Re: [gmx-users] Re: Problem with simulated annealing!!!
A wise man once laid down three rules about the behaviour of computers. 1) Computers are fast 2) Computers are literal 3) Computers are stupid Items 2 and 3 are applicable here. gromacs is very helpful and effective in pointing out when the user may be in breach of the duty of care implied by 2, but it can't recover from 3, unfortunately. Your original error messages were >>>I am getting these warnings: >>> >>>ARNING 1 [file full.mdp, line unknown]: >>> Unknown left-hand coulomb type in parameter file >>> >>>WARNING 2 [file full.mdp, line unknown]: >>> Unknown left-hand anneaing in parameter file >>> >>>WARNING 3 [file full.mdp, line unknown]: >>> Unknown left-hand anneling_npoints in parameter >> >>file Maybe gromacs knew what it was talking about. Your .mdp file contains mis-spelled left-hand keywords. gromacs can spell (see 2 above), but can't correct spelling, or infer correct spelling (see 3 above). That's your job :-) Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Membrane error
Kushal Seth wrote: Dear All! Thanks for your replies.My CPP path seems to be ok as far as the location is concerened and I continue to get the same error messsages. The fact that you are receiving a cpp exit code (32512 in your email) means it is being found and run, so Sukit's suggestion isn't applicable here. Is there any other reason for that ( my top files also seem to be wroking for other simulations ) Reading the error message carefully will usually help you... > --- > Program grompp, VERSION 3.3 > Source code file: grompp.c, line: 427 > > Fatal error: > number of coordinates in coordinate file > (binaryCR-Ochol-box-largeZ.pdb, 10280) > does not match topology (mytop-nowater1.top, 0) The absence of atoms in your .top file suggests that it is not being generated correctly, or is trying to include non-existent files. Have a look at it and try work out what is going wrong. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: Problem with simulated annealing!!!
Hai all, This is my simulated annealing mdp file.. title = simulated annealing test run cpp = /lib/cpp constraints = all-bonds integrator = md dt = 0.002; ps ! nsteps = 5; total 100 ps. nstcomm = 1 nstxout = 500 nstvout = 500 nstfout = 0 nstlog = 500 nstenergy = 500 nstlist = 10 ns_type = grid rlist = 0.9 coulomb type= PME rcoulomb= 0.9 rvdw= 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = system tau_t = 0.5 ref_t = 300 ; Energy monitoring energygrps = Protein SOL ; Isotropic pressure coupling is now on Pcoupl = berendsen Pcoupltype = isotropic tau_p = 5.0 compressibility = 4.5e-5 ref_p = 1.0 ;simulated annealing anneaing= single, single anneling_npoints= 5,5 annealing_time = 20 40 60 80 100 20 40 60 80 100 annealing_temp = 320 338 350 360 370 320 338 350 360 370 ; Generate velocites is off at 300 K. gen_vel = no gen_temp= 300.0 gen_seed= 173529 --- Viswanadham Sridhara <[EMAIL PROTECTED]> wrote: > Hi Poornima, > If you can paste the entire mdp file, then it can be > easy for the users to > suggest you things. > Cheers, > > On 3/31/06, poornima Gajendrarao > <[EMAIL PROTECTED]> wrote: > > > > Dear Bruce, > > > > Thank you very much for your suggestion. > > > > I tried as you said. But the only difference Which > I > > saw is that the temperautre goes upto 314 (I tried > it > > with 10ps MDrun). After that I tried for 100ps > MDrun. > > I used the same parameters which you have > mentioned in > > the previous mail. I didnt change anything. And > while > > running the grompp program for simulated > annealing.. > > > > I am getting these warnings: > > > > ARNING 1 [file full.mdp, line unknown]: > > Unknown left-hand coulomb type in parameter file > > > > WARNING 2 [file full.mdp, line unknown]: > > Unknown left-hand anneaing in parameter file > > > > WARNING 3 [file full.mdp, line unknown]: > > Unknown left-hand anneling_npoints in parameter > file > > > > can any one help to solve this problem!! > > > > Thanks in advance. > > > > with prayers, > > Poornima > > > > > > > > > > > > --- [EMAIL PROTECTED] wrote: > > > > > Hi Poornima, > > > > > > It could be that you are defining two > > > energy/temperature groups: > > > >tc-grps = Protein SOL > > > >tau_t = 0.1 0.1 > > > >ref_t = 300 300 > > > >; Energy monitoring > > > >energygrps = Protein SOL > > > > > > but then only defining annealing protocols for > one > > > group: > > > >;simulated annealing > > > >anneling = single > > > >anneling_npoints = 5 > > > >anneling_time = 2 4 6 8 10 > > > >anneling_temp = 320 338 350 360 370 > > > > > > I think it should be like this: > > > > > > annealing = single single > > > annealing_npoints = 5 5 > > > annealing_time = 2 4 6 8 10 2 4 6 8 10 > > > annealing_temp = 320 338 350 360 370 320 338 350 > 360 > > > 370 > > > > > > Have a look at the mdp options part of the > online > > > manual and check the SA part. > > > > > > Cheers, > > > > > > Bruce > > > > > > -- > > > Dr. Bruce F. Milne PhD > > > CEQOFFUP > > > Faculdade de Farmácia > > > Universidade do Porto > > > Rua Aníbal Cunha - 164 > > > 4050-047 > > > Porto > > > Portugal > > > > > > > > > > > > This message was sent using IMP, the Internet > > > Messaging Program. > > > ___ > > > gmx-users mailing listgmx-users@gromacs.org > > > > http://www.gromacs.org/mailman/listinfo/gmx-users > > > Please don't post (un)subscribe requests to the > > > list. Use the > > > www interface or send it to > > > [EMAIL PROTECTED] > > > Can't post? Read > > > http://www.gromacs.org/mailing_lists/users.php > > > > > > > > > > > > > > __ > > Yahoo! India Matrimony: Find your partner now. Go > to > > http://yahoo.shaadi.com > > ___ > > gmx-users mailing listgmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please don't post (un)subscribe requests to the > list. Use the > > www interface or send it to > [EMAIL PROTECTED] > > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > > > > > > -- > Viswanadham Sridhara, > Graduate Research Assistant, > Old Dominion University, > Norfolk, VA-23529. > > ___ > gmx-users mailing l
Re: [gmx-users] Membrane error
Dear All! Thanks for your replies.My CPP path seems to be ok as far as the location is concerened and I continue to get the same error messsages. Is there any other reason for that ( my top files also seem to be wroking for other simulations ) Need help ASAP. Thanks again to you all. Kris On 4/4/06, Sukit Leekumjorn <[EMAIL PROTECTED]> wrote: I had a similar problem before. Check and see if "cpp" is in/usr/bin/cpp path. Sometime it is in /lib/cpp depending on your operating system. You can check the location of cpp by typing "whichcpp" on the command line.Hope this help, SukitKushal Seth wrote:>>> HI all !> I am gettting this error while doing my simulation... for the > bilayers Back Off! I just backed up emout-nowater.mdp to> ./#emout-nowater.mdp.1#> checking input for internal consistency...> ...ling /usr/bin/cpp > : No such file or directory> cpp exit code: 32512> -I/usr/local/gromacs/share/gromacs/top mytop-nowater1.top >> gromppdriwHo'> ' command is defined in the .mdp file > processing topology...> processing coordinates...> ---> Program grompp, VERSION 3.3> Source code file: grompp.c, line: 427 >> Fatal error:> number of coordinates in coordinate file> (binaryCR-Ochol-box-largeZ.pdb, 10280)> does not match topology (mytop-nowater1.top, 0)> > I would appreciate if anyone can help me out with this.> Thanks> Kris>>> >> ___ > gmx-users mailing listgmx-users@gromacs.org> http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the> www interface or send it to [EMAIL PROTECTED].> Can't post? Read http://www.gromacs.org/mailing_lists/users.php___gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use thewww 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 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] Projecting on Eigen vector
Hi gmxions, I have found out the eigen vectors computed of from a proteins simulation. Now I want to project coordinates of entire simulation on to eigen vectors to see the collective , anharmonic motion of that protein. And doing so for wild and mutant protein, I expect to trace the reason for catalytic efficiency of the proteins in question between its wild and mutant form. Am I Techniquely sound right here? Otherwise eigen vectors compuations is for any other different purpose ? With thanks ! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - And now for something completely different ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] QM/MM Compatible CPMD-3.11.1 Released!
Hi, Sorry, that my message was not clear. Examples on H2O-dimer, Ethane, and P450-heme are available inside the Source code; they are in a folder "qmmm_projects" in "share". I mentioned that I'll upload ADDITIONAL examples SOON; I'm taking that link out till I find some time to select, zip, and upload some files there. The instructions for Compilation and running of Gromacs/CPMD are available in 1) a folder "qmmm_manual" inside "qmmm_projects"; and possibly a more clear instruction is available 2) in the CPMD manual (section 9.15 page 131) pb. Ch On Apr 4, 2006, at 3:20 AM, Florian Haberl wrote: hi, On Monday 03 April 2006 22:54, Pradip Kumar Biswas wrote: Hello Gmxers, This is to inform you that the CPMD code which is now compatible to do QM/MM with Gromacs (as the driver ) is released and is available for free subject to a license agreement with the CPMD developers. The QM/MM modified gromacs code is available at: http://comppsi.csuohio.edu/groups/qmmm.html (We have posted an example of qm/mm with P450 heme and additional examples will be uploaded soon). the example download gives me a 404 error http://comppsi.csuohio.edu/groups/ex_qmmm.tar.gz and the CPMD code is available at: http://www.cpmd.org Cheers, PB. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Florian -- --- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Mailto: florian.haberl AT chemie.uni-erlangen.de --- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] NS in PME
Janne Hirvi wrote: Hello David! I read your interesting new article "The Origin of Layer Structure Artifacts in Simulations of Liquid Water" and I would like to know especially what kind of NS parameters you have used in the simulations with PME and are the following parameters correct otherwise? dt=0.002 nstlist=5 rlist=? coulombtype=PME rcoulomb=0.9 vdwtype=cut-off rvdw=? I'm attaching my mdp file. We have just disabled the option to have rlist != rcoulomb with PME. I am interested especially about the rlist parameter because there seems to be some energy conservation problems in my water simulations. At least I couldn't achieve energy conservation with single precision complilation and with double precision compilation energy is conserved only when switch(shift?) function is used for vdw interactions (rlist>rvdw>rvdw_switch) and PME for coulombic interactions (rlist>rcoulomb). If rlist is equal to rcoulomb I need to update NS list at every time step but with preceding parameters energy is conserved even when nstlist=10. So should I use rlist>rcoulomb with PME when nstlist>1 to take into account movement of atoms/molecules(charge groups) near the real space cut-off limit (rcoulomb) or is there something I don't understand? Atleast from the manual someone could get the picture that rlist should be equal to rcoulomb and there are also different kind of opinions on mailing list? Maybe Berk can comment? Thanks for any comments in advance! Janne -- Janne Hirvi, MSc(Physical Chemistry), Researcher University of Joensuu, Department of Chemistry, P.O.Box 111 80101 Joensuu, FI Tel: +358 13 2514544 & +358 50 3474223 E-mail: [EMAIL PROTECTED] & [EMAIL PROTECTED] -- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ; ; File 'mdout.mdp' was generated ; By user: spoel (291) ; On host: matisse ; At date: Sun Aug 11 22:20:40 2002 ; ; VARIOUS PREPROCESSING OPTIONS = title= cpp = /lib/cpp ; RUN CONTROL PARAMETERS = integrator = md ; start time and timestep in ps = tinit= 0 dt = 0.002 nsteps = 100 ; mode for center of mass motion removal = comm-mode= Linear ; number of steps for center of mass motion removal = nstcomm = 1 ; group(s) for center of mass motion removal = comm-grps= ; LANGEVIN DYNAMICS OPTIONS = ; Temperature, friction coefficient (amu/ps) and random seed = bd-temp = 300 bd-fric = 0 ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS = ; Force tolerance and initial step-size = emtol= 100 emstep = 0.01 ; Max number of iterations in relax_shells = niter= 20 ; Step size (1/ps^2) for minimization of flexible constraints = fcstep = 0 ; Frequency of steepest descents steps when doing CG = nstcgsteep = 1000 ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 0 nstvout = 0 nstfout = 0 ; Output frequency for energies to log file and energy file = nstlog = 1000 nstenergy= 100 ; Output frequency and precision for xtc file = nstxtcout= 250 xtc-precision= 1000 ; This selects the subset of atoms for the xtc file. You can = ; select multiple groups. By default all atoms will be written. = xtc-grps = ; Selection of energy groups = energygrps = ; NEIGHBORSEARCHING PARAMETERS = ; nblist update frequency = nstlist = 5 ; ns algorithm (simple or grid) = ns-type = Grid ; Periodic boundary conditions: xyz or no = pbc = xyz ; nblist cut-off = domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW = ; Method for doing electrostatics = coulombtype = PME rcoulomb-switch = 0 ; Dielectric constant (DC) for
Re: [gmx-users] H211 in ffG53a5
Hi David, Thanks for pursuing this, No, unfortunately h211 is in neither the .hdb nor the .pdb file. I attached the .pdb file to my first post as well as the additions I made to the .hdb file. I've reattached them at the end of this post along with the pdb2gmx error. I did in fact use the -ignh flag in pdb2gmx although the .pdb file is w/out H's. Is there a problem with the format of the .hdb (attached) changes I've made? I would think not, since it removes the "warning, atoms etc. not in .hdb file" problems, but you never know... Could someone with other hardware/OS (I'm running on OS X.3.9/G3 and RedHat/P4) run the test.pdb (1 nucleotide) with a .hdb file containing the modifications to see if the problem is reproducible? On Apr 3, 2006, at 5:26 PM, David Mathog wrote: Ken Rotondi wrote: I've had this in AMBER for some time. I need to use a UAFF. ok There is no H211 in either the .hdb or .pdb file. My first guess would be that even though you say it's not in there, it actually is. Perhaps it's in lower case and you used a case sensitive search? Try grep -i h211 *.hdb *.pdb and see if it turns up. -ignh might also be helpful (doubt it though). If all else fails backtrace through the code from the location of the error message until you find where that atom is coming from. Regards, David Mathog [EMAIL PROTECTED] Manager, Sequence Analysis Facility, Biology Division, Caltech _ ADE 3 1 2 H2* O2* C2* C3* 2 3 H61 N6C6N1 2 3 H62 N6C6N1 GUA 4 1 2 H2* O2* C2* C3* 2 3 H21 N2C2N1 2 3 H22 N2C2N1 1 1 H1N1C6C2 CYT 3 1 2 H2* O2* C2* C3* 2 3 H41 N4C4N3 2 3 H42 N4C4N3 URA 2 1 2 H2* O2* C2* C3* 1 1 H3N3C2C4 _ ATOM 1 P GUA A 1 4.006 48.703 126.810 1.00 58.91 ATOM 2 O2P GUA A 1 4.598 50.201 126.810 1.00 58.91 ATOM 3 O1P GUA A 1 3.130 48.474 125.479 1.00 58.91 ATOM 4 O5* GUA A 1 5.220 47.646 126.843 1.00 58.91 ATOM 5 C5* GUA A 1 6.464 48.349 126.894 1.00 58.91 ATOM 6 C4* GUA A 1 7.236 48.051 128.158 1.00 58.91 ATOM 7 O4* GUA A 1 7.567 46.637 128.194 1.00 58.91 ATOM 8 C1* GUA A 1 8.854 46.462 128.764 1.00 58.91 ATOM 9 N9 GUA A 1 9.716 45.855 127.755 1.00 58.91 ATOM 10 C4 GUA A 1 10.914 45.215 127.975 1.00 58.91 ATOM 11 N3 GUA A 1 11.509 45.032 129.173 1.00 58.91 ATOM 12 C2 GUA A 1 12.655 44.380 129.062 1.00 58.91 ATOM 13 N2 GUA A 1 13.383 44.113 130.156 1.00 58.91 ATOM 14 N1 GUA A 1 13.174 43.942 127.869 1.00 58.91 ATOM 15 C6 GUA A 1 12.580 44.119 126.624 1.00 58.91 ATOM 16 O6 GUA A 1 13.135 43.683 125.607 1.00 58.91 ATOM 17 C5 GUA A 1 11.350 44.818 126.728 1.00 58.91 ATOM 18 N7 GUA A 1 10.447 45.200 125.746 1.00 58.91 ATOM 19 C8 GUA A 1 9.496 45.810 126.400 1.00 58.91 ATOM 20 C2* GUA A 1 9.338 47.838 129.227 1.00 58.91 ATOM 21 O2* GUA A 1 8.990 48.036 130.582 1.00 58.91 ATOM 22 C3* GUA A 1 8.576 48.757 128.282 1.00 58.91 ATOM 23 O3* GUA A 1 8.414 50.063 128.828 1.00 58.91 _ --- Program pdb2gmx, VERSION 3.3 Source code file: add_par.c, line: 221 Fatal error: Atom H211 not found in rtp database in residue GUA, it looks a bit like H21 --- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] NS in PME
Hello David! I read your interesting new article "The Origin of Layer Structure Artifacts in Simulations of Liquid Water" and I would like to know especially what kind of NS parameters you have used in the simulations with PME and are the following parameters correct otherwise? dt=0.002 nstlist=5 rlist=? coulombtype=PME rcoulomb=0.9 vdwtype=cut-off rvdw=? I am interested especially about the rlist parameter because there seems to be some energy conservation problems in my water simulations. At least I couldn't achieve energy conservation with single precision complilation and with double precision compilation energy is conserved only when switch(shift?) function is used for vdw interactions (rlist>rvdw>rvdw_switch) and PME for coulombic interactions (rlist>rcoulomb). If rlist is equal to rcoulomb I need to update NS list at every time step but with preceding parameters energy is conserved even when nstlist=10. So should I use rlist>rcoulomb with PME when nstlist>1 to take into account movement of atoms/molecules(charge groups) near the real space cut-off limit (rcoulomb) or is there something I don't understand? Atleast from the manual someone could get the picture that rlist should be equal to rcoulomb and there are also different kind of opinions on mailing list? Thanks for any comments in advance! Janne -- Janne Hirvi, MSc(Physical Chemistry), Researcher University of Joensuu, Department of Chemistry, P.O.Box 111 80101 Joensuu, FI Tel: +358 13 2514544 & +358 50 3474223 E-mail: [EMAIL PROTECTED] & [EMAIL PROTECTED] -- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] grompp error
Hi,are you sure that the DNA_A and DNA_B groups of atoms are correctly defined in the index.ndx file?Actually, it seems that grompp couldn't find them defined because they aren't default groups, so you have to generate a proper user-defined index.ndx file using make_ndx.hope it helps,MGOn 4/4/06, Super Sayan <[EMAIL PROTECTED]> wrote: Hi, I've a little problem: when i type grompp for the full MD, it return an error: [EMAIL PROTECTED]:~/Desktop/DNA$ grompp -f fullmd_sol.mdp -c minimized_DNA_box_water.gro -p DNA.top -o fullMD.tpr processing index file... Analysing residue names: Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat There are: 43015 OTHER residues There are: 0 PROTEIN residues There are: 0 DNA residues Analysing Other... --- Program grompp, VERSION 3.3 Source code file: readir.c, line: 775 Fatal error: Group DNA_A not found in indexfile. Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n' option. but also with the -n option there aren't any differences. in the .mdp file i used "DNA_A" "DNA_B" "SOL" as group; DNA_A and DNA_B are .itp files, and i've also DNA_posre_A.itp DNA_posre_B.itp files. what can i do? thanks very much PS:i hope that i've been clear. Beniamino Yahoo! Mail: gratis 1GB per i messaggi, antispam, antivirus, POP3 ___gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-usersPlease 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 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] grompp error
Hi, I've a little problem: when i type grompp for the full MD, it return an error: [EMAIL PROTECTED]:~/Desktop/DNA$ grompp -f fullmd_sol.mdp -c minimized_DNA_box_water.gro -p DNA.top -o fullMD.tpr processing index file... Analysing residue names: Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat There are: 43015 OTHER residues There are: 0 PROTEIN residues There are: 0 DNA residues Analysing Other... --- Program grompp, VERSION 3.3 Source code file: readir.c, line: 775 Fatal error: Group DNA_A not found in indexfile. Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n' option. but also with the -n option there aren't any differences. in the .mdp file i used "DNA_A" "DNA_B" "SOL" as group; DNA_A and DNA_B are .itp files, and i've also DNA_posre_A.itp DNA_posre_B.itp files. what can i do? thanks very much PS:i hope that i've been clear. Beniamino Yahoo! Mail: gratis 1GB per i messaggi, antispam, antivirus, POP3___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] topology database
Hello all, while pdb2gmx on my pdb I got following error --- Program pdb2gmx, VERSION 3.3 Source code file: resall.c, line: 438 Fatal error: Residue 'MSE' not found in residue topology database Will it be possible to add MSE in topology database of Gromacs? If yes then how to add it ? if anyone have any other solution please tell me -- Dhananjay ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] energy files
for energy files, eneconv for trjectory, trjcat Yang Ye Raghunadha Reddy Burri wrote: Dear GMX-Users, How to combine more than two energy files into one? I had 10 energy files (as well as .tpr, .trr, .xtc and .gro files) each 4 ns time total 40 ns simulations . To use gmx analysis programs I like to combine energy files. Anyone please give me some suggestions Thank you very much Raghu ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] energy files
Raghunadha Reddy Burri wrote: Dear GMX-Users, How to combine more than two energy files into one? I had 10 energy files (as well as .tpr, .trr, .xtc and .gro files) each 4 ns time total 40 ns simulations . To use gmx analysis programs I like to combine energy files. eneconv Anyone please give me some suggestions Thank you very much Raghu ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [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 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] energy files
Dear GMX-Users, How to combine more than two energy files into one? I had 10 energy files (as well as .tpr, .trr, .xtc and .gro files) each 4 ns time total 40 ns simulations . To use gmx analysis programs I like to combine energy files. Anyone please give me some suggestions Thank you very much Raghu ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] how to remove solvent molecules from xtc files
hi all, i am using this template of commands to remove the solvent molecules from the xtc file.but i found that the solvent molecues are not being deleted from the xtc file.The trajectory shows distorted image in vmd when loaded on pdb file but works fine when loaded on .gro file which also has solvent molecules.(either way of no use).All trajectories run well on ngmx(with and without solvent molecules). (procedure adapted as per a "reply" by Dr.Warren in the gromacs archives). trjconv_mpi -f viimd.trr -o viimd.xtc make_ndx_mpi -f conf.gro -o index.ndx (In this option i chose protein) trjconv_mpi -f viimd.xtc -o ready.xtc -s 1BXL-bclxl-bak-complex.pdb -n index.ndx Can anyone please help me on this as I have some ten trajectory files with the same problem. Thanks in advance. cheers hayagreevan ___Get the FREE email that has everyone talking at http://www.mail2world.com Unlimited Email Storage – POP3 – Calendar – SMS – Translator – Much More!___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: User defined Potential Table
Hi, Rahul Yes. I think that shall be fine. They shall be there for system vs. system, and WCA vs. system, which we did not specified in the mdp. I recommend you to check your energies with previous set-up. You need to check whether *new set-up's energy = original energy - internal potential of 3-4 groups + WCA potential of 3-4 groups.* P.S. Use nstep=1 to get the energy. Yang Ye Rahul Godawat wrote: Thank you Yang, It was really helpful, but after doing this, the mdrun asks me table.xvg and tablep.xvg. I read about these files and I found a fix by just copying the file table6-12.xvg from top directory as table.xvg and tablep.xvg in the working directory seems to work. I think it is correct but I am not sure, any comments. Thanks once again Rahul -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL PROTECTED] Sent: Tuesday, April 04, 2006 2:26 AM To: gmx-users@gromacs.org Subject: gmx-users Digest, Vol 24, Issue 8 Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://www.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to [EMAIL PROTECTED] You can reach the person managing the list at [EMAIL PROTECTED] When replying, please edit your Subject line so it is more specific than "Re: Contents of gmx-users digest..." Today's Topics: 1. QM/MM Compatible CPMD-3.11.1 Released! (Pradip Kumar Biswas) 2. Re: H211 in ffG53a5 (David Mathog) 3. (???) 4. Building Helical Polymer (Rahul B Kasat) 5. User defined Potential Table (Rahul Godawat) 6. (no subject) (raja) 7. Re: User defined Potential Table (Yang Ye) 8. Membrane error (Kushal Seth) 9. Re: Membrane error (X.Periole) -- Message: 1 Date: Mon, 3 Apr 2006 16:54:15 -0400 From: Pradip Kumar Biswas <[EMAIL PROTECTED]> Subject: [gmx-users] QM/MM Compatible CPMD-3.11.1 Released! To: Discussion list for GROMACS users Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=US-ASCII; format=flowed Hello Gmxers, This is to inform you that the CPMD code which is now compatible to do QM/MM with Gromacs (as the driver ) is released and is available for free subject to a license agreement with the CPMD developers. The QM/MM modified gromacs code is available at: http://comppsi.csuohio.edu/groups/qmmm.html (We have posted an example of qm/mm with P450 heme and additional examples will be uploaded soon). and the CPMD code is available at: http://www.cpmd.org Cheers, PB. -- Message: 2 Date: Mon, 03 Apr 2006 14:26:41 -0700 From: "David Mathog" <[EMAIL PROTECTED]> Subject: Re: [gmx-users] H211 in ffG53a5 To: Discussion list for GROMACS users Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=iso-8859-1 Ken Rotondi wrote: I've had this in AMBER for some time. I need to use a UAFF. ok There is no H211 in either the .hdb or .pdb file. My first guess would be that even though you say it's not in there, it actually is. Perhaps it's in lower case and you used a case sensitive search? Try grep -i h211 *.hdb *.pdb and see if it turns up. -ignh might also be helpful (doubt it though). If all else fails backtrace through the code from the location of the error message until you find where that atom is coming from. Regards, David Mathog [EMAIL PROTECTED] Manager, Sequence Analysis Facility, Biology Division, Caltech -- Message: 3 Date: Tue, 4 Apr 2006 06:36:28 +0900 (KST) From: ??? <[EMAIL PROTECTED]> Subject: [gmx-users] To: gmx-users@gromacs.org Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset="us-ascii" An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20060404/1ac551ac/att achment-0001.html -- Message: 4 Date: Mon, 3 Apr 2006 20:01:28 -0400 (EDT) From: Rahul B Kasat <[EMAIL PROTECTED]> Subject: [gmx-users] Building Helical Polymer To: Discussion list for GROMACS users Message-ID: <[EMAIL PROTECTED]> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Hi Everyone: I am a new user of GROMACS. I am interested in building a new helical polymer (6 monomers per helical turn) in gromacs with periodic boundary conditions. Can someone please guide me through this? Thanks, - Rahul * Rahul Kasat Purdue University, West Lafayette, IN 47907 * -- Message: 5 Date: Mon, 3 Apr 2006 19:39:20 -0400 From: "Rahul Godawat" &l
[gmx-users] lincs warning
Hello, gmx-users， i am just simulating a single PEO chain in a large box(vacuum), the EM step went perfectly well for steep and cg, but after MD has started there came the following warnings: Step 1432, time 2.864 (ps) LINCS WARNING relative constraint deviation after LINCS: max 1.600984 (between atoms 141 and 142) rms 0.134828 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 141142 90.00.1000 0.2458 0.0945 Wrote pdb files with previous and current coordinates Step 1433, time 2.866 (ps) LINCS WARNING relative constraint deviation after LINCS: max 0.027914 (between atoms 141 and 142) rms 0.002435 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 141142 90.00.2458 0.0971 0.0945 Step 1434, time 2.868 (ps) LINCS WARNING relative constraint deviation after LINCS: max 1.672527 (between atoms 141 and 142) rms 0.140852 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 141142 90.00.0971 0.2526 0.0945 …… and in a few seconds the core dumped, and system collapsed. i was using oplsaa force field and the [ pairs ] are removed as refered by the mannual i wonder where the problem might exists. any suggestion will be greatly appreciated! Regards Thanks Rongliang Wu [EMAIL PROTECTED] 2006-04-04 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Membrane error
I had a similar problem before. Check and see if "cpp" is in /usr/bin/cpp path. Sometime it is in /lib/cpp depending on your operating system. You can check the location of cpp by typing "which cpp" on the command line. Hope this help, Sukit Kushal Seth wrote: HI all ! I am gettting this error while doing my simulation... for the bilayers Back Off! I just backed up emout-nowater.mdp to ./#emout-nowater.mdp.1# checking input for internal consistency... ...ling /usr/bin/cpp : No such file or directory cpp exit code: 32512 -I/usr/local/gromacs/share/gromacs/top mytop-nowater1.top > gromppdriwHo' ' command is defined in the .mdp file processing topology... processing coordinates... --- Program grompp, VERSION 3.3 Source code file: grompp.c, line: 427 Fatal error: number of coordinates in coordinate file (binaryCR-Ochol-box-largeZ.pdb, 10280) does not match topology (mytop-nowater1.top, 0) I would appreciate if anyone can help me out with this. Thanks Kris ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: User defined Potential Table
Thank you Yang, It was really helpful, but after doing this, the mdrun asks me table.xvg and tablep.xvg. I read about these files and I found a fix by just copying the file table6-12.xvg from top directory as table.xvg and tablep.xvg in the working directory seems to work. I think it is correct but I am not sure, any comments. Thanks once again Rahul -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL PROTECTED] Sent: Tuesday, April 04, 2006 2:26 AM To: gmx-users@gromacs.org Subject: gmx-users Digest, Vol 24, Issue 8 Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://www.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to [EMAIL PROTECTED] You can reach the person managing the list at [EMAIL PROTECTED] When replying, please edit your Subject line so it is more specific than "Re: Contents of gmx-users digest..." Today's Topics: 1. QM/MM Compatible CPMD-3.11.1 Released! (Pradip Kumar Biswas) 2. Re: H211 in ffG53a5 (David Mathog) 3. (???) 4. Building Helical Polymer (Rahul B Kasat) 5. User defined Potential Table (Rahul Godawat) 6. (no subject) (raja) 7. Re: User defined Potential Table (Yang Ye) 8. Membrane error (Kushal Seth) 9. Re: Membrane error (X.Periole) -- Message: 1 Date: Mon, 3 Apr 2006 16:54:15 -0400 From: Pradip Kumar Biswas <[EMAIL PROTECTED]> Subject: [gmx-users] QM/MM Compatible CPMD-3.11.1 Released! To: Discussion list for GROMACS users Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=US-ASCII; format=flowed Hello Gmxers, This is to inform you that the CPMD code which is now compatible to do QM/MM with Gromacs (as the driver ) is released and is available for free subject to a license agreement with the CPMD developers. The QM/MM modified gromacs code is available at: http://comppsi.csuohio.edu/groups/qmmm.html (We have posted an example of qm/mm with P450 heme and additional examples will be uploaded soon). and the CPMD code is available at: http://www.cpmd.org Cheers, PB. -- Message: 2 Date: Mon, 03 Apr 2006 14:26:41 -0700 From: "David Mathog" <[EMAIL PROTECTED]> Subject: Re: [gmx-users] H211 in ffG53a5 To: Discussion list for GROMACS users Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=iso-8859-1 Ken Rotondi wrote: > I've had this in AMBER for some time. I need to use a > UAFF. ok > > > > There is no H211 in either the .hdb or .pdb file. My first guess would be that even though you say it's not in there, it actually is. Perhaps it's in lower case and you used a case sensitive search? Try grep -i h211 *.hdb *.pdb and see if it turns up. -ignh might also be helpful (doubt it though). If all else fails backtrace through the code from the location of the error message until you find where that atom is coming from. Regards, David Mathog [EMAIL PROTECTED] Manager, Sequence Analysis Facility, Biology Division, Caltech -- Message: 3 Date: Tue, 4 Apr 2006 06:36:28 +0900 (KST) From: ??? <[EMAIL PROTECTED]> Subject: [gmx-users] To: gmx-users@gromacs.org Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset="us-ascii" An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20060404/1ac551ac/att achment-0001.html -- Message: 4 Date: Mon, 3 Apr 2006 20:01:28 -0400 (EDT) From: Rahul B Kasat <[EMAIL PROTECTED]> Subject: [gmx-users] Building Helical Polymer To: Discussion list for GROMACS users Message-ID: <[EMAIL PROTECTED]> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Hi Everyone: I am a new user of GROMACS. I am interested in building a new helical polymer (6 monomers per helical turn) in gromacs with periodic boundary conditions. Can someone please guide me through this? Thanks, - Rahul * Rahul Kasat Purdue University, West Lafayette, IN 47907 * -- Message: 5 Date: Mon, 3 Apr 2006 19:39:20 -0400 From: "Rahul Godawat" <[EMAIL PROTECTED]> Subject: [gmx-users] User defined Potential Table To: Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset="us-ascii" Hi Berk, Groamcs user forum has really been extremely useful so far to work with gromacs. I want to apply a user defined potential for selected energy groups. Its hard to interpret the information on the gromacs webpage and even going
Re: [gmx-users] QM/MM Compatible CPMD-3.11.1 Released!
hi, On Monday 03 April 2006 22:54, Pradip Kumar Biswas wrote: > Hello Gmxers, > > This is to inform you that the CPMD code which is now > compatible to do QM/MM with Gromacs (as the driver ) > is released and is available for free subject to a license > agreement with the CPMD developers. > > The QM/MM modified gromacs code is available at: > http://comppsi.csuohio.edu/groups/qmmm.html > (We have posted an example of qm/mm with P450 heme > and additional examples will be uploaded soon). the example download gives me a 404 error http://comppsi.csuohio.edu/groups/ex_qmmm.tar.gz > > and the CPMD code is available at: http://www.cpmd.org > > > Cheers, > PB. > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php Florian -- --- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Mailto: florian.haberl AT chemie.uni-erlangen.de --- pgpmoeNHLwop1.pgp Description: PGP signature ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
