[gmx-users] 1-4 interaction problem with a Thr
Hi group, I'm simulating a protein+drug and always getting the "1-4 interaction between 3013 and 3016 at distance 1.825 which is larger than the 1-4 table size 1.000 nm". These atoms are a CA and a HG1 from a Thr residue. My mdp file is enclosed. What should I encrease or decrease to be able to continue my simulation without this error? Thanks, Aline Rossi ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] 1-4 interaction problem with a Thr
Sorry, I forgot to enclose the .mdp file: ; ; User spoel (236) ; Wed Nov 3 17:12:44 1993 ; Input file ; title = PEP MD cpp = /lib/cpp constraints = none integrator = md tinit = 0 dt = 0.002; ps ! nsteps = 50; total 1ns. ;mode for centre of mass motio removal ;comm-mode = linear ;number of steps for centre of mass motion removal nstcomm = 1 nstxout = 5000;output coordinates every 0.5 ps nstvout = 5000; output velocities every 0,5ps nstlog = 5000 nstenergy= 250 nstxtcout= 250 xtc-precision = 1000 ;Selection of energy groups ;NEIGHBORSEARCHING PARAMETERES ;nblist update frequency nstlist = 10 ;ns algorithm (simple or grid) ns_type = grid ;nblist cut-off rlist = 0.9 ;domain-decomposition= no ;OPTIONS FOR ELECTROSTATICS AND VDW ;method for doing electrostatics coulombtype = PME rcoulomb= 0.9 ;method for doing van der waals rvdw= 0.9 ;spacing for the PME FFT grid fourierspacing = 0.12 ;FFT grid size fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ;Ewald/PME/PPPM parameters pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes constraint_algorithm = lincs lincs_order = 4 ;OPTIONS FOR WEAK COUPLING ALGORITHMS ; Berendsen temperature coupling is off in two groups ;TEMPERATURE COUPLING Tcoupl = berendsen tc-grps = Protein ISZ SOL NA+ tau_t = 0.1 0.1 0.1 0.1 ref_t = 310 310 310 310 ;table-extension = 1.2 ; Energy monitoring ;energygrps = ProteinISZ ; Isotropic pressure coupling is on Pcoupl = berendsen Pcoupltype = isotropic tau_p = 1 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 310 K. gen_vel = yes gen_temp= 310.0 gen_seed= 173529 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] SGI Altix stack traceback
Hi All, the 3.3.1 version of gromacs was installed on A SGI Altix 3700 BX2. When I run mdrun_mpi_f using 8 processors for a ~500k atoms system, i receive the follwing error. But when I run the same system with 4, 2 or 1 processor, the symulation goes fine. I´ve already tried to enhance the amount of memory to 16gb, but received the same error. Can any one advise me where might be the problem? With regards, Aline MPI: On host altix, Program /usr/local/gromacs-3.3.1/bin/mdrun_mpi_f, Rank 3, Process 10691 received signal SIGSEGV(11) MPI: stack traceback--- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Problem with trjconv
* **I have a 100ps .trr file. If I use: **trjconv -f in.trr -o out.gro -dump 95 -s in.tpr ** **trjconv stops returning the following warning: **"Reading frame 20 time 95.000 ** **WARNING no output, trajectory ended at 100" ** ** **Same warning if I -dump with any other value, as well with -b 95 -e 95. ** **Why does the trjconv does not give me the output file? The gromacs version is 3.3.1. ** **Thanks for your help. ** **Aline Rossi* ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Problem with trjconv
Aline wrote: * Greetings, *>* *>* I have a 100ps .trr file. If I use: *>* trjconv -f in.trr -o out.gro -dump 95 -s in.tpr *>* *>* trjconv stops returning the following warning: *>* "Reading frame 20 time 95.000 *>* *>* WARNING no output, trajectory ended at 100" *>* *>* *>* Same warning if I -dump with any other value, as well with -b 95 -e 95. *>* *>* Why does the trjconv does not give me the output file? *>* *>* Thanks for your help. *>* *>* Aline *>* *>* *David wrote: Which gromacs version? This has probably been fixed in the development code already. -- David. The gromacs version is 3.3.1. Aline ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Problem with trjconv
Greetings, I have a 100ps .trr file. If I use: trjconv -f in.trr -o out.gro -dump 95 -s in.tpr trjconv stops returning the following warning: "Reading frame 20 time 95.000 WARNING no output, trajectory ended at 100" Same warning if I -dump with any other value, as well with -b 95 -e 95. Why does the trjconv does not give me the output file? Thanks for your help. Aline ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] how to create a .top file from a .gro?
Hi list, I want to create a .top form an already run dinamics, using the .gro result from the last trajetory frame. I already used the pdb2gmx, but when i run the grompp, using the already cited .gro and new .top, i receive the error that my .gro and .top doesnt have the same number of atoms. is there something im missing? thanks for advices ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Not enough ref_t and tau_t values!
Hi list, Im dealing with a problem when trying to monitoring energygrps. When I run the grompp i receive this output: creating statusfile for 1 node... Back Off! I just backed up mdout.mdp to ./#mdout.mdp.16# checking input for internal consistency... calling /lib/cpp... processing topology... Generated 279 of the 1225 non-bonded parameter combinations Excluding 3 bonded neighbours for Protein_A 1 Excluding 3 bonded neighbours for Protein_B 1 Excluding 3 bonded neighbours for Protein_C 1 Excluding 2 bonded neighbours for SOL 30314 Excluding 1 bonded neighbours for NA+ 2 processing coordinates... double-checking input for internal consistency... Velocities were taken from a Maxwell distribution at 312 K renumbering atomtypes... converting bonded parameters... # G96BONDS: 6825 # G96ANGLES: 9964 # PDIHS: 3583 # IDIHS: 3430 # LJ14: 10944 # SETTLE: 30314 initialising group options... processing index file... Making dummy/rest group for T-Coupling containing 90944 elements --- Program grompp, VERSION 3.3 Source code file: readir.c, line: 1131 Fatal error: Not enough ref_t and tau_t values! my index file is: 0 System : 96772 atoms 1 Protein : 6694 atoms 2 Protein-H : 5213 atoms 3 C-alpha : 666 atoms 4 Backbone: 1998 atoms 5 MainChain : 2667 atoms 6 MainChain+Cb: 3268 atoms 7 MainChain+H : 3306 atoms 8 SideChain : 3388 atoms 9 SideChain-H : 2546 atoms 10 Prot-Masses : 6694 atoms 11 Non-Protein : 90078 atoms 12 Mg : 7 atoms 13 SOL : 90069 atoms 14 NA+ : 2 atoms 15 Other : 90078 atoms 16 alpha&beta : 6648 atoms 17 his159 :12 atoms 18 arg157 :17 atoms 19 ecdw:51 atoms 20 glu1:12 atoms 21 cys2: 8 atoms 22 asp3: 9 atoms 23 trp4:22 atoms 24 tyr458 :18 atoms 25 ala585 : 6 atoms 26 prot+pep: 6703 atoms 27 prot+pep+mg : 6706 atoms 28 alpha : 4453 atoms 29 beta: 2202 atoms 30 pep :51 atoms title = PEP MD cpp = /lib/cpp constraints = none integrator = md dt = 0.0015 ; ps ! nsteps = 1000 ; total 500 ps. nstcomm = 3000 nstxout = 3000 nstvout = 5000 nstfout = 3000 nstlog = 1500 nstenergy = 3000 nstlist = 5 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb= 0.9 rvdw= 0.9 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes unconstrained-start = yes ; Berendsen temperature coupling is off in two groups Tcoupl = berendsen tc-grps = alpha beta pep tau_t = 0.1 0.1 0.1 ref_t = 312 312 312 ; Energy monitoring energygrps = alphabetapep ; Isotropic pressure coupling is on Pcoupl = berendsen Pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 312 K. gen_vel = yes gen_temp= 312.0 gen_seed= 173529 What should be wrong with my imputs?? Thanks for help and my .mdp file is: ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
