[gmx-users] gcc problem
Dear all: I have a problem when I was running mdrun on different computers. I made a .tpr file including coordinate and velocity of each atom from a crash of mdrun and upload it to four computers whose distribution version of linux and gcc were as follows: computer A: Redhat 9.0, gcc 3.2.2 computer B: Turbo Linux 10,gcc 3.4.3 computer C: Redhat 7.2, gcc 2.96 computer D: Fedora core 6, gcc 3.4.6(the default version is 4.1.1, so I reinstalled an old version on it) All the gmx are compiled in float and mpi mode. The results of mdrun (the final .gro file, the trajectory file and the energy file) that start from the same .tpr file obtained on these computers are totally different, but if I ran mdrun on one computer from this .tpr file twice or more times, the results are all the same. So I don't know why the "mdrun" compiled by different versions of gcc would give such different results and which result should I trust. Does anybody know why it happens? I beg for your help... this is the content of my .mdp file, I have modified nstlist, ns_type, pbc, rlist, rvdw and rcoulomb for many times, but it does not work. title= cpp = /usr/bin/cpp include = define = -DFLEXIBLE integrator = md tinit= 0 dt = 0.002 nsteps = 12000 init_step= 0 comm-mode= Angular nstcomm = 1 comm-grps= bd-fric = 0 ld-seed = 1993 emtol= 100 emstep = 0.01 niter= 20 fcstep = 0 nstcgsteep = 1000 nbfgscorr= 10 nstxout = 100 nstvout = 1000 nstfout = 0 nstcheckpoint= 1000 nstlog = 1000 nstenergy= 100 nstxtcout= 0 xtc-precision= 1000 xtc-grps = energygrps = nstlist = 1 ns_type = grid pbc = xyz rlist= 0.9 domain-decomposition = no coulombtype = Cut-off rcoulomb-switch = 0 rcoulomb = 1.2 epsilon_r= 1 epsilon_rf = 1 vdw-type = Cut-off rvdw-switch = 0 rvdw = 0.9 DispCorr = No table-extension = 1 energygrp_table = fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order= 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no gb_algorithm = Still nstgbradii = 1 rgbradii = 2 gb_saltconc = 0 implicit_solvent = No Tcoupl = nose-hoover tc-grps = System tau-t= 0.1 ref-t= 600 Pcoupl = no Pcoupltype = Isotropic tau-p= 1 compressibility = ref-p= andersen_seed= 815131 QMMM = no QMMM-grps= QMmethod = QMMMscheme = normal QMbasis = QMcharge = QMmult = SH = CASorbitals = CASelectrons = SAon = SAoff= SAsteps = MMChargeScaleFactor = 1 bOPT = bTS = annealing= no annealing_npoints= 11 annealing_time = annealing_temp = gen_vel = no gen-temp = 600 gen-seed = 173529 constraints = none constraint-algorithm = Lincs unconstrained-start = no Shake-SOR= no shake-tol= 0.0001 lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 morse= no energygrp_excl = disre= No disre-weighting = Conservative disre-mixed = no disre-fc = 1000 disre-tau= 0 nstdisreout = 100 orire= no orire-fc = 0 orire-tau= 0 orire-fitgrp = nstorireout = 100 dihre= No dihre-fc = 1000 dihre-tau= 0 nstdihreout = 100 free-energy = no init-lambda = 0 delta-lambda = 0 sc-alpha = 0 sc-power = 0 sc-sigma = 0.3 ; Non-equilibrium MD stuff acc-grps =
Re: [gmx-users] Fatal error:Atom index (1) in settles out of bounds (1-0)
Hi, To use GROMACS' spc topology with ffamber, you may create a new spc topology, e.g. spc-amber.itp. Following is its content. If you know C preprocessor, you can merge it with original spc.itp. [ moleculetype ] ; molname nrexcl SOL 2 [ atoms ] ; nr type resnr residue atom cgnr charge mass 1 amber99_54 1 SOL OW 1 -0.82 15.99940 2 amber99_55 1 SOLHW1 1 0.41 1.00800 3 amber99_55 1 SOLHW2 1 0.41 1.00800 #ifdef FLEXIBLE [ bonds ] ; i j funct length force.c. 1 2 1 0.1 345000 0.1 345000 1 3 1 0.1 345000 0.1 345000 [ angles ] ; i j k funct angle force.c. 2 1 3 1 109.47 383 109.47 383 #else [ settles ] ; OW funct doh dhh 1 1 0.1 0.16333 [ exclusions ] 1 2 3 2 1 3 3 1 2 #endif On 11/5/2007 2:59 PM, willting wrote: Hi, I added ffamber_v3.3.1 to gromacs-3.3.1 and wanted to use the AMBER99 Wang protein/nucleic acid forcefield. Run the commands: pdb2gmx -ignh -f sev.pdb -o sev.gro -p sev.top -missing -water spc editconf -bt cubic -f sev.gro -o sev_box.gro -c -d 1 genbox -cp sev_box.gro -cs -p sev.top -o sev_water.gro grompp -v -f em.mdp -c sev.gro -p sev.top -o sev_em.tpr then it showed: --- Program grompp, VERSION 3.3.1 Source code file: toppush.c, line: 1108 Fatal error: [ file "/usr/local/gromacs/share/gromacs/top/spc.itp", line 41 ]: Atom index (1) in settles out of bounds (1-0) --- what should I do ? Thanks, will * My pdb: ATOM 3072 N NPHE P 1 49.900 57.324 4.858 1.00 17.05 N ATOM 3073 CA NPHE P 1 49.015 58.449 4.532 1.00 17.68 C ATOM 3074 C NPHE P 1 48.529 58.242 3.088 1.00 17.14 C ATOM 3075 O NPHE P 1 49.336 58.259 2.133 1.00 18.44 O ATOM 3076 CB NPHE P 1 49.786 59.754 4.742 1.00 1850 C ATOM 3077 CG NPHE P 1 48.955 60.964 4.622 1.00 22.19 C ATOM 3078 CD1 NPHE P 1 48.146 61.341 5.652 1.00 28.37 C ATOM 3079 CD2 NPHE P 1 48.962 61.710 3.451 1.00 30.13 C ATOM 3080 CE1 NPHE P 1 47.364 62.498 5.562 1.00 33.16 C ATOM 3081 CE2 NPHE P 1 48.231 62.874 3.360 1.00 31.49 C ATOM 3082 CZ NPHE P 1 47.415 63.254 4.420 1.00 33.03 C ATOM 3083 N ALA P 2 47.231 57.937 3.024 1.00 17.87 N ATOM 3084 CA ALA P 2 46.514 57.524 1.824 1.00 18.82 C ATOM 3085 C ALA P 2 46.531 58.561 0.717 1.00 19.39 C ATOM 3086 O ALA P 2 46.622 59.753 0.962 1.00 18.85 O ATOM 3087 CB ALA P 2 45.082 57.093 2.184 1.00 18.07 C ATOM 3088 N PRO P 3 46.475 58.093 -0.513 1.00 20.13 N ATOM 3089 CA PRO P 3 46.273 59.006 -1.620 1.00 23.52 C ATOM 3090 C PRO P 3 44.935 59.714 -1.371 1.00 26.20 C ATOM 3091 O PRO P 3 43.968 59.104 -0.883 1.00 30.44 O ATOM 3092 CB PRO P 3 46.123 58.061 -2.834 1.00 22.88 C ATOM 3093 CG PRO P 3 46.724 56.802 -2.456 1.00 20.87 C ATOM 3094 CD PRO P 3 46.550 56.684 -0.930 1.00 18.82 C ATOM 3095 N GLY P 4 44.860 60.944 -1.765 1.00 30.11 N ATOM 3096 CA GLY P 4 43.552 61.581 -1.771 1.00 32.23 C ATOM 3097 C GLY P 4 43.266 61.997 -3.211 1.00 30.90 C ATOM 3098 O GLY P 4 44.171 62.226 -3.966 1.00 34.59 O ATOM 3099 N ASN P 5 42.016 62.091 -3.590 1.00 33.27 N ATOM 3100 CA ASN P 5 41.666 62.673 -4.864 1.00 32.62 C ATOM 3101 C ASN P 5 41.960 61.777 -6.056 1.00 31.39 C ATOM 3102 O ASN P 5 42.610 62.291 -6.989 1.00 33.62 O ATOM 3103 CB ASN P 5 42.445 63.999 -5.073 1.00 35.10 C ATOM 3104 CG ASN P 5 42.229 65.016 -3.907 1.00 40.06 C ATOM 3105 OD1 ASN P 5 41.098 65.202 -3.404 1.00 47.96 O ATOM 3106 ND2 ASN P 5 43.323 65.656 -3.468 1.00 47.14 N ATOM 3107 N TYR P 6 41.551 60.487 -6.012 1.00 24.72 N ATOM 3108 CA TYR P 6 41.616 59.590 -7.164 1.00 22.15 C ATOM 3109 C TYR P 6 40774 60.234 -8.266 1.00 21.95 C ATOM 3110 O TYR P 6 39.555 60.176 -8.207 1.00 21.25 O ATOM 3111 CB TYR P 6 41.068 58.202 -6.866 1.00 21.39 C ATOM 3112 CG TYR P 6 41.847 57.366 -5.863 1.00 19.06 C ATOM 3113 CD1 TYR P 6 41.589 57.466 -4.512 1.00 16.12 C ATOM 3114 CD2 TYR P 6 42.800 56.441 -6.274 1.00 15.31 C ATOM 3115 CE1 TYR P 6 42.257 56.717 -3.628 1.00 15.10 C ATOM 3116 CE2 TYR P 6 43.510 55.696 -5.390 1.00 13.45 C ATOM 3117 CZ TYR P 6 43.226 55.805 -4.054 1.00 15.29 C ATOM 3118 OH TYR P 6 43.914 55.071 -3.133 1.00 14.56 O ATOM 3119 N PRO P 7 41.417 60.776 -9.285 1.00 21.63 N ATOM 3120 CA PRO P 7 40.708 61.437 -10.395 1.00 21.38 C ATOM 3121 C PRO P 7 39.731 60.470 -11.044 1.00 20.08 C ATOM 3122 O PRO P 7 40.005 59.287 -11.207 1.00 18.00 O ATOM 3123 CB PRO P 7 41.824 61.799 -11.375 1.00 23.11 C ATOM 3124 CG PRO P 7 43.064 61.687 -10.604 1.00 25.67 C ATOM 3125 CD PRO P 7 42.862 60.695 -9.527 1.00 23.44 C ATOM 3126 N ALA P 8 38.590 60.992 -11.468 1.00 18.89 N ATOM 3127 CA ALA P 8 37.595 60.159 -12.075 1.00 18.81 C ATOM 3128 C ALA P 8 38.061 59.569 -13.390 1.00 17.43 C ATOM 3129 O ALA P 8 38.796 60.195 -14.168 1.00 18.08 O ATOM 3130 CB ALA P 8 36.306 60.943 -12.286 1.00 19.45 C ATOM 3131 N CLEU P 9 37.637 58.345 -13.643 1.00 16.96 N ATOM 3132 CA CLEU P 9 37.959 57.644 -14.866 1.00 18.11 C ATOM 3133 C CLEU P 9 37
Re: [gmx-users] How to calculate total enery of a protein
[EMAIL PROTECTED] wrote: Hi, I am new to gromacs, I wold like to calculate the total energy of a protein molecule, in other words i have pdb structures what is the energy of this molecule? Is there any option to in GROMACS to do this. Yes, but a single total energy doesn't mean anything. It's like me telling you that there's a single rock in the Himalayas that has gravitational potential energy of -10.234 megajoules. It sounds like you might need to do some background textbook reading on molecular simulations and computational chemistry in general :-) Mark ___ 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
Re: [gmx-users] How to calculate total enery of a protein
[EMAIL PROTECTED] wrote: Hi, I am new to gromacs, I wold like to calculate the total energy of a protein molecule, in other words i have pdb structures what is the energy of this molecule? Is there any option to in GROMACS to do this. What kind of energy? You can not compute things like heat of formation like you would in a quantum code. -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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] Fatal error:Atom index (1) in settles out of bounds (1-0)
Hi, I added ffamber_v3.3.1 to gromacs-3.3.1 and wanted to use the AMBER99 Wang protein/nucleic acid forcefield. Run the commands: pdb2gmx -ignh -f sev.pdb -o sev.gro -p sev.top -missing -water spc editconf -bt cubic -f sev.gro -o sev_box.gro -c -d 1 genbox -cp sev_box.gro -cs -p sev.top -o sev_water.gro grompp -v -f em.mdp -c sev.gro -p sev.top -o sev_em.tpr then it showed: --- Program grompp, VERSION 3.3.1 Source code file: toppush.c, line: 1108 Fatal error: [ file "/usr/local/gromacs/share/gromacs/top/spc.itp", line 41 ]: Atom index (1) in settles out of bounds (1-0) --- what should I do ? Thanks, will * My pdb: ATOM 3072 N NPHE P 1 49.900 57.324 4.858 1.00 17.05 N ATOM 3073 CA NPHE P 1 49.015 58.449 4.532 1.00 17.68 C ATOM 3074 C NPHE P 1 48.529 58.242 3.088 1.00 17.14 C ATOM 3075 O NPHE P 1 49.336 58.259 2.133 1.00 18.44 O ATOM 3076 CB NPHE P 1 49.786 59.754 4.742 1.00 18.50 C ATOM 3077 CG NPHE P 1 48.955 60.964 4.622 1.00 22.19 C ATOM 3078 CD1 NPHE P 1 48.146 61.341 5.652 1.00 28.37 C ATOM 3079 CD2 NPHE P 1 48.962 61.710 3.451 1.00 30.13 C ATOM 3080 CE1 NPHE P 1 47.364 62.498 5.562 1.00 33.16 C ATOM 3081 CE2 NPHE P 1 48.231 62.874 3.360 1.00 31.49 C ATOM 3082 CZ NPHE P 1 47.415 63.254 4.420 1.00 33.03 C ATOM 3083 N ALA P 2 47.231 57.937 3.024 1.00 17.87 N ATOM 3084 CA ALA P 2 46.514 57.524 1.824 1.00 18.82 C ATOM 3085 C ALA P 2 46.531 58.561 0.717 1.00 19.39 C ATOM 3086 O ALA P 2 46.622 59.753 0.962 1.00 18.85 O ATOM 3087 CB ALA P 2 45.082 57.093 2.184 1.00 18.07 C ATOM 3088 N PRO P 3 46.475 58.093 -0.513 1.00 20.13 N ATOM 3089 CA PRO P 3 46.273 59.006 -1.620 1.00 23.52 C ATOM 3090 C PRO P 3 44.935 59.714 -1.371 1.00 26.20 C ATOM 3091 O PRO P 3 43.968 59.104 -0.883 1.00 30.44 O ATOM 3092 CB PRO P 3 46.123 58.061 -2.834 1.00 22.88 C ATOM 3093 CG PRO P 3 46.724 56.802 -2.456 1.00 20.87 C ATOM 3094 CD PRO P 3 46.550 56.684 -0.930 1.00 18.82 C ATOM 3095 N GLY P 4 44.860 60.944 -1.765 1.00 30.11 N ATOM 3096 CA GLY P 4 43.552 61.581 -1.771 1.00 32.23 C ATOM 3097 C GLY P 4 43.266 61.997 -3.211 1.00 30.90 C ATOM 3098 O GLY P 4 44.171 62.226 -3.966 1.00 34.59 O ATOM 3099 N ASN P 5 42.016 62.091 -3.590 1.00 33.27 N ATOM 3100 CA ASN P 5 41.666 62.673 -4.864 1.00 32.62 C ATOM 3101 C ASN P 5 41.960 61.777 -6.056 1.00 31.39 C ATOM 3102 O ASN P 5 42.610 62.291 -6.989 1.00 33.62 O ATOM 3103 CB ASN P 5 42.445 63.999 -5.073 1.00 35.10 C ATOM 3104 CG ASN P 5 42.229 65.016 -3.907 1.00 40.06 C ATOM 3105 OD1 ASN P 5 41.098 65.202 -3.404 1.00 47.96 O ATOM 3106 ND2 ASN P 5 43.323 65.656 -3.468 1.00 47.14 N ATOM 3107 N TYR P 6 41.551 60.487 -6.012 1.00 24.72 N ATOM 3108 CA TYR P 6 41.616 59.590 -7.164 1.00 22.15 C ATOM 3109 C TYR P 6 40.774 60.234 -8.266 1.00 21.95 C ATOM 3110 O TYR P 6 39.555 60.176 -8.207 1.00 21.25 O ATOM 3111 CB TYR P 6 41.068 58.202 -6.866 1.00 21.39 C ATOM 3112 CG TYR P 6 41.847 57.366 -5.863 1.00 19.06 C ATOM 3113 CD1 TYR P 6 41.589 57.466 -4.512 1.00 16.12 C ATOM 3114 CD2 TYR P 6 42.800 56.441 -6.274 1.00 15.31 C ATOM 3115 CE1 TYR P 6 42.257 56.717 -3.628 1.00 15.10 C ATOM 3116 CE2 TYR P 6 43.510 55.696 -5.390 1.00 13.45 C ATOM 3117 CZ TYR P 6 43.226 55.805 -4.054 1.00 15.29 C ATOM 3118 OH TYR P 6 43.914 55.071 -3.133 1.00 14.56 O ATOM 3119 N PRO P 7 41.417 60.776 -9.285 1.00 21.63 N ATOM 3120 CA PRO P 7 40.708 61.437 -10.395 1.00 21.38 C ATOM 3121 C PRO P 7 39.731 60.470 -11.044 1.00 20.08 C ATOM 3122 O PRO P 7 40.005 59.287 -11.207 1.00 18.00 O ATOM 3123 CB PRO P 7 41.824 61.799 -11.375 1.00 23.11 C ATOM 3124 CG PRO P 7 43.064 61.687 -10.604 1.00 25.67 C ATOM 3125 CD PRO P 7 42.862 60.695 -9.527 1.00 23.44 C ATOM 3126 N ALA P 8 38.590 60.992 -11.468 1.00 18.89 N ATOM 3127 CA ALA P 8 37.595 60.159 -12.075 1.00 18.81 C ATOM 3128 C ALA P 8 38.061 59.569 -13.390 1.00 17.43 C ATOM 3129 O ALA P 8 38.796 60.195 -14.168 1.00 18.08 O ATOM 3130 CB ALA P 8 36.306 60.943 -12.286 1.00 19.45 C ATOM 3131 N CLEU P 9 37.637 58.345 -13.643 1.00 16.96 N ATOM 3132 CA CLEU P 9 37.959 57.644 -14.866 1.00 18.11 C ATOM 3133 C CLEU P 9 37.229 58.236 -16.066 1.00 18.76 C ATOM 3134 OC1 CLEU P 9 36.273 59.002 -15.893 1.00 19.22 O ATOM 3135 CB CLEU P 9 37.536 56.180 -14.732 1.00 18.89 C ATOM 3136 CG CLEU P 9 38.185 55.363 -13.653 1.00 19.67 C ATOM 3137 CD1 CLEU P 9 37.635 53.964 -13.635 1.00 21.54 C ATOM 3138 CD2 CLEU P 9 39.637 55.309 -13.857 1.00 20.00 C ATOM 3139 OC2 CLEU P 9 37.619 57.946 -17.224 1.00 17.47 O TER 3140 LEU P 9 ___ 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 calculate total enery of a protein
Hi, I am new to gromacs, I wold like to calculate the total energy of a protein molecule, in other words i have pdb structures what is the energy of this molecule? Is there any option to in GROMACS to do this. Thanks in advance Regards Chandu -- C.Chandra Sekhar Reddy (Research Scholar) Laboratoire de Biochimie et Génétique Moléculaire Université de La Réunion 15, avenue René Cassin 97715 Saint Denis Messag Cedex 09 La Réunion, France Tel : +262 262 93 8641 MOB +262 (0)692 44 49 42 Fax : +262 262 93 8237 -- ___ 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
Re: [gmx-users] Node assignment using openmpi for multiple simulations in the same submission script in PBS
My apologies for not reading the reference properly. Thanks, Mark However, the --byslot option is not being able to do the needful. I will update if I learn something new. On Nov 2, 2007 11:50 PM, Mark Abraham <[EMAIL PROTECTED]> wrote: > himanshu khandelia wrote: > > I get bad scaling with 8 cpus. > > http://www.gromacs.org/index.php?option=com_wrapper&Itemid=84 > > > > > >> I'm not seeing how openmpi (the implementation) can be > >> allocating cpus "depending on what options gromacs was originally > >> compiled with". > > > > I do not see immediately how either, but just seemed logical to me. I > > may be wrong > > When describing material like this, you'd do well to separate your > speculation from your knowledge in your description, and limit the > former. If your speculation was so hot, you'd have probably fixed the > problem by now :-) > > http://www.open-mpi.org/faq/?category=running#mpirun-scheduling suggests > that the interplay of --byslot and --bynode with your machine will > depend how the hostfile is set up. You need to find out what the > defaults for the machine are and how to tweak them to what you want > under PBS. > > hostfile: > node0 slots=4 max_slots=4 > node1 slots=4 max_slots=4 > > and then two "mpirun -np 4 --byslot --hostfile hostfile mdrun" look > right to me. > > > Mark > ___ > 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 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] soft-core and coulomb transformation
Dear all, i am trying some very basic transformations by thermodynamic integration to calculate free energy difference. By following mailing-list archive, i learned that it is efficient to do coulomb transformations and LJ transformations separately. i use David Mobley's tutorial values for soft-coring, i.e., sc-alpha=0.5, sc-power=1, sc-sigma=0.3. As per list, since charge transformations are not "hard", we are at liberty to use soft-core potentials for coulombs and that is quite logical, and yes, without sc, there is no problem in coulomb transformation. Everything goes fine till this point. Now, i do reverse transformations to check for hysteresis. For vdw transformations, i get almost perfect overlap of dG/dlambda vs lambda for forward and reverse transformations, but for coloumb transformations, if i don't use soft-core potentials, i don't get any overlap (i understand that getting overlap in forward and reverse transformations is not the accurate-enough measure of absence of hysteresis, but for smaller systems 5 ns at each lambda value should be sufficiently enough sampling). Ny doubt is why should this happen? if there is no problem like singularities in potentials, why should not using sc-potentials make such a difference? i tried this for simple ala->gly and ethane->methane transformations. please give me some insight into the problem... bharat -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. ___ 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
Re: [gmx-users] Placing a peptide at the air/water interface
OZGE ENGIN wrote: Hi Mark, I am so sorry, but I erased your mail before reading it. So, could you please send the mail one more time? It is important to me. you can find it in the archives on the website. Thank you very much Ozge -Original Message- From: "OZGE ENGIN" <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Date: Sun, 04 Nov 2007 13:36:02 +0200 Subject: [gmx-users] Placing a peptide at the air/water interface Hi all, I am performing a simulation of an amphilic peptide at air/water interface. I want to start to simulation in which the peptide is placed at the interface. I changed the center of the system so that the center is now located at interface. Then, I used editconf command with -c option in order to center the peptide. I expect to place the peptide at interface. However, instead of placing it at interface, the center of the box is changed its old values. How can I place the peptide at air/water interface before starting a simulation? Thanks in advance Ozge. ___ 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 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 -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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
Re: [gmx-users] Placing a peptide at the air/water interface
Hi Mark, I am so sorry, but I erased your mail before reading it. So, could you please send the mail one more time? It is important to me. Thank you very much Ozge -Original Message- From: "OZGE ENGIN" <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Date: Sun, 04 Nov 2007 13:36:02 +0200 Subject: [gmx-users] Placing a peptide at the air/water interface Hi all, I am performing a simulation of an amphilic peptide at air/water interface. I want to start to simulation in which the peptide is placed at the interface. I changed the center of the system so that the center is now located at interface. Then, I used editconf command with -c option in order to center the peptide. I expect to place the peptide at interface. However, instead of placing it at interface, the center of the box is changed its old values. How can I place the peptide at air/water interface before starting a simulation? Thanks in advance Ozge. ___ 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 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] MSD analysis
Dear all: I've got a DOPC/cholesterol system, and I want to get the MSD of the DOPCs near cholesterols. According to the literature, the overall movement of the each monolayer should be removed prior to the MSD analysis of individual molecules, my question is how should I do this? Thank you in advance. Jian ___ 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
Re: [gmx-users] Placing a peptide at the air/water interface
OZGE ENGIN wrote: Hi all, I am performing a simulation of an amphilic peptide at air/water interface. I want to start to simulation in which the peptide is placed at the interface. I changed the center of the system so that the center is now located at interface. Then, I used editconf command with -c option in order to center the peptide. I expect to place the peptide at interface. However, instead of placing it at interface, the center of the box is changed its old values. editconf -c doesn't place a solute in a box... How can I place the peptide at air/water interface before starting a simulation? I think you want to construct your solvent box as above, then use genbox -cp solute.gro -cs twophases.gro with an appopriate -box setting. Alternatively, set up your peptide with its hydrophobic face parallel to the x-y plane, solvate in a box of water and then delete all waters with z coordinates past a certain value. Then solvate the water+peptide in a cunningly chosen box of air. Mark ___ 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] Placing a peptide at the air/water interface
Hi all, I am performing a simulation of an amphilic peptide at air/water interface. I want to start to simulation in which the peptide is placed at the interface. I changed the center of the system so that the center is now located at interface. Then, I used editconf command with -c option in order to center the peptide. I expect to place the peptide at interface. However, instead of placing it at interface, the center of the box is changed its old values. How can I place the peptide at air/water interface before starting a simulation? Thanks in advance Ozge. ___ 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] Placing a peptide at the air/water interface
Hi all, I am performing a simulation of an amphilic peptide at air/water interface. I want to start to simulation in which the peptide is placed at the interface. I changed the center of the system so that the center is now located at interface. Then, I used editconf command with -c option in order to center the peptide. I expect to place the peptide at interface. However, instead of placing it at interface, the center of the box is changed its old values. How can I place the peptide at air/water interface before starting a simulation? Thanks in advance Ozge. ___ 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
Re: [gmx-users] g_rdf problem
avinash kumar wrote: Dear all, I am having a problem in running some post analysis commands like g_rdf on my computer . When my simulation is complete I type in the following command to calculate the radial distribution function for the system " g_rdf -f traj.trr -s topol.tpr -o rdf.xvg -b 0 -e 20 " and the program gives a message like this probably installation issues. which version and how was it compiled on which platform? :-) G R O M A C S (-: Gallium Rubidium Oxygen Manganese Argon Carbon Silicon :-) VERSION 3.3.1 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2006, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) g_rdf (-: Select a reference group and 1 group Opening library file /usr/share/gromacs/top/aminoacids.dat Group 0 ( System) has 648 elements Group 1 ( SOL) has 648 elements Select a group: 1 Selected 1: 'SOL' Select a group: 1 Selected 1: 'SOL' trn version: GMX_trn_file (single precision) Reading frame 0 time0.000 After displaying this line the program does nothing further . I checked for the installation of g_rdf and found it to be installed . My simulation was completed and for command like "trjconv" can read all the frames . Then why is "g_rdf" command failing to read all the frames? eagerly waiting for a reply. Avinash Kumar 3rd year undergraduate IIT Khragpur,India Mechanical Engineering Department ___ 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 -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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
