RE: [gmx-users] mdp file for local pressure
Is there a local pressure version of Gromacs 4? I can only find Gromacs version 3.02 with local pressure. If there is, could you tell me where to get it? Thanks. Daniel From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of anirban polley Sent: Monday, May 18, 2009 7:39 PM To: gmx-users@gromacs.org Subject: [gmx-users] mdp file for local pressure --- Program grompp_mpi, VERSION 4.0.2_localpressure Source code file: readir.c, line: 454 Fatal error: Expected 2 elements for wall_atomtype, found 0 --- Could you please tell me where my fault is? Thanks a lot in advance. Anirban This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] mdp file for local pressure
The error message explicitly tells you what is wrong: "Expected 2 elements for wall_atomtype, found 0" And looking in your .mdp file ... ;WALLS ; Number of walls, type, atom types, densities and box-z scale factor for Ewald nwall= 2 wall_type= 9-3 wall_r_linpot= -1 wall_atomtype= wall_density = wall_ewald_zfac = 3 On the wall_atomtype line, you have defined zero elements and you should have two. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] mdp file for local pressure
Dear sir, I am calculating local pressure by gromacs-localp. My .mdp file is following integrator = sd ; stochastic dynamics -> Langevin! ld_seed = -1 ; random seed for sd dt = 0.002 ; ps ! nsteps = 5 ; total 500/5=100 ps nstcomm = 1 ; freq. for cm-motion removal tinit= 0 ; starting time (ps) constraints = all-bonds ; constraint for all bond lengths constraint_algorithm = lincs ; default lincs_order = 4 ; default nstxout = 1000; T(x_out) 10 ps nstvout = 1000; T(v_out) 10 ps nstfout = 0 ; T(f_out) nstlog = 250 ; energies to log (0.5 ps) nstenergy= 250 ; energies to energy file ns_type = grid; nl type nstlist = 10 ; Freq. to update neighbour list rlist= 1.0 ; nm (cutoff for short-range nl) ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = xy coulombtype = PME ;Reaction-Field ; Coulomb interactions rcoulomb = 1.0 ;2.0 ; nm (Coulomb cut-off!!) epsilon_r= 80.0; dielectric constant for reaction field vdwtype = Cut-off ; Wan der Waals interactions rvdw = 1.0 ; nm (LJ cut-off) optimize_fft = yes ; Temperature coupling Tcoupl = no ; no effect when integrator = sd tc-grps = POPC SM CHOL SOL tau_t= 0.1 0.1 0.1 0.1 ref_t= 296 296 296 296 ; Pressure coupling ;Pcoupl = no Pcoupl = berendsen Pcoupltype = semiisotropic tau_p= 1.01.0 ; ps compressibility = 4.5e-5 4.5e-5; 1/bar (water: 1 atm, 300 K) ref_p= 1.01.0 ; bar ; Generate velocites in the beginning gen_vel = yes gen_temp = 296.0 gen_seed = 173529 ;WALLS ; Number of walls, type, atom types, densities and box-z scale factor for Ewald nwall= 2 wall_type= 9-3 wall_r_linpot= -1 wall_atomtype= wall_density = wall_ewald_zfac = 3 It gives following error --- Program grompp_mpi, VERSION 4.0.2_localpressure Source code file: readir.c, line: 454 Fatal error: Expected 2 elements for wall_atomtype, found 0 --- Could you please tell me where my fault is? Thanks a lot in advance. Anirban ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
