Brazil) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] simulating liquid SO2 (Sulphur dioxide)
Em 05/04/2015 14:44, Jashimuddin Ashraf jashimuddin.ashra...@gmail.com escreveu: Dear gromacs users, I am trying to simulate liquid SO2 (Sulphur dioxide). So I tried to create an equilibrated structure of SO2 molecules using the gmx insert-molecules function. As I try to minimize the energy of the system, I always get this- Energy minimization has stopped, but the forces have not converged to the requested precision Fmax 10 (which may not be possible for your system). It stopped because the algorithm tried to make a new step whose size was too small, or there was no change in the energy since last step. Either way, we regard the minimization as converged to within the available machine precision, given your starting configuration and EM parameters. That isn't necessarily a problem here, unless the maximum force is too high. You have requested a low threshold (emtol =10) and the machine precision can't reach it on simple precision. I tried to analyze my .gro file that the gmx insert-molecules function is returning me and found that some of my SO2 have a bond in between them. Is this what causes the energy minimization to crash? Also, the .gro file just outputs atoms coordinates. There is no 'bonds' on it. Usualy, that is a visualization problem. Is there any way I can prepare an equilibrated system of liquid SO2 ? Yes. Read the paper 'Force field benchmark for organic liquids' and you might get an idea how to do it. My SO2.itp file is like this (I made this an .itp because I wish to study this system along with some other molecules)- [ moleculetype ] ; Name nrexcl SO23 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB 1 opls_202 1 SR S 1 0.6512 32.07 ;qtot 0.6512 2 opls_326 1 SR O1 2-0.3256 15.99940 ;qtot 0.3256 3 opls_326 1 SR O2 3-0.3256 15.99940 ; qtot 0 ; opls_202 S 16 32.07 0.6512 A3.61500e-01 1.2125232 ; opls_326 O 8 15.99940-0.3256 A3.00500e-01 0.47756176 [ bonds ] ; aiaj functc0c1c2c3 1 2 1 0.1434 635968.0 1 3 1 0.1434635968.0 [ distance_restraints ] ; aiaj type index type' low up1 up2 fac 1 2 1 0 1 1.149 1.490 1.490 1.0 1 3 1 0 1 1.149 1.490 1.490 1.0 [ angles ] ; aiajak functc0c1 c2c3 2 1 3 1119.51359.8 I have also uploaded the .gro file that the gmx insert-molecules function is returning me after this text. SO2_box300.gro https://docs.google.com/file/d/0B8p1k0KkNddyUEN3dzZRZE5keXM/edit?usp=drive_web Thanks in advance. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Explicit Hydrogen LJ param
Hi all! It might be a silly question, but I am wondering why explicit hydrogens do not have LJ parameters in Gromos forcefields (they are set 0), while HC hydrogens (aromatic) has some value: ;name at.num masscharge ptype c6 c12 HC1 0.000 0.000 A 8.464e-05 1.5129e-08 H1 0.000 0.000 A 0 0 Best regards, -- Marcelo Depólo Polêto Group of Structural Bioinformatics - Center of Biotechnology Student of MSc Cell and Molecular Biology - UFRGS (Brazil) B.Sc. Biochemistry - University of Viçosa (Brazil) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Fatal error: Index contains atom numbers larger than the topology
Hi! I am running a DoS calculation using g_dos on 5.0.6 version, using the .tpr used to generate a .trr trajectory. Hence, the topology and index should contain the same number of atoms and I confirmed this by looking the number of atoms on the generated .gro. Still, I got the error: Command = *g_dos_506 -s ani.DOS.tpr -f ani.DOS.trr -beginfit 20 -endfit 40 -T 298 -dos ani.dos.xvg* *Reading file ani.DOS.tpr, VERSION 5.0.6 (single precision)Reading file ani.DOS.tpr, VERSION 5.0.6 (single precision)Group 0 ( System) has 14000 elementsGroup 1 ( Other) has 14000 elementsGroup 2 (ANI) has 14000 elementsSelect a group: 0---Program g_dos_506, VERSION 5.0.6Fatal error:Index contains atom numbers larger than the topology* Does anyone have an idea about it? Cheers! -- Marcelo Depólo Polêto Group of Structural Bioinformatics - Center of Biotechnology Student of MSc Cell and Molecular Biology - UFRGS (Brazil) B.Sc. Biochemistry - University of Viçosa (Brazil) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] gromacs 5 pdb2gmx does not faithfully reproduce the AMBER99sb-ILDN force field
Em 22/07/2015 14:51, Christopher Neale chris.ne...@alum.utoronto.ca escreveu: Dear Users: I believe that gromacs 5 pdb2gmx does not faithfully reproduce the AMBER99sb-ILDN force field. It is not exclusive behavior for any particular FF. I've got same error for Gromos54a7. If one uses multiple terms to describe a dihedral in any force field in Gromacs 5.X series, it is strongly recommended to check the topology twice. I wanted to make a notice here so that people who are using that combination can compare the topologies they get out of gromacs 5 pdb2gmx to gromacs 4 pdb2gmx. Details are here: http://redmine.gromacs.org/issues/1778 Thank you, Chris. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] gmx dos - Possible bug on 5.0.6
Hi all! I've been running gmx dos (version 5.0.4) in some trajectories with the following: echo BEN | gmx_504 dos -s ben.DOS.tpr -f ben.DOS.trr -g ben.log -dos dos.xvg -vacf vacf.xvg -mvacf mvacf.xvg and it runs just fine. But when I run the same line with 5.0.6, I get: *---Program gmx_506, VERSION 5.0.6Source code file: /home/marcelodepolo/Downloads/BACKUP-softwares/gromacs-5.0.6/src/gromacs/gmxana/gmx_dos.c, line: 93Fatal error:Index contains atom numbers larger than the topology* Did anyone already come across this? Cheers! -- Marcelo Depólo Polêto Group of Structural Bioinformatics - Center of Biotechnology Student of MSc Cell and Molecular Biology - UFRGS (Brazil) B.Sc. Biochemistry - University of Viçosa (Brazil) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Calculation of Cv
2015-08-31 12:43 GMT-03:00 Sunil Ghimire <ghimiresuni...@gmail.com>: > No sir.i want to know whether it is possible to obtain from energies and > enthalpy obtained from g_energy? > The answer was just one google away: http://manual.gromacs.org/programs/gmx-energy.html Still, read about Heat Capacities calculations using g_energy and DoS simulations. On 31 Aug 2015 19:57, "David van der Spoel" <sp...@xray.bmc.uu.se> wrote: > > > On 31/08/15 14:15, Sunil Ghimire wrote: > > > >> Dear sir, > >> Thanks for suggestion.This is the theoritical approach.I want to > >> known > >> how can we obtain Cv from the production run done with NVT ensemble? Is > it > >> possible to obtain from g_energy ? > >> > > Have you tried? > > > > On 31 Aug 2015 17:18, "Justin Lemkul" <jalem...@vt.edu> wrote: > >> > >> > >>> > >>> On 8/30/15 10:41 PM, Sunil Ghimire wrote: > >>> > >>> Dear sir, > >>>>How can we calculate the value of Cv for noble gases? > >>>> > >>>> > >>>> http://hyperphysics.phy-astr.gsu.edu/hbase/kinetic/shegas.html > >>> > >>> -Justin > >>> > >>> -- > >>> == > >>> > >>> Justin A. Lemkul, Ph.D. > >>> Ruth L. Kirschstein NRSA Postdoctoral Fellow > >>> > >>> Department of Pharmaceutical Sciences > >>> School of Pharmacy > >>> Health Sciences Facility II, Room 629 > >>> University of Maryland, Baltimore > >>> 20 Penn St. > >>> Baltimore, MD 21201 > >>> > >>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 > >>> http://mackerell.umaryland.edu/~jalemkul > >>> > >>> == > >>> -- > >>> Gromacs Users mailing list > >>> > >>> * Please search the archive at > >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >>> posting! > >>> > >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >>> > >>> * For (un)subscribe requests visit > >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >>> send a mail to gmx-users-requ...@gromacs.org. > >>> > >>> > > > > -- > > David van der Spoel, Ph.D., Professor of Biology > > Dept. of Cell & Molec. Biol., Uppsala University. > > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. > > sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Marcelo Depólo Polêto Group of Structural Bioinformatics - Center of Biotechnology Student of MSc Cell and Molecular Biology - UFRGS (Brazil) B.Sc. Biochemistry - University of Viçosa (Brazil) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] gmx dos - Possible bug on 5.0.6
2015-08-25 17:29 GMT-03:00 David van der Spoel sp...@xray.bmc.uu.se: On 25/08/15 18:24, Marcelo Depólo wrote: Hi all! I've been running gmx dos (version 5.0.4) in some trajectories with the following: echo BEN | gmx_504 dos -s ben.DOS.tpr -f ben.DOS.trr -g ben.log -dos dos.xvg -vacf vacf.xvg -mvacf mvacf.xvg and it runs just fine. But when I run the same line with 5.0.6, I get: That means the results from previous versions may not have been what you thought they would be. What are you trying to accomplish? gmx dos does not do anything useful with an index file. I am calculating Cv from DoS simulations. Still, I haven't use any index file in my line. I used precisely the same one as above. I have checked both gmx_dos.c and there is a new code implemented on 5.0.6, exactly in the part of counting atoms (if I am not mistaken). *---Program gmx_506, VERSION 5.0.6Source code file: /home/marcelodepolo/Downloads/BACKUP-softwares/gromacs-5.0.6/src/gromacs/gmxana/gmx_dos.c, line: 93Fatal error:Index contains atom numbers larger than the topology* Did anyone already come across this? Cheers! -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Marcelo Depólo Polêto Group of Structural Bioinformatics - Center of Biotechnology Student of MSc Cell and Molecular Biology - UFRGS (Brazil) B.Sc. Biochemistry - University of Viçosa (Brazil) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] K+ ions instead of NA+ for neutralization
Depends on what you are simulating. Na+ concentration inside cell is very low, comparing to K+. Thus, if you are simulating cell biomolecules, you should go for K+, and for other cases, Na+. Still, there are some issues with KCl crystal formation on some forcefields when simulating polyelectronic biomolecules (nucleic acids and membranes), widely reported. I would check this cases before designing any simulation Cheers, -- Marcelo Depólo Polêto Structural Bioinformatics Group Master Student - BCM/UFRGS B.Sc. Biochemistry - UFV Em 13/09/2015 09:42, "Vitaly V. Chaban" <vvcha...@gmail.com> escreveu: > Perhaps, K+ is even better. > > > > > On Sun, Sep 13, 2015 at 4:10 AM, Andrew Bostick <andrew.bosti...@gmail.com > > > wrote: > > > Dear gromacs users, > > > > For neutralizing the simulation system, can I use K+ ions instead of NA+? > > > > Best, > > Andrew > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Density of States syntax question
Hi! That's an bug that was not corrected yet for the 5.1 version. Its somehow linked to a safety measure that went nuts. The issue was already directed to the admins. Try to use 501 version. For me, it works just fine. Cheers! 2016-05-31 10:59 GMT-03:00 Chapman, Christopher W. <chapma...@ornl.gov>: > Hello all, > > I am new to Gromacs, so I apologize if this is a trivial question. I'm > running a Gromacs tutorial (found at > https://github.com/wesbarnett/gromacs-tutorials/tree/master/1_tip4pew_water) > using Gromacs v5.1.2, and I was trying to get the Density of States from > the production run. When I type in the following: > > gmx dos -f prd.cpt -s prd.tpr > > and choose any of the Groups listed (0 for 'System', 1 for 'Water', 2 for > 'SOL'), I get the following: > > Program gmx dos, VERSION 5.1.2 > Source code file: > /build/gromacs-z6bPBg/gromacs-5.1.2/src/gromacs/gmxana/gmx_dos.c, line: 94 > > Fatal error: > Index contains atom numbers larger than the topology > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > > What exactly does this mean, and how do I go about fixing this (assuming > it's possible)? Also, is it possible to get the density of states for each > individual atom (Oxygen and Hydrogen, in this case), or is it only > available for the molecule as a whole? > > Sincerely, > > Chris W. Chapman > Computational Reactor and Medical Physics Group > Nuclear and Radiological Engineering > Georgia Institute of Technology > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- -- Marcelo Depólo Polêto MSc Cell and Molecular Biology - UFRGS (Brazil) Group of Structural Bioinformatics - Room 202 Center of Biotechnology - UFRGS Phone: + 55 51 3308-7770 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Hbond residence time
Hi all! I have been looking into the autocorrelation function outputs of 'gmx hbond' in order to calculate the residence time for my water hbond to a specific heteroatom. It turns out that I couldn't find any detailed explanation about each 'type' outputted. In my case: Type Rate (1/ps) Time (ps) DG (kJ/mol) Chi^2 Forward 3.384 0.296 1.506 0.0290557 Backward -0.183 -5.477-666.000 One-way 8.291 0.121 -0.716 Integral 0.802 1.247 5.075 Relaxation 0.767 1.303 5.185 Does anyone have a suggestion of what each of these types mean? Thanks in advance! -- Marcelo Depólo Polêto DSc. Cell and Molecular Biology - UFRGS (Brazil) Group of Structural Bioinformatics - Room 202 Center of Biotechnology - UFRGS Phone: + 55 51 3308-7770 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Donors and Acceptors - gmx hbond
Hi all! I've been wondering how donors and acceptors are defined in gmx hbond. In the help output: "(...) OH and NH groups are regarded as donors, O is an acceptor always, N is an acceptor by default, but this can be switched using -nitacc. Dummy hydrogen atoms are assumed to be connected to the first preceding non-hydrogen atom. You need to specify two groups for analysis, which must be either identical or non-overlapping. All hydrogen bonds between the two groups are analyzed." So if I evaluate a 'OH' group (in MeOH - water solution, for example), will I be calculating the h-bonds donated by H atom and accepted by the O atom at the same time? If so, is there anyway to calculate both separately? Cheers! -- Marcelo Depólo Polêto DSc. Cell and Molecular Biology - UFRGS (Brazil) Group of Structural Bioinformatics - Room 202 Center of Biotechnology - UFRGS Phone: + 55 51 3308-7770 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Donors and Acceptors - gmx hbond - gromacs.org_gmx-users Digest, Vol 160, Issue 67
Hi Mark, I've tried your suggestion. I've made an index file with my oxygen (O) and my hydroxyl group (OH). Here my results: H-bond average (calculated using num.xvg): O = 1.10 +/- 0.62 OH = 2.06 +/- 0.66 (The first line from .log for each group) # DonorHydrogen Acceptor O= SOL2OW SOL2HW1 MET1O OH = MET1O MET1HHSOL2OW My command line for each group was: gmx_507 hbond -s met.SIM.tpr -f met.SIM-traj.xtc -n wat_ana.ndx -shell 0.5 -r 0.35 -a 30 -num met.num.xvg -hbn met.hbn.ndx -don met.donors.xvg -dan met.dan.xvg -g met.log So I am a bit confused. I was expecting only 1 H-bond from OH group (since O is able to donate only one H), and 2 H-bonds accepted for O. Based on the .log, gmx hbond doesn't seem to be calculating H-bond for acceptors and donors at the same time, what would justify this value of 2 for OH (1 accepted and 1 donated). So, I ran out of ideas. Does anyone have any? Does these values make sense? Cheers! Marcelo -- > > Message: 2 > Date: Mon, 14 Aug 2017 12:13:38 + > From: Mark Abraham <mark.j.abra...@gmail.com> > To: gmx-us...@gromacs.org, gromacs.org_gmx-users@maillist.sys.kth.se > Subject: Re: [gmx-users] Donors and Acceptors - gmx hbond > Message-ID: > <CAMNuMAQ2LLXpSQ1ChMoKiBd-YJP4s+76Dou0Wvn5sLmj_UGJng@ > mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Hi, > > I would use the selection groups judiciously, for example have one of them > with only donor atoms in it. > > Mark > > -- -- Marcelo Depólo Polêto DSc. Cell and Molecular Biology - UFRGS (Brazil) Group of Structural Bioinformatics - Room 202 Center of Biotechnology - UFRGS Phone: + 55 51 3308-7770 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] HBond for F and S (Justin Lemkul)
Thanks, Justin! It worked just fine. I guess using a flag to include different atomtypes into the analyses would be a nice feature for next GROMACS versions. Cheers! -- Marcelo Depólo Polêto DSc. Cell and Molecular Biology - UFRGS (Brazil) Group of Structural Bioinformatics - Room 202 Center of Biotechnology - UFRGS Phone: + 55 51 3308-7770 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] HBond for F and S
Hi, Can gmx hbond also calculates hbonds between non-canonical atoms like S or F as well? If so, how can I do it? Cheers! -- Marcelo -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] atomname2types.n2t explanation
Hi Can someone explain what does each column on atomname2types.n2t mean? For gromos53a5 it is: H H0.408 1.008 1 O 0.1 O OA -0.674 15.9994 2 C 0.14 H 0.1 C CH3 0.000 15.0351 C 0.15 C CH0 0.266 12.0114 C 0.15 C 0.15 C 0.15 O 0.14 I suppose the first column is the target atom name, the second is the atom type, the third is charge and the fourth is mass. Is the fifth the number of bonds? And the others? Thanks in advance! -- Marcelo -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Poor GPU Performance with GROMACS 5.1.4
Hi, I had the same struggle benchmarking a similar system last week. Just for curiosity, could you tell us the performance you get when sharing your GPU with multiple jobs? In my case (6k atoms + Reaction field + 8 cores 2.2Ghz + TitanX Pascal), I've got ~440 ns/day. However, I get ~280 ns/day running 2 jobs and sharing the GPU. Cheers! -- Marcelo -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] gmx hbond -tu error
Hi! I am running ACF calculations in gmx hbond tool in 5.0.7 version. When running: gmx hbond -s mol.tpr -f mol.xtc -tu ns -b 0 -e 10 -ac acf_0-10ns.xvg and gmx hbond -s mol.tpr -f mol.xtc -b 0 -e 1 -ac acf_0-10ns.xvg The results given for the ACF are completely different (example: CHI^2 = 0.000347 and CHI^2 = 22.9131, respectively). It seems -tu flag is not working properly here. Still, all graphs generated make sense (going until 5ns, the half of trajectory time analyzed). Does anyone already encountered this error? Thanks! -- Marcelo -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] gmx sorient interpretation
Hi, I am not sure how to interpret the cos(theta1) around my reference atom. The help printed is not straightforward when comes to set which atoms forms the angle theta1. For instance. "theta_1: the angle with the vector from the first atom of the solvent molecule to the midpoint between atoms 2 and 3. theta_2: the angle with the normal of the solvent plane, defined by the same three atoms, or, when the option -v23 is set, the angle with the vector between atoms 2 and 3." In case of water (using default Water group), is oxygen the atom 1 and the hydrogens the atoms 2 and 3? Does it follows the index given by .tpr used for analyses? If so, the distribution as a function of distance gives positive and negative values for cos(theta1). Does positive values means that water oxygen is orient towards my reference at that distance? Cheers! -- Marcelo -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] cmaptypes format
Hi everyone! I was wondering about the cmaptypes format within cmap.itp file. [ cmaptypes ] C N CT C N 1 24 24\ I understand that C-N-CT-C = phi, N-CT-C-N = psi and 24x24 is the grid size. What does this '1' mean? Thanks in advance! -- Marcelo Depólo Polêto Postdoctoral Researcher BIOAGRO - Room T07 Department of General Biology - UFV Contact: + 55 31 3612-2464 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Residue-Specific CMAPS in GROMACS
Hi all, I've been investigating the implementation of CMAP in GROMACS and, as far as I understood, the current CMAP format does not allow the use of residue-specific CMAPS, since it is based on atomtypes and not on function numbers, as GROMACS normally do. For example, for AMBER, the function number '9' is defined for dihedral format: [ dihedrals ] ; aiajakal funct 2 1 5 6 9 Considering that FFSB19 ( https://pubs.acs.org/doi/abs/10.1021/acs.jctc.9b00591) uses residue-specific CMAPs, it I create two different CMAPs for ALA and LEU residues, it would lead to the same header format for both: [ cmaptypes ] C N CT C N 1 24 24\ Therefore, would it be possible to implement the use of function numbers for CMAPs in GROMACS as well? That dummy '1' could be used as a CMAP ID and called from the topology designed in .rtp file. I am not expert in GROMACS code so I would appreciate any inputs that you may find relevant. Thanks in advance! -- Marcelo Depolo Poleto Postdoctoral Researcher BIOAGRO - Room T07 Department of General Biology - UFV Contact: + 55 31 3612-2464 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] CMAP format on GROMACS
t; >yet removed the GROMOS force fields, but you should be aware of these > >issues and check if molecules in your system are affected before > >proceeding. Further information is available at > >https://redmine.gromacs.org/issues/2884 , and a longer explanation > of our > >decision to remove physically incorrect algorithms can be found at > >https://doi.org/10.26434/chemrxiv.11474583.v1 . > > > > > > WARNING 2 [file md_umbrella.mdp]: > >With Nose-Hoover T-coupling and Parrinello-Rahman p-coupling, tau-p > (1) > >should be at least twice as large as tau-t (1) to avoid resonances > > > > I solved this problem with using -maxwarn option but I am wondering > whether thses warning is passed over. > > What do you think what I happend? dears. Any idea on what caused this > problem? > > The first warning is very verbose and provides you with substantial > justification and background reading. > > As for the second, change tau-p to 2 as suggested. Note that I have not > made any attempt to update the tutorials for the 2020 version, and they > are only guaranteed to be compatible with GROMACS 2018.x versions. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ========== > > > > -- > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > > End of gromacs.org_gmx-users Digest, Vol 189, Issue 13 > ** > -- -- Marcelo Depólo Polêto Postdoctoral Researcher BIOAGRO - Room T07 Department of General Biology - UFV Contact: + 55 31 3612-2464 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] CMAP format on GROMCACS
Hi everybody! Happy new year! =) I would like to understand a little bit better the CMAP format of charmm27.ff within GROMACS. I've looked up in the manual but found little information. I understand that it is defined by 5 atoms (1-4 phi and 2-5 psi), a arbitrary identification number (e.g. 1) and the grid size (e.g. 24x24). But the following grid values are lines with just 10 values each, ended with a "\", instead of a 24 columns- 24 lines matrix. How are those values of CMAP formatted in GMX? Does GMX automatically transform those values in a matrix and, if so, can I consider that its "y-axis" would be PSI and "x-axis" would be PHI? Cheers! -- Marcelo Depólo Polêto Postdoctoral Researcher BIOAGRO - Room T07 Department of General Biology - UFV Contact: + 55 31 3612-2464 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
