Re: [gmx-users] Martini Cg-model can not be downloaded!
Could you download this with another bowser? On Feb 11, 2009, at 5:22 AM, weixin wrote: Oh, sorry. I mean the browser. (IE= internet explorer) 2009/2/10 XAvier Periole x.peri...@rug.nl On Feb 10, 2009, at 9:54 AM, weixin wrote: It's caused by the IE. what is IE ? 2009/2/10 xi zhao zhaoxiitc2...@yahoo.com.cn well.. it seems that there is a problem in the page for downloading files from http://md.chem.rug.nl/~marrink/MARTINI/Parameters.html, the cg model parameters can not be downloaded! Thank you for help! 好玩贺卡等你发，邮箱贺卡全新上线！ ___ 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 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 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 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 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] Re: gmx-users Digest, Vol 58, Issue 59
Robert Fenwick wrote: Hi, I wanted to run one of the gromacs 4.0 benchmarks on a new cluster that we have and also wanted to see the affect of this 4 fs time step. If it would not be too much trouble would it be possible for the setups of either the PLINCS paper or the GROMACS 4.0 paper to be placed somewhere on the website. Specifically I am intersted in the lysozyme benchmark, however I suspect others might like the membrane system to as well. I have tried to set a similar simulation up, but it is not able to run with 4 fs integration. So what exactly is going wrong? What is in your .mdp file? It is probably better for you to post this information here and receive feedback, so that others can make use of it later. I've followed what I think is a sensible setup, which comes from the GROMACS workshop pre-workshop tutorial. Comments are wellcome, I generate this using a bash script for convenience: grep -v HOH original/1LYD.pdb ./prot1LYD.pdb pdb2gmx -f prot1LYD.pdb -ter -ignh -vsite hydrogens -water tip3p select OPLS, 0, 0 editconf -f conf.gro -bt dodecahedron -d 0.7 -o box.gro genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro grompp -f em.mdp -p topol.top -c solvated.gro -o sol.tpr genion -s sol.tpr -nn 8 -nname CL- -nq -1 -np 0 -pname NA+ -pq 1 -p topol.top -o solvatedIon.gro select 12 (SOL) grompp -f em.mdp -p topol.top -c solvatedIon.gro -o em.tpr mdrun -v -deffnm em grompp -f pr.mdp -p topol.top -c em.gro -o pr.tpr mpirun -np 16 mdrun_mpi -v -deffnm pr -npme 8 grompp -f run.mdp -p topol.top -c pr.gro -o run.tpr mpirun -np 16 mdrun_mpi -v -deffnm run -npme 8 The inputs are, and come directly from the article Hess et al., 2008 JCTC GROMACS 4 : :: em.mdp :: integrator = steep nsteps = 200 nstlist = 10 rlist = 1.0 coulombtype = pme fourierspacing = 0.125 rcoulomb= 1.0 vdw-type= cut-off rvdw= 1.0 lincs-order = 6 nstenergy = 10 :: pr.mdp :: integrator = md nsteps = 5 dt = 0.002 nstlist = 10 rlist = 1.0 coulombtype = pme fourierspacing = 0.125 rcoulomb= 1.0 vdw-type= cut-off rvdw= 1.0 lincs-order = 6 tcoupl = Berendsen tc-grps = protein non-protein tau-t = 0.1 0.1 ref-t = 298 298 Pcoupl = Berendsen tau-p = 1.0 compressibility = 1e-5 1e-5 1e-5 0 0 0 ref-p = 1.0 nstenergy = 100 define = -DPOSRES :: run.mdp :: integrator = md nsteps = 5 dt = 0.004 nstlist = 5 rlist = 1.0 coulombtype = pme fourierspacing = 0.125 rcoulomb= 1.0 vdw-type= cut-off rvdw= 1.0 lincs-order = 6 tcoupl = Berendsen tc-grps = protein non-protein tau-t = 0.1 0.1 ref-t = 298 298 nstxout = 1000 nstvout = 1000 nstxtcout = 100 nstenergy = 100 The simulation dies with: Step 6, time 0.024 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.222533, max 1.229818 (between atoms 328 and 329) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 1970 1973 90.00.2413 0.3543 0.1930 1888 1891 65.80.4413 0.1879 0.1930 447449 59.20.2406 0.1939 0.1939 656660 90.00.1930 0.4267 0.1930 616619 90.00.1924 0.2612 0.1930 477480 89.90.2945 0.3802 0.1930 319329 65.30.1670 0.1816 0.1670 328329 90.00.0915 0.2039 0.0915 762765 42.40.1584 0.1554 0.1583 762766 44.00.1581 0.1616 0.1583 t = 0.024 ps: Water molecule starting at atom 16419 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates Warning: 1-4 interaction between 949 and 963 at distance 6.212 which is larger than the 1-4 table size 2.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size Warning: 1-4 interaction between 747 and 753 at distance 14.118 which is larger than the 1-4 table size 2.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size --- Program mdrun_mpi, VERSION 4.0.3 Source code file: pme.c, line: 518 Fatal error: 11 particles communicated to PME node 3 are more than a cell length out of the domain decomposition cell of their charge group --- The
Re: [gmx-users] Re: gmx-users Digest, Vol 58, Issue 59
Robert Fenwick wrote: pdb2gmx -f prot1LYD.pdb -ter -ignh -vsite hydrogens -water tip3p select OPLS, 0, 0 The benchmarks were done with SPC/E; don't know if that will make a difference or not (probably not, but just FYI). editconf -f conf.gro -bt dodecahedron -d 0.7 -o box.gro This box will be smaller than what was described in the paper. Try -box 7 7 7 for a more reasonable size (and total number of water molecules). genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro grompp -f em.mdp -p topol.top -c solvated.gro -o sol.tpr genion -s sol.tpr -nn 8 -nname CL- -nq -1 -np 0 -pname NA+ -pq 1 -p topol.top -o solvatedIon.gro select 12 (SOL) grompp -f em.mdp -p topol.top -c solvatedIon.gro -o em.tpr mdrun -v -deffnm em grompp -f pr.mdp -p topol.top -c em.gro -o pr.tpr mpirun -np 16 mdrun_mpi -v -deffnm pr -npme 8 You're bound to get bad performance doing this. You've got a 1:1 PP:PME ratio. If you've done everything correctly, grompp should estimate that the PME load be about 33%, thus 2:1 PP:PME. I ran this particular benchmark on our cluster using 12 nodes, with 4 for PME. grompp -f run.mdp -p topol.top -c pr.gro -o run.tpr mpirun -np 16 mdrun_mpi -v -deffnm run -npme 8 The inputs are, and come directly from the article Hess et al., 2008 JCTC GROMACS 4 : :: em.mdp :: integrator = steep nsteps = 200 nstlist = 10 rlist = 1.0 coulombtype = pme fourierspacing = 0.125 rcoulomb= 1.0 vdw-type= cut-off rvdw= 1.0 lincs-order = 6 nstenergy = 10 :: pr.mdp :: integrator = md nsteps = 5 dt = 0.002 nstlist = 10 rlist = 1.0 coulombtype = pme fourierspacing = 0.125 rcoulomb= 1.0 vdw-type= cut-off rvdw= 1.0 lincs-order = 6 tcoupl = Berendsen tc-grps = protein non-protein tau-t = 0.1 0.1 ref-t = 298 298 Pcoupl = Berendsen tau-p = 1.0 compressibility = 1e-5 1e-5 1e-5 0 0 0 ref-p = 1.0 nstenergy = 100 define = -DPOSRES :: run.mdp :: integrator = md nsteps = 5 dt = 0.004 nstlist = 5 rlist = 1.0 coulombtype = pme fourierspacing = 0.125 rcoulomb= 1.0 vdw-type= cut-off rvdw= 1.0 lincs-order = 6 tcoupl = Berendsen tc-grps = protein non-protein tau-t = 0.1 0.1 ref-t = 298 298 nstxout = 1000 nstvout = 1000 nstxtcout = 100 nstenergy = 100 Try applying constraints = all-bonds (based on Table 3 of Berk's JCTC paper about P-LINCS). -Justin The simulation dies with: Step 6, time 0.024 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.222533, max 1.229818 (between atoms 328 and 329) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 1970 1973 90.00.2413 0.3543 0.1930 1888 1891 65.80.4413 0.1879 0.1930 447449 59.20.2406 0.1939 0.1939 656660 90.00.1930 0.4267 0.1930 616619 90.00.1924 0.2612 0.1930 477480 89.90.2945 0.3802 0.1930 319329 65.30.1670 0.1816 0.1670 328329 90.00.0915 0.2039 0.0915 762765 42.40.1584 0.1554 0.1583 762766 44.00.1581 0.1616 0.1583 t = 0.024 ps: Water molecule starting at atom 16419 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates Warning: 1-4 interaction between 949 and 963 at distance 6.212 which is larger than the 1-4 table size 2.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size Warning: 1-4 interaction between 747 and 753 at distance 14.118 which is larger than the 1-4 table size 2.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size --- Program mdrun_mpi, VERSION 4.0.3 Source code file: pme.c, line: 518 Fatal error: 11 particles communicated to PME node 3 are more than a cell length out of the domain decomposition cell of their charge group --- The methodology for the lysozyme benchmark is pretty explicit in the Gromacs 4 paper; is there some aspect that is not clear? I agree that the paper is clear, I ask because it is obvious that I am doing something wrong the system should be stable! -Justin Bryn
[gmx-users] Barostat Density decreasing to zero
Dear All, I have simulated a protein inside a box with water and ions. I began by minimizing my system (which has a total charge of zero), until the maximum gradient was small enough and the potential energy become negative. Then I heated it, slowly, to 300K at constant volume (using berendsen thermostat and tcoupl = 1 ps). Then I performed 500 ps NVT simulation to equilibrate the temperature, at 300K. Then, I tried to equilibrate the pressure and run NPT simulation, using Berendsen barostat (p=1, pcoupl=10) and Berendsen thermostat (T=300K, tcoupl = 0.1). My problem is, that with the barostat thermostat both active in the same MD run, my density drops to a very low value (at the first MD steps, the density is 1000, dropping later to 100 kg/m^3). That is- my box dimensions increase significantly (from around 6x6x6 to 12x12x12 nm^3. If I change the pressure coupling constant, the speed of the expansion changes but all simulation converged to a small density between 50-100 kg/m3. Your help is appreciated; Probably, I am not controlling the simulation like I should. I will appreciate any advice. Thank you, Omer Markovitch. I have used gromacs version 3.3.3, Here is my .MDP file for the NPT run: integrator = md dt = 0.001 nsteps = 50 comm_grps= system nstxout = 500 nstvout = 500 nstcheckpoint= 1000 nstlog = 500 nstenergy= 500 nstlist = 10 ns_type = simple pbc = xyz rlist= 1.0 coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.0 epsilon_r= 80 epsilon_rf = 80 vdw-type = Cut-off rvdw-switch = 0 rvdw = 1.0 table-extension = 1 fourierspacing = 0.12 pme_order= 4 ewald_rtol = 1e-05 ewald_geometry = 3d optimize_fft = yes tcoupl = berendsen tc-grps = system tau_t= 0.1 ref_t= 300 Pcoupl = berendsen Pcoupltype = Isotropic tau-p= 10 compressibility = 4.5E-5 ref-p= 1 andersen_seed= 815131 constraints = none ___ 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] Barostat Density decreasing to zero
Hi Omer, You use a dielectric constant is 80, which means that the electrostatic interactions are screened. Perhaps that's why your density is low. Ran. Omer Markovitch wrote: Dear All, I have simulated a protein inside a box with water and ions. I began by minimizing my system (which has a total charge of zero), until the maximum gradient was small enough and the potential energy become negative. Then I heated it, slowly, to 300K at constant volume (using berendsen thermostat and tcoupl = 1 ps). Then I performed 500 ps NVT simulation to equilibrate the temperature, at 300K. Then, I tried to equilibrate the pressure and run NPT simulation, using Berendsen barostat (p=1, pcoupl=10) and Berendsen thermostat (T=300K, tcoupl = 0.1). My problem is, that with the barostat thermostat both active in the same MD run, my density drops to a very low value (at the first MD steps, the density is 1000, dropping later to 100 kg/m^3). That is- my box dimensions increase significantly (from around 6x6x6 to 12x12x12 nm^3. If I change the pressure coupling constant, the speed of the expansion changes but all simulation converged to a small density between 50-100 kg/m3. Your help is appreciated; Probably, I am not controlling the simulation like I should. I will appreciate any advice. Thank you, Omer Markovitch. I have used gromacs version 3.3.3, Here is my .MDP file for the NPT run: integrator = md dt = 0.001 nsteps = 50 comm_grps= system nstxout = 500 nstvout = 500 nstcheckpoint= 1000 nstlog = 500 nstenergy= 500 nstlist = 10 ns_type = simple pbc = xyz rlist= 1.0 coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.0 epsilon_r= 80 epsilon_rf = 80 vdw-type = Cut-off rvdw-switch = 0 rvdw = 1.0 table-extension = 1 fourierspacing = 0.12 pme_order= 4 ewald_rtol = 1e-05 ewald_geometry = 3d optimize_fft = yes tcoupl = berendsen tc-grps = system tau_t= 0.1 ref_t= 300 Pcoupl = berendsen Pcoupltype = Isotropic tau-p= 10 compressibility = 4.5E-5 ref-p= 1 andersen_seed= 815131 constraints = none ___ 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 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] Re: gmx-users Digest, Vol 58, Issue 61
Re Benchmarks, Fixed! After making all the changes that Justin suggested the dynamics run as expected, if anyone wants the scripts to run the exact same system then I am happy to send them on. Bryn ___ 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] funny zero-step mdrun results in 4.0.3
David, Both your gro files are wrong, the definition of gro files has never changed. Do you mean to say this has ever worked? Yes, it worked fine in 3.3.x. I would point out that trjconv has an -ndec option which, if used to output a gro file, will generate high-precision gro files as output. Presumably these are acceptable gro files?!? What exactly is wrong with it? Here's one that works (an output with -ndec from trjconv); I'm not clear on why this one works and the one I sent doesn't: Generated by trjconv : 9 system in water t= 0.0 17 1ASN C41 20.166000366211 20.479019165039 20.427963256836 0.0 0.0 0.0 1ASN H12 20.146055221558 20.570739746094 20.372158050537 0.0 0.0 0.0 1ASN H23 20.098955154419 20.395944595337 20.404985427856 0.0 0.0 0.0 1ASN H34 20.166000366211 20.499057769775 20.535308837891 0.0 0.0 0.0 1ASN C75 20.29576294 20.426000595093 20.385000228882 0.0 0.0 0.0 1ASN O16 20.315000534058 20.30465942 20.349000930786 0.0 0.0 0.0 1ASN N27 20.393997192383 20.515981674194 20.393993377686 0.0 0.0 0.0 1ASN H48 20.489086151123 20.482969284058 20.386993408203 0.0 0.0 0.0 1ASN H59 20.374940872192 20.611291885376 20.421081542969 0.0 0.0 0.0 2SOL OW 10 20.548002243042 20.120998382568 20.291999816895 0.0 0.0 0.0 2SOLHW1 11 20.5000 20.046926498413 20.254966735840 0.0 0.0 0.0 2SOLHW2 12 20.479961395264 20.183086395264 20.318038940430 0.0 0.0 0.0 2SOL MW 13 20.535623550415 20.119720458984 20.290826797485 -0.0009536742582 0.0 0.0 3SOL OW 14 20.242019653320 20.178009033203 20.123998641968 0.0 0.0 0.0 3SOLHW1 15 20.164087295532 20.143032073975 20.167186737061 0.0 0.0 0.0 3SOLHW2 16 20.300615310669 20.201835632324 20.195838928223 0.0 0.0 0.0 3SOL MW 17 20.239955902100 20.176818847656 20.136268615723 -0.0085830679163 -0.0038146970328 0.0 40.642551422119 40.642551422119 40.642551422119 Maybe this is just wishful thinking, but it would be nice if the manual actually explained the specifications of the gro file format. For example, it is clearly not fixed-width, as the number of digits in the columns can vary, but at the same time it doesn't appear to be tab/space delimited, as the columns of velocities can occasionally run together (if I'm using the -ndec option, especially). Obviously one can look at the code (perhaps I should do this) but it seems it should be documented. Thanks, David If you want high precision use g96. ___ 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 -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org 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 gmx-users-requ...@gromacs.org. 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] funny zero-step mdrun results in 4.0.3
Hi, I checked the gro manual page: http://www.gromacs.org/documentation/reference_4.0/online/gro.html and found out that it is actually pretty clear. Note that it is fixed format, but with flexible precision which is derived from the space between the decimal points. I found out a while ago that in 3.3 gro was not read fixed format, but in some messy way which was close to free format for the coordinates. For 4.0 I changed the reading so it is really fixed format and one can store coordinates of 1000 nm or larger and -100 nm and smaller. Note that the different precision gro files do not adhere to the original GROMOS format and might not be read correctly by some software. Berk Date: Wed, 11 Feb 2009 10:46:26 -0600 Subject: Re: [gmx-users] funny zero-step mdrun results in 4.0.3 From: dmob...@gmail.com To: gmx-users@gromacs.org David, Both your gro files are wrong, the definition of gro files has never changed. Do you mean to say this has ever worked? Yes, it worked fine in 3.3.x. I would point out that trjconv has an -ndec option which, if used to output a gro file, will generate high-precision gro files as output. Presumably these are acceptable gro files?!? What exactly is wrong with it? Here's one that works (an output with -ndec from trjconv); I'm not clear on why this one works and the one I sent doesn't: Generated by trjconv : 9 system in water t= 0.0 17 1ASN C41 20.166000366211 20.479019165039 20.427963256836 0.0 0.0 0.0 1ASN H12 20.146055221558 20.570739746094 20.372158050537 0.0 0.0 0.0 1ASN H23 20.098955154419 20.395944595337 20.404985427856 0.0 0.0 0.0 1ASN H34 20.166000366211 20.499057769775 20.535308837891 0.0 0.0 0.0 1ASN C75 20.29576294 20.426000595093 20.385000228882 0.0 0.0 0.0 1ASN O16 20.315000534058 20.30465942 20.349000930786 0.0 0.0 0.0 1ASN N27 20.393997192383 20.515981674194 20.393993377686 0.0 0.0 0.0 1ASN H48 20.489086151123 20.482969284058 20.386993408203 0.0 0.0 0.0 1ASN H59 20.374940872192 20.611291885376 20.421081542969 0.0 0.0 0.0 2SOL OW 10 20.548002243042 20.120998382568 20.291999816895 0.0 0.0 0.0 2SOLHW1 11 20.5000 20.046926498413 20.254966735840 0.0 0.0 0.0 2SOLHW2 12 20.479961395264 20.183086395264 20.318038940430 0.0 0.0 0.0 2SOL MW 13 20.535623550415 20.119720458984 20.290826797485 -0.0009536742582 0.0 0.0 3SOL OW 14 20.242019653320 20.178009033203 20.123998641968 0.0 0.0 0.0 3SOLHW1 15 20.164087295532 20.143032073975 20.167186737061 0.0 0.0 0.0 3SOLHW2 16 20.300615310669 20.201835632324 20.195838928223 0.0 0.0 0.0 3SOL MW 17 20.239955902100 20.176818847656 20.136268615723 -0.0085830679163 -0.0038146970328 0.0 40.642551422119 40.642551422119 40.642551422119 Maybe this is just wishful thinking, but it would be nice if the manual actually explained the specifications of the gro file format. For example, it is clearly not fixed-width, as the number of digits in the columns can vary, but at the same time it doesn't appear to be tab/space delimited, as the columns of velocities can occasionally run together (if I'm using the -ndec option, especially). Obviously one can look at the code (perhaps I should do this) but it seems it should be documented. Thanks, David If you want high precision use g96. ___ 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 -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___
[gmx-users] gromacs 4.0.3 tests validations
Hi, I am compiling gromacs on CentOS-3 x86_64 both serial and LAM-MPI version (7.1.4) and I would like to validate the builds. [...@sillage gmxtest]$ rpm -q gcc fftw3 perl gcc-3.2.3-59.x86_64 fftw3-3.0.1-2_centos3.x86_64 perl-5.8.0-98.EL3.x86_64 ./configure --prefix=... --with-x --enable-shared make make install test validation as stated at http://wiki.gromacs.org/index.php/Test-set wget -O - ftp://ftp.gromacs.org/pub/tests/gmxtest-3.3.2.tgz| tar xzvf - make tests ... All 16 simple tests PASSED All 14 complex tests PASSED All 63 kernel tests PASSED Error not all 45 pdb2gmx tests have been done successfully Only 0 energies in the log file - The PASSED lines are fine to me, but what about the last 2 lines? I also compiled the double precision version with: ./configure --prefix=... --with-x --enable-shared --disable-float and the tests yields: [...@sillage gmxtest]$ ./gmxtest.pl -double all All 16 simple tests PASSED All 14 complex tests PASSED All 63 kernel tests PASSED readline() on closed filehandle PIPE at ./gmxtest.pl line 343. readline() on closed filehandle PIPE at ./gmxtest.pl line 348. ... readline() on closed filehandle PIPE at ./gmxtest.pl line 348. readline() on closed filehandle PIPE at ./gmxtest.pl line 343. readline() on closed filehandle PIPE at ./gmxtest.pl line 348. Error not all 45 pdb2gmx tests have been done successfully Only 0 energies in the log file Should I be worried? About the parallel test (grompp -np N for gromacs 3.x) as previoulsy stated on the mailing list, one should use: grompp -c system.gro -p topology.top -f something.mdp mpirun -np N mdrun so gmxtest.pl should read: system($grompp -maxwarn 10 $ndx /dev/null 21); system(mpirun -$par mdrun -maxwarn 10 $ndx grompp.out 21); instead of: system($grompp -maxwarn 10 $ndx $par grompp.out 21); [...@sillage gmxtest]$ ./gmxtest.pl -np 1 all Will test on 1 processors All 16 simple tests PASSED All 14 complex tests PASSED All 63 kernel tests PASSED Error not all 45 pdb2gmx tests have been done successfully Only 0 energies in the log file [...@sillage gmxtest]$ ./gmxtest.pl -np 2 all Will test on 2 processors FAILED. Check files in bham 1 out of 16 simple tests FAILED FAILED. Check files in acetonitrilRF FAILED. Check files in aminoacids FAILED. Check files in argon FAILED. Check files in sw FAILED. Check files in tip4p FAILED. Check files in urea FAILED. Check files in water 7 out of 14 complex tests FAILED All 63 kernel tests PASSED Error not all 45 pdb2gmx tests have been done successfully Only 0 energies in the log file Thanks. Tru -- Dr Tru Huynh | http://www.pasteur.fr/recherche/unites/Binfs/ mailto:t...@pasteur.fr | tel/fax +33 1 45 68 87 37/19 Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France ___ 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] funny zero-step mdrun results in 4.0.3
Hi, I just had a look at the gro files you mailed. They have one space too little between the x and y columns and the y and z columns. Or stricktly speaking according to the format, the space between the x and y decimal point does not match the space between the y and z decimal point. I will add a check for this. Berk Date: Wed, 11 Feb 2009 10:46:26 -0600 Subject: Re: [gmx-users] funny zero-step mdrun results in 4.0.3 From: dmob...@gmail.com To: gmx-users@gromacs.org David, Both your gro files are wrong, the definition of gro files has never changed. Do you mean to say this has ever worked? Yes, it worked fine in 3.3.x. I would point out that trjconv has an -ndec option which, if used to output a gro file, will generate high-precision gro files as output. Presumably these are acceptable gro files?!? What exactly is wrong with it? Here's one that works (an output with -ndec from trjconv); I'm not clear on why this one works and the one I sent doesn't: Generated by trjconv : 9 system in water t= 0.0 17 1ASN C41 20.166000366211 20.479019165039 20.427963256836 0.0 0.0 0.0 1ASN H12 20.146055221558 20.570739746094 20.372158050537 0.0 0.0 0.0 1ASN H23 20.098955154419 20.395944595337 20.404985427856 0.0 0.0 0.0 1ASN H34 20.166000366211 20.499057769775 20.535308837891 0.0 0.0 0.0 1ASN C75 20.29576294 20.426000595093 20.385000228882 0.0 0.0 0.0 1ASN O16 20.315000534058 20.30465942 20.349000930786 0.0 0.0 0.0 1ASN N27 20.393997192383 20.515981674194 20.393993377686 0.0 0.0 0.0 1ASN H48 20.489086151123 20.482969284058 20.386993408203 0.0 0.0 0.0 1ASN H59 20.374940872192 20.611291885376 20.421081542969 0.0 0.0 0.0 2SOL OW 10 20.548002243042 20.120998382568 20.291999816895 0.0 0.0 0.0 2SOLHW1 11 20.5000 20.046926498413 20.254966735840 0.0 0.0 0.0 2SOLHW2 12 20.479961395264 20.183086395264 20.318038940430 0.0 0.0 0.0 2SOL MW 13 20.535623550415 20.119720458984 20.290826797485 -0.0009536742582 0.0 0.0 3SOL OW 14 20.242019653320 20.178009033203 20.123998641968 0.0 0.0 0.0 3SOLHW1 15 20.164087295532 20.143032073975 20.167186737061 0.0 0.0 0.0 3SOLHW2 16 20.300615310669 20.201835632324 20.195838928223 0.0 0.0 0.0 3SOL MW 17 20.239955902100 20.176818847656 20.136268615723 -0.0085830679163 -0.0038146970328 0.0 40.642551422119 40.642551422119 40.642551422119 Maybe this is just wishful thinking, but it would be nice if the manual actually explained the specifications of the gro file format. For example, it is clearly not fixed-width, as the number of digits in the columns can vary, but at the same time it doesn't appear to be tab/space delimited, as the columns of velocities can occasionally run together (if I'm using the -ndec option, especially). Obviously one can look at the code (perhaps I should do this) but it seems it should be documented. Thanks, David If you want high precision use g96. ___ 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 -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] funny zero-step mdrun results in 4.0.3
Hi, It is slightly more subtle. The spacing of the decimals points is correct, but the last digit of x and y ends up in y and z. Berk From: g...@hotmail.com To: gmx-users@gromacs.org Subject: RE: [gmx-users] funny zero-step mdrun results in 4.0.3 Date: Wed, 11 Feb 2009 18:01:31 +0100 Hi, I just had a look at the gro files you mailed. They have one space too little between the x and y columns and the y and z columns. Or stricktly speaking according to the format, the space between the x and y decimal point does not match the space between the y and z decimal point. I will add a check for this. Berk Date: Wed, 11 Feb 2009 10:46:26 -0600 Subject: Re: [gmx-users] funny zero-step mdrun results in 4.0.3 From: dmob...@gmail.com To: gmx-users@gromacs.org David, Both your gro files are wrong, the definition of gro files has never changed. Do you mean to say this has ever worked? Yes, it worked fine in 3.3.x. I would point out that trjconv has an -ndec option which, if used to output a gro file, will generate high-precision gro files as output. Presumably these are acceptable gro files?!? What exactly is wrong with it? Here's one that works (an output with -ndec from trjconv); I'm not clear on why this one works and the one I sent doesn't: Generated by trjconv : 9 system in water t= 0.0 17 1ASN C41 20.166000366211 20.479019165039 20.427963256836 0.0 0.0 0.0 1ASN H12 20.146055221558 20.570739746094 20.372158050537 0.0 0.0 0.0 1ASN H23 20.098955154419 20.395944595337 20.404985427856 0.0 0.0 0.0 1ASN H34 20.166000366211 20.499057769775 20.535308837891 0.0 0.0 0.0 1ASN C75 20.29576294 20.426000595093 20.385000228882 0.0 0.0 0.0 1ASN O16 20.315000534058 20.30465942 20.349000930786 0.0 0.0 0.0 1ASN N27 20.393997192383 20.515981674194 20.393993377686 0.0 0.0 0.0 1ASN H48 20.489086151123 20.482969284058 20.386993408203 0.0 0.0 0.0 1ASN H59 20.374940872192 20.611291885376 20.421081542969 0.0 0.0 0.0 2SOL OW 10 20.548002243042 20.120998382568 20.291999816895 0.0 0.0 0.0 2SOLHW1 11 20.5000 20.046926498413 20.254966735840 0.0 0.0 0.0 2SOLHW2 12 20.479961395264 20.183086395264 20.318038940430 0.0 0.0 0.0 2SOL MW 13 20.535623550415 20.119720458984 20.290826797485 -0.0009536742582 0.0 0.0 3SOL OW 14 20.242019653320 20.178009033203 20.123998641968 0.0 0.0 0.0 3SOLHW1 15 20.164087295532 20.143032073975 20.167186737061 0.0 0.0 0.0 3SOLHW2 16 20.300615310669 20.201835632324 20.195838928223 0.0 0.0 0.0 3SOL MW 17 20.239955902100 20.176818847656 20.136268615723 -0.0085830679163 -0.0038146970328 0.0 40.642551422119 40.642551422119 40.642551422119 Maybe this is just wishful thinking, but it would be nice if the manual actually explained the specifications of the gro file format. For example, it is clearly not fixed-width, as the number of digits in the columns can vary, but at the same time it doesn't appear to be tab/space delimited, as the columns of velocities can occasionally run together (if I'm using the -ndec option, especially). Obviously one can look at the code (perhaps I should do this) but it seems it should be documented. Thanks, David If you want high precision use g96. ___ 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 -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org
Re: [gmx-users] P-N vector orientation
Hello, Is that thread solved? I've got a bunch of TCL scripts for VMD that can do this calculation. They are not really user friendly or incredibly fast, but they give a correct answer. I can send those scripts off the list if you are interested. Nicolas ANINDITA GAYEN a écrit : Dear Xavier Periole I am a GROMACS user, presently working with DMPC bilayer.. I want to calculate the orientation of the head groups P-N vector. From gmx-users, I have came to know that you have a program that can determine the angle of the PN vector (or what ever pair of atoms) relative to the z axis. If possible, can you please provide me that program or tell me how can i calculate that? Thanks in advance. Ms. Anindita Gayen C/O Dr. Chaitali Mukhopadhyay Senior Research Fellow Department of Chemistry University of Calcutta 92, A. P. C. Road Kolkata-700 009 India Add more friends to your messenger and enjoy! Invite them now. http://in.rd.yahoo.com/tagline_messenger_6/*http://messenger.yahoo.com/invite/ ___ 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 begin:vcard fn:Nicolas Sapay n:Sapay;Nicolas org:University of Calgary;Biological department adr:;;2500 University drive NW;Calgary;AB;T2N 1N4;Canada email;internet:nsa...@ucalgary.ca title:Post-doctoral fellow tel;work:403-220-6869 x-mozilla-html:TRUE url:http://moose.bio.ucalgary.ca/ version:2.1 end:vcard ___ 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] funny zero-step mdrun results in 4.0.3
Hi, I added a format check for 4.0.4. Berk From: g...@hotmail.com To: gmx-users@gromacs.org Subject: RE: [gmx-users] funny zero-step mdrun results in 4.0.3 Date: Wed, 11 Feb 2009 18:08:43 +0100 Hi, It is slightly more subtle. The spacing of the decimals points is correct, but the last digit of x and y ends up in y and z. Berk From: g...@hotmail.com To: gmx-users@gromacs.org Subject: RE: [gmx-users] funny zero-step mdrun results in 4.0.3 Date: Wed, 11 Feb 2009 18:01:31 +0100 Hi, I just had a look at the gro files you mailed. They have one space too little between the x and y columns and the y and z columns. Or stricktly speaking according to the format, the space between the x and y decimal point does not match the space between the y and z decimal point. I will add a check for this. Berk Date: Wed, 11 Feb 2009 10:46:26 -0600 Subject: Re: [gmx-users] funny zero-step mdrun results in 4.0.3 From: dmob...@gmail.com To: gmx-users@gromacs.org David, Both your gro files are wrong, the definition of gro files has never changed. Do you mean to say this has ever worked? Yes, it worked fine in 3.3.x. I would point out that trjconv has an -ndec option which, if used to output a gro file, will generate high-precision gro files as output. Presumably these are acceptable gro files?!? What exactly is wrong with it? Here's one that works (an output with -ndec from trjconv); I'm not clear on why this one works and the one I sent doesn't: Generated by trjconv : 9 system in water t= 0.0 17 1ASN C41 20.166000366211 20.479019165039 20.427963256836 0.0 0.0 0.0 1ASN H12 20.146055221558 20.570739746094 20.372158050537 0.0 0.0 0.0 1ASN H23 20.098955154419 20.395944595337 20.404985427856 0.0 0.0 0.0 1ASN H34 20.166000366211 20.499057769775 20.535308837891 0.0 0.0 0.0 1ASN C75 20.29576294 20.426000595093 20.385000228882 0.0 0.0 0.0 1ASN O16 20.315000534058 20.30465942 20.349000930786 0.0 0.0 0.0 1ASN N27 20.393997192383 20.515981674194 20.393993377686 0.0 0.0 0.0 1ASN H48 20.489086151123 20.482969284058 20.386993408203 0.0 0.0 0.0 1ASN H59 20.374940872192 20.611291885376 20.421081542969 0.0 0.0 0.0 2SOL OW 10 20.548002243042 20.120998382568 20.291999816895 0.0 0.0 0.0 2SOLHW1 11 20.5000 20.046926498413 20.254966735840 0.0 0.0 0.0 2SOLHW2 12 20.479961395264 20.183086395264 20.318038940430 0.0 0.0 0.0 2SOL MW 13 20.535623550415 20.119720458984 20.290826797485 -0.0009536742582 0.0 0.0 3SOL OW 14 20.242019653320 20.178009033203 20.123998641968 0.0 0.0 0.0 3SOLHW1 15 20.164087295532 20.143032073975 20.167186737061 0.0 0.0 0.0 3SOLHW2 16 20.300615310669 20.201835632324 20.195838928223 0.0 0.0 0.0 3SOL MW 17 20.239955902100 20.176818847656 20.136268615723 -0.0085830679163 -0.0038146970328 0.0 40.642551422119 40.642551422119 40.642551422119 Maybe this is just wishful thinking, but it would be nice if the manual actually explained the specifications of the gro file format. For example, it is clearly not fixed-width, as the number of digits in the columns can vary, but at the same time it doesn't appear to be tab/space delimited, as the columns of velocities can occasionally run together (if I'm using the -ndec option, especially). Obviously one can look at the code (perhaps I should do this) but it seems it should be documented. Thanks, David If you want high precision use g96. ___ 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 -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax:
Re: [gmx-users] funny zero-step mdrun results in 4.0.3
Berk, I checked the gro manual page: http://www.gromacs.org/documentation/reference_4.0/online/gro.html and found out that it is actually pretty clear. Note that it is fixed format, but with flexible precision which is derived from the space between the decimal points. Thanks. I was looking at the 3.3 paper manual. I found out a while ago that in 3.3 gro was not read fixed format, but in some messy way which was close to free format for the coordinates. For 4.0 I changed the reading so it is really fixed format and one can store coordinates of 1000 nm or larger and -100 nm and smaller. OK, that's good to know. Note that the different precision gro files do not adhere to the original GROMOS format and might not be read correctly by some software. Thanks, David Berk Date: Wed, 11 Feb 2009 10:46:26 -0600 Subject: Re: [gmx-users] funny zero-step mdrun results in 4.0.3 From: dmob...@gmail.com To: gmx-users@gromacs.org David, Both your gro files are wrong, the definition of gro files has never changed. Do you mean to say this has ever worked? Yes, it worked fine in 3.3.x. I would point out that trjconv has an -ndec option which, if used to output a gro file, will generate high-precision gro files as output. Presumably these are acceptable gro files?!? What exactly is wrong with it? Here's one that works (an output with -ndec from trjconv); I'm not clear on why this one works and the one I sent doesn't: Generated by trjconv : 9 system in water t= 0.0 17 1ASN C4 1 20.166000366211 20.479019165039 20.427963256836 0.0 0.0 0.0 1ASN H1 2 20.146055221558 20.570739746094 20.372158050537 0.0 0.0 0.0 1ASN H2 3 20.098955154419 20.395944595337 20.404985427856 0.0 0.0 0.0 1ASN H3 4 20.166000366211 20.499057769775 20.535308837891 0.0 0.0 0.0 1ASN C7 5 20.29576294 20.426000595093 20.385000228882 0.0 0.0 0.0 1ASN O1 6 20.315000534058 20.30465942 20.349000930786 0.0 0.0 0.0 1ASN N2 7 20.393997192383 20.515981674194 20.393993377686 0.0 0.0 0.0 1ASN H4 8 20.489086151123 20.482969284058 20.386993408203 0.0 0.0 0.0 1ASN H5 9 20.374940872192 20.611291885376 20.421081542969 0.0 0.0 0.0 2SOL OW 10 20.548002243042 20.120998382568 20.291999816895 0.0 0.0 0.0 2SOL HW1 11 20.5000 20.046926498413 20.254966735840 0.0 0.0 0.0 2SOL HW2 12 20.479961395264 20.183086395264 20.318038940430 0.0 0.0 0.0 2SOL MW 13 20.535623550415 20.119720458984 20.290826797485 -0.0009536742582 0.0 0.0 3SOL OW 14 20.242019653320 20.178009033203 20.123998641968 0.0 0.0 0.0 3SOL HW1 15 20.164087295532 20.143032073975 20.167186737061 0.0 0.0 0.0 3SOL HW2 16 20.300615310669 20.201835632324 20.195838928223 0.0 0.0 0.0 3SOL MW 17 20.239955902100 20.176818847656 20.136268615723 -0.0085830679163 -0.0038146970328 0.0 40.642551422119 40.642551422119 40.642551422119 Maybe this is just wishful thinking, but it would be nice if the manual actually explained the specifications of the gro file format. For example, it is clearly not fixed-width, as the number of digits in the columns can vary, but at the same time it doesn't appear to be tab/space delimited, as the columns of velocities can occasionally run together (if I'm using the -ndec option, especially). Obviously one can look at the code (perhaps I should do this) but it seems it should be documented. Thanks, David If you want high precision use g96. ___ gmx-users mailing list gmx-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 -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please
