Re: [gmx-users] Subtract structure to a trajectory
Dear Marco, If no-one can suggest a Gromacs tool, it would be easy to output all the co-ordinates of the atoms and then calculate (atom position) - (average structure position) during post-processing. But maybe you know this already. James On 10 July 2014 22:59, Marco Gerolin marco.gero...@studenti.unipd.it wrote: Dear Gromacs users, I have an MD trajectory, and I need to subtract for each atom and each frame, the coordinate of an average structure. Has Gromacs a tool capable of this? Thank you -- Marco Gerolin Dipartimento di Scienze Chimiche Università degli Studi di Padova Via Marzolo 1, 35131 Padova -- 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] Error in system_inflate.gro coordinates does not match
hello gromacs users thank you justin i got system_shrink.gro after 20 energy minimization and shrinking next step is solvate your syetem but no command is there the command is there is grompp -f ions.mdp -c system_solv.gro -p topol.top -o ions.tpr genion -s ions.tpr -o system_solv_ions.gro -p topol.top -pname NA -nname CL -nn 4 which one is i have to use if both then i do not have system_solv.gro or system_solv_ions.gro (output) i have shrinking and minimize structure files kindly help On Thu, Jul 10, 2014 at 6:02 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/10/14, 5:44 AM, RINU KHATTRI wrote: hello every one i have been removed all the error of previous output but still i got one new error Fatal error: [ file strong_posre.itp, line 3886 ]: Atom index (3882) in position_restraints out of bounds (1-3881). This probably means that you have inserted topology section position_restraints in a part belonging to a different molecule than you intended to. In that case move the position_restraints section to the right molecule. i have been changed the position_restrints but no out put same error please help It's not the location within the .top that's the problem, it's the contents of the actual restraint .itp file. You made a mistake in creating the file, likely including multiple molecules or molecules that are not part of the restrained [moleculetype]. -Justin topol.top ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Strong position restraints for InflateGRO #ifdef STRONG_POSRES #include strong_posre.itp #endif ; Include ligand topology #include drag.itp ; Include POPC chain topology #include popc.itp ; Include water topology #include gromos53a6_lipid.ff/spc.itp On Thu, Jul 10, 2014 at 10:46 AM, RINU KHATTRI nickname.mi...@gmail.com wrote: hello every one ohk i havbben pasted UNK portion from old files because it is still missing in system.gro now after running minimization i got new error old problem has resolved :-) grompp (-: Option Filename Type Description -f minim.mdp Inputgrompp input file with MD parameters -po mdout.mdp Output grompp input file with MD parameters -c system_inflated.gro InputStructure file: gro g96 pdb tpr etc. -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc. -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc. -n index.ndx Input, Opt. Index file -p topol.top InputTopology file -pp processed.top Output, Opt. Topology file -oconfout.tpr Output Run input file: tpr tpb tpa -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt -e ener.edr Input, Opt. Energy file Option Type Value Description -- -[no]h bool no Print help info and quit -[no]version bool no Print version info and quit -niceint0 Set the nicelevel -[no]v bool no Be loud and noisy -timereal -1 Take frame at or first after this time. -[no]rmvsbds bool yes Remove constant bonded interactions with virtual sites -maxwarn int2 Number of allowed warnings during input processing. Not for normal use and may generate unstable systems -[no]zerobool no Set parameters for bonded interactions without defaults to zero instead of generating an error -[no]renum bool yes Renumber atomtypes and minimize number of atomtypes Back Off! I just backed up mdout.mdp to ./#mdout.mdp.8# Generated 813 of the 2346 non-bonded parameter combinations ERROR 1 [file topol.top, line 22752]: No default Proper Dih. types Excluding 3 bonded neighbours molecule type 'Protein_chain_A' Excluding 3 bonded neighbours molecule type 'UNK' Excluding 3 bonded neighbours molecule type 'POPC' NOTE 1 [file topol.top, line 24831]: System has non-zero total charge: 14.788998 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. There was 1 note --- Program grompp, VERSION 4.5.5 Source code file: /build/buildd/gromacs-4.5.5/src/kernel/grompp.c, line: 1388 Fatal error: There was 1 error in input file(s) kindly help On Thu, Jul 10, 2014 at 10:17 AM, RINU KHATTRI nickname.mi...@gmail.com wrote: hello gromacs users ohk justin but if unk is deleted then how to put it back in system_inflate.gro On Wed, Jul 9, 2014 at 5:16 PM, Justin Lemkul jalem...@vt.edu wrote:
Re: [gmx-users] Error in system_inflate.gro coordinates does not match
hello i am following the lysozyme tutorial editconf -f system_shrink20.gro -o newbox.gro -bt dodecahedron -d 1.0 solvate -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro but after running second command i got error solvate command not found gmx solvate is also not working On Fri, Jul 11, 2014 at 12:27 PM, RINU KHATTRI nickname.mi...@gmail.com wrote: hello gromacs users thank you justin i got system_shrink.gro after 20 energy minimization and shrinking next step is solvate your syetem but no command is there the command is there is grompp -f ions.mdp -c system_solv.gro -p topol.top -o ions.tpr genion -s ions.tpr -o system_solv_ions.gro -p topol.top -pname NA -nname CL -nn 4 which one is i have to use if both then i do not have system_solv.gro or system_solv_ions.gro (output) i have shrinking and minimize structure files kindly help On Thu, Jul 10, 2014 at 6:02 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/10/14, 5:44 AM, RINU KHATTRI wrote: hello every one i have been removed all the error of previous output but still i got one new error Fatal error: [ file strong_posre.itp, line 3886 ]: Atom index (3882) in position_restraints out of bounds (1-3881). This probably means that you have inserted topology section position_restraints in a part belonging to a different molecule than you intended to. In that case move the position_restraints section to the right molecule. i have been changed the position_restrints but no out put same error please help It's not the location within the .top that's the problem, it's the contents of the actual restraint .itp file. You made a mistake in creating the file, likely including multiple molecules or molecules that are not part of the restrained [moleculetype]. -Justin topol.top ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Strong position restraints for InflateGRO #ifdef STRONG_POSRES #include strong_posre.itp #endif ; Include ligand topology #include drag.itp ; Include POPC chain topology #include popc.itp ; Include water topology #include gromos53a6_lipid.ff/spc.itp On Thu, Jul 10, 2014 at 10:46 AM, RINU KHATTRI nickname.mi...@gmail.com wrote: hello every one ohk i havbben pasted UNK portion from old files because it is still missing in system.gro now after running minimization i got new error old problem has resolved :-) grompp (-: Option Filename Type Description -f minim.mdp Inputgrompp input file with MD parameters -po mdout.mdp Output grompp input file with MD parameters -c system_inflated.gro InputStructure file: gro g96 pdb tpr etc. -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc. -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc. -n index.ndx Input, Opt. Index file -p topol.top InputTopology file -pp processed.top Output, Opt. Topology file -oconfout.tpr Output Run input file: tpr tpb tpa -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt -e ener.edr Input, Opt. Energy file Option Type Value Description -- -[no]h bool no Print help info and quit -[no]version bool no Print version info and quit -niceint0 Set the nicelevel -[no]v bool no Be loud and noisy -timereal -1 Take frame at or first after this time. -[no]rmvsbds bool yes Remove constant bonded interactions with virtual sites -maxwarn int2 Number of allowed warnings during input processing. Not for normal use and may generate unstable systems -[no]zerobool no Set parameters for bonded interactions without defaults to zero instead of generating an error -[no]renum bool yes Renumber atomtypes and minimize number of atomtypes Back Off! I just backed up mdout.mdp to ./#mdout.mdp.8# Generated 813 of the 2346 non-bonded parameter combinations ERROR 1 [file topol.top, line 22752]: No default Proper Dih. types Excluding 3 bonded neighbours molecule type 'Protein_chain_A' Excluding 3 bonded neighbours molecule type 'UNK' Excluding 3 bonded neighbours molecule type 'POPC' NOTE 1 [file topol.top, line 24831]: System has non-zero total charge: 14.788998 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. There was 1 note --- Program grompp, VERSION 4.5.5 Source code file:
Re: [gmx-users] Graphene topology file
Hi Justin, Thanks for the reply. I changed define= -dflexible to -dposres_water and removed freeze graphene group in my .mdp file and ran the energy minimization and npt again. This time for pbc= xyz, the water doesn't fly away but the graphene sheet curves and does not remain in xy plane. Is it ok for the sheet to bend during simulation and will it not effect the pbc? Also for pbc=xy, the same problem persists as the previous one i.e. following error occurs: Step 20: The charge group starting at atom 796 moved than the distance allowed by the domain decomposition in direction X distance out of cell -0.290927 New coordinates:2.4112.0060.982 Old cell boundaries in direction X:0.0002.702 New cell boundaries in direction X:0.0002.702 --- Program mdrun, VERSION 4.5.5 Source code file: /build/buildd/gromacs-4.5.5/src/mdlib/domdec.c, line: 4124 Fatal error: A charge group moved too far between two domain decomposition steps This usually means that your system is not well equilibrated For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors. Can you please suggest what can be causing the error to occur? Thanks and Regards Sukriti From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul jalem...@vt.edu Sent: Thursday, July 10, 2014 8:50 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Graphene topology file On 7/10/14, 8:46 AM, #SUKRITI GUPTA# wrote: Hi Justin, Thanks for the reply. Following is my npt.mdp file for pbc in xy direction: title = example cpp = define = -DFLEXIBLE You shouldn't use flexible water during MD. The water models in Gromacs were designed to be rigid. constraints = none integrator = md dt = 0.001 nsteps = 10 ;Output control parameters nstxout = 100 nstvout = 100 nstfout = 0 ;Checking for crashes nstcheckpoint = 1000 ; Output frequency for energies to log file and energy file nstlog = 100 nstenergy = 100 ; Output frequency and precision for xtc file nstxtcout = 0 xtc-precision = 1000 ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 10 ; ns algorithm (simple or grid) ns-type = Grid ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = xy ; nblist cut-off domain-decomposition= no rlist = 1.2 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = Cut-off rcoulomb-switch = 0 rcoulomb= 1.2 ; ; Method for doing Van der Waals vdw-type= Switch ; cut-off lengths rvdw-switch = 0 rvdw= 1.0 ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling = yes tcoupl = Berendsen The Berendsen algorithm has known deficiencies. For initial equilibration, it's OK, but don't use it for a production simulation. ; Groups to couple separately tc-grps = Other SOL ; Time constant (ps) and reference temperature (K) tau-t= .25 .25 ref-t= 300 300 ; Pressure coupling Pcoupl = Berendsen Pcoupltype = Semiisotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau-p = 1 1 compressibility = 0 4.5e-5 ref-p= 1.01325 1.01325 ; ; GENERATE VELOCITIES FOR STARTUP RUN gen-vel = yes gen-temp = 300 gen-seed= 173529 nwall = 2 wall_type = 12-6 wall_density = 5 5 wall_atomtype = opls_995 opls_996 wall_r_linpot = 1 wall_ewald_zfac = 3 periodic_molecules=yes freezegrps = GRA freezedim = Y Y Y Freezing the graphene is probably going to generate a lot of problems. You get totally unphysical forces unless you use energygrp_excl properly, but even then, freezing is a severe perturbation to the system. For pbc in xyz, nwall options are not there and I used Isotropic Pcoupletype with compressibility 4.5e-5. Gromacs Userlist is not allowing me to attach images as the size of the mail is increasing to more than 50KB. So can I mail the images to your mail id? No. Post them to an image-sharing site and provide a URL. -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
Re: [gmx-users] Subtract structure to a trajectory
Hello James, actually I don't need to calculate the RMSF, i need the subtracted trajectory to calculate some correlation functions. It seems to me that the unique solution is to write a TCL script ad hoc. I'm totally new with TCL , so probably it would take some time, but it's not a problem. Thank you for helping! 2014-07-11 8:56 GMT+02:00 James jamesresearch...@gmail.com: Dear Marco, If no-one can suggest a Gromacs tool, it would be easy to output all the co-ordinates of the atoms and then calculate (atom position) - (average structure position) during post-processing. But maybe you know this already. James On 10 July 2014 22:59, Marco Gerolin marco.gero...@studenti.unipd.it wrote: Dear Gromacs users, I have an MD trajectory, and I need to subtract for each atom and each frame, the coordinate of an average structure. Has Gromacs a tool capable of this? Thank you -- Marco Gerolin Dipartimento di Scienze Chimiche Università degli Studi di Padova Via Marzolo 1, 35131 Padova -- 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. -- Marco Gerolin Dipartimento di Scienze Chimiche Università degli Studi di Padova Via Marzolo 1, 35131 Padova -- 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] Running job on GPUs
Hello all I am trying to run my job on 2 nodes by utilizing all available cores. On each node of the cluster, we have two GPUs and two sockets with 8 cores each. Every time I am submitting the job, we find that it is running on one node. How to make use of the other node? Till now, I have used following trial commands as suggested in http://www.gromacs.org/Documentation/Acceleration_and_parallelization 1) mpirun -n 2 mdrun_mpi -v -deffnm nvt -ntomp 16 output: Using 2 MPI processes Using 16 OpenMP threads per MPI process WARNING: Oversubscribing the available 16 logical CPU cores with 32 threads. This will cause considerable performance loss! 2) mpirun -n 4 mdrun_mpi -v -deffnm nvt -ntomp 8 output: Incorrect launch configuration: mismatching number of PP MPI processes and GPUs per node. mdrun_mpi was started with 4 PP MPI processes per node, but only 2 GPUs were detected. I understand that the above error comes when number of MPI ranks is not a multiple of number of GPUs intended to be used. But in my case 4 is a multiple of 2. 3) mpirun -n 4 -npernode 2 mdrun_mpi -v -deffnm nvt The job still runs on 1 node. How can I run my job on 2 nodes utilizing all cores and GPUs? Thanks Nidhi -- 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] Running job on GPUs
On Fri, Jul 11, 2014 at 12:18 PM, Nidhi Katyal nidhikatyal1...@gmail.com wrote: Hello all I am trying to run my job on 2 nodes by utilizing all available cores. On each node of the cluster, we have two GPUs and two sockets with 8 cores each. Every time I am submitting the job, we find that it is running on one node. How to make use of the other node? Till now, I have used following trial commands as suggested in http://www.gromacs.org/Documentation/Acceleration_and_parallelization 1) mpirun -n 2 mdrun_mpi -v -deffnm nvt -ntomp 16 output: Using 2 MPI processes Using 16 OpenMP threads per MPI process WARNING: Oversubscribing the available 16 logical CPU cores with 32 threads. This will cause considerable performance loss! You are starting two ranks and these get placed on the first node (presumably because of the job scheduler commands you used). That's why mdrun warns that you are oversubscribing because the 32 threads you meant to spread out across two nodes got started on only one. Note that this will still not work with two GPUs per node, though; as the docs indicate, you need (at least) as many PP ranks as GPUs. 2) mpirun -n 4 mdrun_mpi -v -deffnm nvt -ntomp 8 output: Incorrect launch configuration: mismatching number of PP MPI processes and GPUs per node. mdrun_mpi was started with 4 PP MPI processes per node, but only 2 GPUs were detected. I understand that the above error comes when number of MPI ranks is not a multiple of number of GPUs intended to be used. But in my case 4 is a multiple of 2. The automatic PP rank to GPU mapping only works if the number of PP ranks is equal to the number of GPUs detected. Otherwise, you need to specify manual mapping. The above command should work if you were running those four ranks on two compute nodes, but as before, these get launched on a single node. 3) mpirun -n 4 -npernode 2 mdrun_mpi -v -deffnm nvt -npernode is not an mdrun argument. The job still runs on 1 node. How can I run my job on 2 nodes utilizing all cores and GPUs? I'm afraid this is not an issue with mdrun, but with the way your ranks get places on compute nodes. Are you using a job scheduler? Cheers, -- Szilárd Thanks Nidhi -- 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] Running job on GPUs
On Fri, Jul 11, 2014 at 12:18 PM, Nidhi Katyal nidhikatyal1...@gmail.com wrote: Hello all I am trying to run my job on 2 nodes by utilizing all available cores. On each node of the cluster, we have two GPUs and two sockets with 8 cores each. Every time I am submitting the job, we find that it is running on one node. How to make use of the other node? Till now, I have used following trial commands as suggested in http://www.gromacs.org/Documentation/Acceleration_and_parallelization 1) mpirun -n 2 mdrun_mpi -v -deffnm nvt -ntomp 16 output: Using 2 MPI processes Using 16 OpenMP threads per MPI process WARNING: Oversubscribing the available 16 logical CPU cores with 32 threads. This will cause considerable performance loss! 2) mpirun -n 4 mdrun_mpi -v -deffnm nvt -ntomp 8 output: Incorrect launch configuration: mismatching number of PP MPI processes and GPUs per node. mdrun_mpi was started with 4 PP MPI processes per node, but only 2 GPUs were detected. I understand that the above error comes when number of MPI ranks is not a multiple of number of GPUs intended to be used. But in my case 4 is a multiple of 2. 3) mpirun -n 4 -npernode 2 mdrun_mpi -v -deffnm nvt The job still runs on 1 node. That can only be because your options to mpirun and local settings specify that. mdrun_mpi uses all of whatever mpirun has given it. Consult the mpirun docs for -n and -npernode and seek alternatives. Mark How can I run my job on 2 nodes utilizing all cores and GPUs? Thanks Nidhi -- 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] Interaction energy between helices
Thanks a lot Justin for your time. Best regards!! 2014-07-10 18:46 GMT-04:00 Justin Lemkul jalem...@vt.edu: On 7/10/14, 3:02 PM, Natalia Alveal F. wrote: Dear Justin, i do that you tell me, and when i do mdrun -rerun -deffnm new.tpr, there is a error, because Can not open file: md-energy.xtc You need to pass a valid file name to the -rerun flag, i.e. the trajectory that already exists for which you wish to recalculate energies. The command above would not have produced that error; please always be sure you're providing copied and pasted commands rather than retyping what you think you did from memory. -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. -- Natalia Alveal Fuentealba Ingeniera en Bioinformática Laboratory of Membranes Proteins Structure and Signalling Departamento de Fisiología Pontificia Universidad Católica de Chile Alameda 340, Santiago, Chile Fono: 56-2-3542877 -- 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-5.0 does not seem to honour plus/minus signs in topology files
I'm getting correct +/- behavior for proteins; is this maybe related to the fact that you have atom C2 in both the current and the preceding residue? It would be useful for debugging if you could create a minimal test case that uses different atom names between the residues. That's not how it's done in proteins! A residue has N, and C binding to +N. Maybe it helps to start with copying a residue and modifying it, retaining the names for connecting atoms. If that works you can start modifying more. Cheers, Tsjerk -- 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-5.0 does not seem to honour plus/minus signs in topology files
On 7/11/14, 5:01 PM, Tsjerk Wassenaar wrote: I'm getting correct +/- behavior for proteins; is this maybe related to the fact that you have atom C2 in both the current and the preceding residue? It would be useful for debugging if you could create a minimal test case that uses different atom names between the residues. That's not how it's done in proteins! A residue has N, and C binding to +N. Indeed, and perhaps I should have been more clear in what I was saying. The error message he's getting is related to duplicated atom indices (something I've never seen), and the .rtp entries have bonds for -C2 C1 and C1 C2 so it is quite likely that something in pdb2gmx is getting screwed up and it's causing repetition. This is why the proteins are still a good control; the linkages are between non-consecutive atoms, i.e. -C N but not N C. -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.
Re: [gmx-users] Graphene topology file
On 7/11/14, 5:42 AM, #SUKRITI GUPTA# wrote: Hi Justin, Thanks for the reply. I changed define= -dflexible to -dposres_water and removed freeze graphene group in my .mdp file and ran the energy minimization and npt again. This time for pbc= xyz, the water doesn't fly away but the graphene sheet curves and does not remain in xy plane. Is it ok for the sheet to bend during simulation and will it not effect the pbc? Applying pressure along the plane of the sheet can cause deformation. Whether or not this is physically relevant, I have no idea. Also for pbc=xy, the same problem persists as the previous one i.e. following error occurs: Step 20: The charge group starting at atom 796 moved than the distance allowed by the domain decomposition in direction X distance out of cell -0.290927 New coordinates:2.4112.0060.982 Old cell boundaries in direction X:0.0002.702 New cell boundaries in direction X:0.0002.702 --- Program mdrun, VERSION 4.5.5 Source code file: /build/buildd/gromacs-4.5.5/src/mdlib/domdec.c, line: 4124 Fatal error: A charge group moved too far between two domain decomposition steps This usually means that your system is not well equilibrated For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors. Can you please suggest what can be causing the error to occur? That's a generic error suggesting the system is blowing up. http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System I know nothing about using walls, so that's the best I can suggest. -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.
Re: [gmx-users] g_wham and hist question
On 7/11/14, 1:17 PM, ANDRES ADOLFO ORTEGA GUERRERO wrote: Hi Dear Gromacs User, I use g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal for a PMF calculation of a molecule permeating an ion channel, i use the version 5-rc1 and a flat bottom potential , with 63 windows, in the terminal said that i should look the poor sampling between z=3.38 and z=3.42 , and i use direction i have a problem with the histogram.xvg. because just appear 1 histogram , should be 63 ? what could be the problem? You're plotting it wrong. xmgrace -nxy histo.xvg -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.
Re: [gmx-users] Trouble with gmx distance
On 7/10/14, 11:55 PM, Teemu Murtola wrote:
The help text explains this: Each selection specifies an independent set
of distances to calculate. Each selection should consist of pairs of
positions, and the distances are computed between positions 1-2, 3-4, etc.
In other words, the selections resemble those that were earlier required by
g_bond, not those by g_dist. The wiki page on tool changes for 5.0 shows an
example if using plus in a selection to get the behavior of g_dist to
compute the distance between centers-of-mass of two groups.
Thanks, Teemu. I guess this just comes down to perhaps a need for a bit of
better wording in the documentation. I guess I didn't recall that there was an
example on that page.
-Justin
On Jul 11, 2014 2:04 AM, Justin Lemkul jalem...@vt.edu wrote:
Hi All,
I have encountered a very annoying problem with gmx distance (the 5.0
replacement for g_dist/g_bond) - selections must have an even number of
atoms. Can anyone explain why this is necessary? I designed a minimal test
system (distance between two atoms), and got:
---
Program: gmx distance, VERSION 5.0
Source file: src/gromacs/trajectoryanalysis/modules/distance.cpp (line
198)
Function:void gmx::analysismodules::{anonymous}::checkSelections(const
SelectionList)
Inconsistency in user input:
Selection 'first' does not evaluate into an even number of positions (there
are 1 positions)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---
Indeed, the code makes sure the selection size is a multiple of 2, but
why? Is there a workaround? Not all groups are even :)
-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
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Re: [gmx-users] inconsistency in obtained temperature values by traj and g_energy tools
On Fri, Jul 11, 2014 at 10:27 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/10/14, 9:30 PM, Rasoul Nasiri wrote: On Fri, Jul 11, 2014 at 12:58 AM, Justin Lemkul jalem...@vt.edu wrote: On 7/10/14, 7:09 PM, Rasoul Nasiri wrote: Because 1- Estimation of T for different sub-systems say phases of gas, interface and liquid. Can be obtained with g_energy? No, not unless they are assigned as separate tc-grps in the .mdp file, as sub-systems are changing during the simulation in terms of number of atoms in a non-equilibrium situation, I don't think g_energy can give relevant temperature values, even tc-grps are specified in mdp. Isn't? No, you can't then. This also makes any sort of interpretation non-trivial; if an atom dissociates from one group to which it was linked, the interpretation of its new velocity when bonding to another group is now somewhat discontinuous, is it not? So it could make clrea why I did not select g_energy for determination of T and replied your question! but then (1) you shouldn't be designing something affecting the physics purely based on what you hope to analyze and (2) you then already know the outcome. This is actually what g_traj can do; like I said, you just have to account for restraints. can you clarify how it can be practically done? You need to recalculate the number of degrees of freedom based on whatever constraints there might be. You said there are none, so that may not be the case. Please excuse the typo in the earlier message, restraints should be constraints. Which DOFs, do I need consider translational and rotational as well as vibrational ones? And how this number will affact crude values obtained by g_traj? Please consider constrained MD simulation done using OPLS. 2- My trajectory is not constrain one as it has been recorded using reactive FF. I need to estimate T with converted trajectory (reaxffgro). Converted trajectory? yes, since non-reactive FF at high temperatures cannot be reliable due to vibrational effects, all my MD has been done by reactive one. Your first post suggested the run was done with Gromacs (being that you had .tpr and .edr files). I have produced .tpr file but not .edr. The outcomes you posted agree perfectly with constrained molecules, The posted data refereed to un-reliability of g_traj for obtaining of T. I just wanted to know the reason via comparison with g_energy. Those obtained by non-reactive FF of OPLS. This is where I was getting confused. Your very first message said you had the same trajectory and input files but clearly this is not true. You're comparing apples and oranges; an accurate statement of what's really going on is very important and saves everyone time. That means all posted values in my first message obtained by ONLY OPLS FF just to understand how much g_traj and g_energy give us different T values on same trajectory and input file. but without more details on what you're actually doing, I'm not going to hazard a guess. Recall that even if you set constraints = none, SETTLE is still applied to water molecules unless you use -DFLEXIBLE (which you shouldn't for most normal purposes). My molecules are not water and g_traj gave following T values for same system using two different FFs 1- ReaxFF 0 399.321 1 400.25 2 401.08 3 401.271 4 400.67 5 400.264 6 400.752 7 401.178 8 401.391 9 399.065 10 401.78 As i said already I just converted reaxff trajectory to gro one and also used tpr file (constrain=none in mdp) for estimation of T with g_traj. 2- OPLS 0 269.581 1 271.064 2 271.309 3 271.205 4 271.499 5 270.868 6 272.247 7 271.59 8 271.614 9 270.598 10 271.662 How constrained MD results (OPLS) can be corrected? Now you're losing me again. You're talking about converting some ReaxFF trajectory without constraints, but were there constraints in the OPLS trajectory? here there are two different values of T obtained by ReaxFF and OPLS. As you told there are no constrains in ReaxFF trajectory BUT there should be constrain in OPLS trajectory. Can you give an actual listing of commands and .mdp files (if applicable) for what you're doing? This is all very confusing. Please just tell me how values of obtained T by g_traj can be corrected when I use trajectory and tpr files of constrain MD simulations (OPLS) as an input? command: g_traj_d -f md.trr -s topol -n n.ndx -ot T.xvg mdp file: ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit= 0 dt = 0.002 nsteps = 1000 ;20ns ; For exact run continuation or redoing part of a run init_step= 0 ; Part index is updated
Re: [gmx-users] gmx-5.0 does not seem to honour plus/minus signs in topology files
Hi, I haven't really followed the thread, but one of https://gerrit.gromacs.org/#/c/3686/ or https://gerrit.gromacs.org/#/c/3656/ might be a guilty party - e.g. see what happens if you check out their respective parents. Mark On Fri, Jul 11, 2014 at 11:14 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/11/14, 5:01 PM, Tsjerk Wassenaar wrote: I'm getting correct +/- behavior for proteins; is this maybe related to the fact that you have atom C2 in both the current and the preceding residue? It would be useful for debugging if you could create a minimal test case that uses different atom names between the residues. That's not how it's done in proteins! A residue has N, and C binding to +N. Indeed, and perhaps I should have been more clear in what I was saying. The error message he's getting is related to duplicated atom indices (something I've never seen), and the .rtp entries have bonds for -C2 C1 and C1 C2 so it is quite likely that something in pdb2gmx is getting screwed up and it's causing repetition. This is why the proteins are still a good control; the linkages are between non-consecutive atoms, i.e. -C N but not N C. -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. -- 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.
