[gmx-users] regarding error in editconf
Dear friends when I am trying command editconf, it is showing error File input/output error I have protein of 700 amino acids and its of inverted T shape and we are giving boxtype dodecahedron. input command is: editconf_d -bt dodecahedron -f input.gro -o box.gro -c -d 10.0 with regards Anamika -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] regarding installation
Dear friends, i have installed gromacs 4.5-beta3 and fftw-3.2.8 on root, now when I am giving command ./configure --enable-threads, it is showing error: cannot find fftw3f library. please let me know, why this error is showing here? thank you in advance Anamika -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] trying to install gromacs on linux single processor
hello all, I am trying to install new version of gromacs on linux single processor, getting this error ./configure --enable-threads --enable-float checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... configure: error: newly created file is older than distributed files! Check your system clock -- gmx-users mailing listgmx-users@gromacs.org http://lists.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] need help
Dear gromacs user, I want to install gromacs new version on my linux system. can u all please guide me, Thanking u in advance Anamika -- gmx-users mailing listgmx-users@gromacs.org http://lists.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] RMSD graph
Dear All, Please tell, what should I predict from this graph? I can understand this is normal type of graph. Sorry for inconvenience, but I want to ask some questions, my this job crashed many time, because of power shut down and I had to restart this again and again, I used tpbconv for the same. but now when I was trying to get rmsd plot from my running job..its not reading the tpr file, which I got from tpbconv , its reading previous tpr file. Is it okey? Thanks in advance Anamika <>___ 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] regarding rmsd !!
Dear All, My protein is simulating for 20 ns and 16 ns has already over, but I want to analyze RMSD and RMSF for this 16 ns simulation, without stopping the running simulation.it was crashed before, so I used tpbconv -f previous.trr -e previous.edr -s previous.tpr -o new.tpr -until 2 then gave the command --> mdrun -s new.tpr -o new.trr -c new.gro -g new.log -e new.edr now job is running now for analysis I am giving this command g_rms new.tpr -f new.trr -o new_rmsd.xvg -xvgr it is giving this output :-) g_rms (-: Option Filename Type Description -s topol.tpr InputStructure+mass(db): tpr tpb tpa gro g96 pdb xml -f new.trr Input Generic trajectory: xtc trr t pdb -f2 traj.xtc Input, Opt. Generic trajectory: xtc trr trj gro g96 pdb -n index.ndx Input, Opt. Index file -o new_rmsd.xvg Output xvgr/xmgr file -mirrmsdmir.xvg Output, Opt. xvgr/xmgr file -a avgrp.xvg Output, Opt. xvgr/xmgr file -dist rmsd-dist.xvg Output, Opt. xvgr/xmgr file -m rmsd.xpm Output, Opt. X PixMap compatible matrix file -bin rmsd.dat Output, Opt. Generic data file -bm bond.xpm Output, Opt. X PixMap compatible matrix file Option Type Value Description -- -[no]h bool no Print help info and quit -[no]X bool no Use dialog box GUI to edit command line options -niceint 19 Set the nicelevel -b time 0 First frame (ps) to read from trajectory -e time 0 Last frame (ps) to read from trajectory -dt time 0 Only use frame when t MOD dt = first time (ps) -tu enum ps Time unit: ps, fs, ns, us, ms, s, m or h -[no]w bool no View output xvg, xpm, eps and pdb files -[no]xvgr boolyes Add specific codes (legends etc.) in the output xvg files for the xmgrace program -what enum rmsd Structural difference measure: rmsd, rho or rhosc -[no]pbc boolyes PBC check -fit enum rot+trans Fit to reference structure: rot+trans, translation or none -prevint 0 Compare with previous frame -[no]split bool no Split graph where time is zero -skipint 1 Only write every nr-th frame to matrix -skip2int 1 Only write every nr-th frame to matrix -max real -1 Maximum level in comparison matrix -min real -1 Minimum level in comparison matrix -bmax real -1 Maximum level in bond angle matrix -bmin real -1 Minimum level in bond angle matrix -nlevelsint 80 Number of levels in the matrices -ngint 1 Number of groups to compute RMS between --- Program g_rms, VERSION 3.3 Source code file: statutil.c, line: 787 Invalid command line argument: new.tpr --- WHY THIS IS SHOWING THIS ERROR? Thanks in advance Anamika ___ 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] regarding trjconv
Dear all, RMSD and RMSF of my protein is showing abnormal flucutuation. To overcome this problem I am using following commands--> trjconv -f *.trr -o trajout_whole.xtc -s *.tpr -pbc whole trjconv -f trajout_whole.xtc -o trajout_nojump .xtc -pbc nojump but this second command is showing fatal error: Index[35] 334 is larger than the number of atoms in the trajectory file (330) pls help me to understand this and to sort out this problem. Thank you Anamika ___ 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 in minimization
Dear Friends, I extracted few conformation from my running job by using trjconv. but now as I want to minimize this conformation it is showing Fatal error that *.pdb and *.top coordinates does not match. I gave this command for my minimization grompp -f em.mdp -c *.pdb -o em.tpr -p *.top Thanks Anamika ___ 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] extract conformations !!
Dear Friends, I want to extract conformations of each 1 ns from my 10 ns simulation. My this job is running for 20 ns, so shall I first stop my job and then do this? I tried this command without stopping my job trjconv -f *.trr -o *.pdb -s *.tpr -b -0 -e -10 -dump -1000 Please tell me the solution of my this problem Thanks Anamika ___ 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] Re:confusion regarding tpbconv
> shall we mention in this way? > steps: > 1- tpbconv -f old.trr -e old.edr -s old.tpr -o new.tpr > 2- mdrun -v -deffnm new.tpr hello Sudheer. As i know about this command, this is only a shortcut and it takes all the filename as default, so if we will do mdrun after a second or third crash, all the .edr .trr and other filenames can confuse us. I dont know, How much I am correct. Anamika check (gmxcheck -h) the content of trr and edr files! .trr should contain coordinates and velocities .edr should contain energies at the same time, 7 ns you mention I think. > Thanks in advance. > > > On Mon, 12 May 2008 15:10:32 +0530 > "Anamika Awasthi" <[EMAIL PROTECTED]> wrote: >> Dear Friends, >>If my simulation crashed because of power failure, then as I know >> there are two option to restart the Job. >> One is GROMPP and another is 'tpbconv', in 'grompp' we have to do >> some changes in md.mdp, but 'tpbconv' takes everything automatically, >> tpbconv needs only .trr and .edr and it takes previous simulation's frame > as >> initial frame for restart and generate new .tpr file. >> This .tpr we should use for md rerun. > your concept is correct but you should just run the new tpr file, not rerun > it > with mdrun. > steps: > 1- tpbconv -f old.trr -e old.edr -s old.tpr -o new.tpr > 2- mdrun -s new.tpr >> I just want to ask, whether my this concept is correct or not. If > I >> am not correct please help me to correct this. >> >> Thanks in advance >> Anamika ___ 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] confusion regarding tpbconv
Dear Xavier Thanks for your help, after running my tpbconv I got this Reading toplogy and shit from 2ao2_tpxout.tpr Reading file 2ao2_tpxout.tpr, VERSION 3.3 (single precision) READING COORDS, VELS AND BOX FROM TRAJECTORY 2ao2_tpxout.trr... trn version: GMX_trn_file (single precision) Read frame 7745: step 0 time0.000 Using frame of step 0 time 0 Opened md2.edr as single precision energy file Reading frame 0 time0.000 READ 3 PRESSURE COUPLING MU'S FROM md2.edr nsteps = 1000, run_step = 0, current_t = 0, until = 2 Extending remaining runtime until 2 ps (now 1000 steps) Writing statusfile with starting step 0 and length 1000 steps... time 0.000 and length 2.000 here it is written that strating step is 0. Sorry for asking silly questions again and again, but really I am confused that it is taking step 0 from last frame of my old.trr and generating new.trr file. My 7ns simulation had over before crash and I want to simulate my job for 20ns. So, Hope It will strat simulation from 7ns and will rum tilll 20 ns. Please Help me to understand this. Thanks a lot Anamika > > > > ___ 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] confusion regarding tpbconv
Dear Friends, If my simulation crashed because of power failure, then as I know there are two option to restart the Job. One is GROMPP and another is 'tpbconv', in 'grompp' we have to do some changes in md.mdp, but 'tpbconv' takes everything automatically, tpbconv needs only .trr and .edr and it takes previous simulation's frame as initial frame for restart and generate new .tpr file. This .tpr we should use for md rerun. I just want to ask, whether my this concept is correct or not. If I am not correct please help me to correct this. Thanks in advance Anamika ___ 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] about fourier grid
Dear Gromacs user, Please tell me what is the significance of fourier grid and spacing in MD simulation? Thanks in advance ___ 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] log file has converted into.log.swp file
Dear Gromacs Users, Please help me to recover my important log file from swap file, How can I do this? I am wondering wheather I can get my original file or not. E325: ATTENTION Found a swap file by the name ".md2.log.swp" owned by: anamika dated: Wed Apr 16 04:21:09 2008 file name: ~anamika/MD/cm_A/test/md2.log modified: no user name: anamika host name: cdfd-grid-node16 process ID: 29468 (still running) While opening file "md2.log" dated: Thu Mar 20 16:09:42 2008 (1) Another program may be editing the same file. If this is the case, be careful not to end up with two different instances of the same file when making changes. Quit, or continue with caution. (2) An edit session for this file crashed. If this is the case, use ":recover" or "vim -r md2.log" to recover the changes (see ":help recovery"). If you did this already, delete the swap file ".md2.log.swp" to avoid this message. Swap file ".md2.log.swp" already exists! [O]pen Read-Only, (E)dit anyway, (R)ecover, (Q)uit: Thanks in advance ___ 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 can I restart simulation
Dear Gromacs Users, I have done MD simulation for 15 ns and I need simulation for further 5 ns. I am wondering how is this possible? Thank you in advance Anamika ___ 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] wants to simulate for more timesteps
Dear Gromacs Users, I have simulated my protein for 15 ns, I need to simulate it for more. How can I do this? Is this any easy way that it can restart after previous 15 ns? Thanks in advance -- Anamika Awasthi, PhD DBT-Postdoctoral Fellow Laboratory of Structural Biology Centre for DNA Fingerprinting and Diagnostics (CDFD) ECIL Road, Nacharam Hyderabad 500 076 INDIA ___ 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] abnormal RMSD
Justin I already tried this I tried this command---> trjconv -f myprotein.trr -o trajout_whole.trr -pbc whole this was showing this error "can not open file topol.tpr" then I repeated the same command with "-s topol.tpr" then trjconv -f trajout_whole.trr -o trajout_nojump.trr -pbc nojump then g_rms -s topol.tpr -f trajout_nojump.trr -o trajout_nojump_rmsd.xvg -xvgr but now this is showing Fatal Error " Molecule in topology has atom numbers below and above natoms. you are probably trying to use a trajectory which does not match the first 330 atoms of the run input file. You can make a matching run input file with tpbconv." with regards Anamika -- Anamika Awasthi, PhD DBT-Postdoctoral Fellow Laboratory of Structural Biology Centre for DNA Fingerprinting and Diagnostics (CDFD) ECIL Road, Nacharam Hyderabad 500 076 INDIA ___ 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] Abnormal RMSD
Dear all, Thanks Florian and Justin for your suggestions I am an beginner, so I am writing all the commands which I used pdb2gmx -f *.pdb -o *.gro -p *.top then editconf -f *.gro -o *out.gro -c -d 0.8 genbox -cp *out.gro -cs -o *b4ion.gro -p *.top grompp -f em.mdp -po *out.mdp -c *b4ion.gro -p *.top -o *b4ion.tpr neutralized system genion -s *b4ion.tpr -o *b4em.gro -pname Na -np 10 -g *ion.log select group 12 editing in *.top file grompp -f em.mdp -c *b4em.gro -p *.top -o *em.tpr mdrun -s *em.tpr -o *em.trr -c *b4pr.gro -g em.log -e em.edr grompp -f pr.mdp -c *b4pr.gro -p *.top -o *pr.tpr mdrun -s *pr.tpr -o *pr.trr -c *b4md.gro -g pr.log -e pr.edr grompp -f md.mdp -c *b4md.gro -p *.top -o *md.tpr mdrun -s *md.tpr -o *md.trr -c *pmd.gro -g md.log -e md.edr HOPE this will help to understand my problem with regards Anamika ___ 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] abnormal RMSD
Thankyou Justin for your suggestion I tried this command---> trjconv -f myprotein.trr -o trajout_whole.trr -pbc whole this was showing this error "can not open file topol.tpr" then I repeated the same command with "-s topol.tpr" then trjconv -f trajout_whole.trr -o trajout_nojump.trr -pbc nojump then g_rms -s topol.tpr -f trajout_nojump.trr -o trajout_nojump_rmsd.xvg -xvgr but now this is showing Fatal Error " Molecule in topology has atom numbers below and above natoms. you are probably trying to use a trajectory which does not match the first 330 atoms of the run input file. You can make a matching run input file with tpbconv." with regards Anamika ___ 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] Abnormal fluctuation in RMSD
Dear all, I am working on a biological dimer of 330 residues. I dont think that I got any error message when I did grompp. Please find pr.mdp filesbelow and RMSD as attachment. Please tell me why it happened? pr.mdp ; ; User spoel (236) ; Wed Nov 3 17:12:44 1993 ; Input file title = CM_2ao2_A cpp = /usr/bin/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.001 nsteps = 10 nstcomm = 1 nstxout = 250 nstvout = 1000 nstfout = 0 nstlog = 10 nstlist = 10 ns_type = grid rlist = 1 coulombtype = PME rcoulomb= 1.0 rvdw= 1.0 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; ; Berendsen temperature coupling is on Tcoupl = berendsen tau_t = 0.01 0.01 tc_grps = protein non-protein ref_t = 300 300 ; 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 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 Thanking you With best regards Anamika <>___ 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] subscription
-- Anamika Awasthi, PhD DBT-Postdoctoral Fellow Laboratory of Structural Biology Centre for DNA Fingerprinting and Diagnostics (CDFD) ECIL Road, Nacharam Hyderabad 500 076 INDIA ___ 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] Hello
Dear Gromacs users, I am beginner in using using GROMACS and MD simulations, Please help me in solving my problem. I simulate my protein for 5 ns and after simulations RMSD in C-alpha is showing a big fluctuation after 3 ns and til 3.5 ns to 4.5 ns its fine and again its showing fluctuation its till 2.5 nm. Please Tell me how should I analyze this and How can I sort out this problem. Thanking you -- Anamika Awasthi, PhD DBT-Postdoctoral Fellow Laboratory of Structural Biology Centre for DNA Fingerprinting and Diagnostics (CDFD) ECIL Road, Nacharam Hyderabad 500 076 INDIA ___ 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
