[gmx-users] Error message in output file.
Hi, I am trying to run the gromacs and am getting the following error message in the status file.I would like to know what is the significance of the error message,is it going to impact my ouptut???.I am running the mpi version with 6 nodes. p0_2593: p4_error: interrupt SIGFPE: 8 p3_2608: p4_error: net_recv recv: EOF on socket: 1 p0_2593: (4.278990) net_send: could not write to fd=7, , errno = 32 p4_2613: p4_error: interrupt SIGx: 13 p5_2618: p4_error: interrupt SIGx: 13 bash-3.00$ Thanks in advance, Mike ___ 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] Not enough ref_t and tau_t values!
On 10/18/2006 8:10 AM, Aline Rossi wrote: Hi list, Im dealing with a problem when trying to monitoring energygrps. When I run the grompp i receive this output: creating statusfile for 1 node... Back Off! I just backed up mdout.mdp to ./#mdout.mdp.16# checking input for internal consistency... calling /lib/cpp... processing topology... Generated 279 of the 1225 non-bonded parameter combinations Excluding 3 bonded neighbours for Protein_A 1 Excluding 3 bonded neighbours for Protein_B 1 Excluding 3 bonded neighbours for Protein_C 1 Excluding 2 bonded neighbours for SOL 30314 Excluding 1 bonded neighbours for NA+ 2 processing coordinates... double-checking input for internal consistency... Velocities were taken from a Maxwell distribution at 312 K renumbering atomtypes... converting bonded parameters... # G96BONDS: 6825 # G96ANGLES: 9964 # PDIHS: 3583 # IDIHS: 3430 # LJ14: 10944 # SETTLE: 30314 initialising group options... processing index file... Making dummy/rest group for T-Coupling containing 90944 elements --- Program grompp, VERSION 3.3 Source code file: readir.c, line: 1131 Fatal error: Not enough ref_t and tau_t values! my index file is: 0 System : 96772 atoms 1 Protein : 6694 atoms 2 Protein-H : 5213 atoms 3 C-alpha : 666 atoms 4 Backbone: 1998 atoms 5 MainChain : 2667 atoms 6 MainChain+Cb: 3268 atoms 7 MainChain+H : 3306 atoms 8 SideChain : 3388 atoms 9 SideChain-H : 2546 atoms 10 Prot-Masses : 6694 atoms 11 Non-Protein : 90078 atoms 12 Mg : 7 atoms 13 SOL : 90069 atoms 14 NA+ : 2 atoms 15 Other : 90078 atoms 16 alphabeta : 6648 atoms 17 his159 :12 atoms 18 arg157 :17 atoms 19 ecdw:51 atoms 20 glu1:12 atoms 21 cys2: 8 atoms 22 asp3: 9 atoms 23 trp4:22 atoms 24 tyr458 :18 atoms 25 ala585 : 6 atoms 26 prot+pep: 6703 atoms 27 prot+pep+mg : 6706 atoms 28 alpha : 4453 atoms 29 beta: 2202 atoms 30 pep :51 atoms title = PEP MD cpp = /lib/cpp constraints = none integrator = md dt = 0.0015; ps ! nsteps = 1000; total 500 ps. nstcomm = 3000 nstxout = 3000 nstvout = 5000 nstfout = 3000 nstlog = 1500 nstenergy = 3000 nstlist = 5 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb= 0.9 rvdw= 0.9 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes unconstrained-start = yes ; Berendsen temperature coupling is off in two groups Tcoupl = berendsen tc-grps= alpha beta pep tau_t = 0.1 0.1 0.1 ref_t = 312 312 312 ; Energy monitoring energygrps = alphabetapep beside the proteins, solvent also needs t-coupl. Try this tc-grps= alpha beta pep rest tau_t = 0.1 0.1 0.10.1 ref_t = 312 312 312 312 ; Energy monitoring energygrps = alphabetapep rest ; Isotropic 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 312 K. gen_vel = yes gen_temp= 312.0 gen_seed= 173529 What should be wrong with my imputs?? Thanks for help and my .mdp file is: ___ 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] Error message in output file.
coderrr c wrote: Hi, I am trying to run the gromacs and am getting the following error message in the status file.I would like to know what is the significance of the error message,is it going to impact my ouptut???.I am running the mpi version with 6 nodes. p0_2593: p4_error: interrupt SIGFPE: 8 p3_2608: p4_error: net_recv recv: EOF on socket: 1 p0_2593: (4.278990) net_send: could not write to fd=7, , errno = 32 p4_2613: p4_error: interrupt SIGx: 13 p5_2618: p4_error: interrupt SIGx: 13 bash-3.00$ most likely your calculation has crashed already. FPE means floating point error, which could be due to large force. Thanks in advance, Mike ___ 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
Re: [gmx-users] what to do if CU1+ warning appears after grompp?
Stefan Schöbel wrote: Hi, I installed the latest gromacs version but after the grompp command i got this warning that CU1+ is redifined. I tried a new ions.itp that I found in the mailing list but I didn't succeeded. How to solve this problem? Thanks in advance Stefan more info please. which force field? did you edit force field files? -- 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
Re: [gmx-users] Error message in output file.
coderrr c wrote: Hi, I am trying to run the gromacs and am getting the following error message in the status file.I would like to know what is the significance of the error message,is it going to impact my ouptut???.I am running the mpi version with 6 nodes. p0_2593: p4_error: interrupt SIGFPE: 8 p3_2608: p4_error: net_recv recv: EOF on socket: 1 p0_2593: (4.278990) net_send: could not write to fd=7, , errno = 32 p4_2613: p4_error: interrupt SIGx: 13 p5_2618: p4_error: interrupt SIGx: 13 This is indicative of a problem with a low-level interaction of your MPI library with other stuff I don't understand. 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
[gmx-users] Large input Files
Hi, I am trying to run Gromacs(mpi) on Sun-Grid.Can someone provide with a large input files,which can utilise good amount of cpu time on Sun-Grid setup. Thanks in advance, Mike ___ 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] Large input Files
coderrr c wrote: Hi, I am trying to run Gromacs(mpi) on Sun-Grid.Can someone provide with a large input files,which can utilise good amount of cpu time on Sun-Grid setup. Thanks in advance, Mike ___ 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 try the benchmark. you can use genconf to make it bigger. -- 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
Re: [gmx-users] Not enough ref_t and tau_t values!
Hi Aline, Maybe a word of warning is in place. It is probably not a good idea to couple different parts of the same protein to different heat baths. It is definitely not a good idea to couple one peptide of 51 atoms to its private bath. You are likely better off with the division Protein Non-Protein (two tc-groups). This stands apart from the energy groups, where you can make the division alpha/beta/pept. Noting that you do have some magnesium ions, it may be necessary to have these in one index group, which you have actually, and for the solvent just make the complementary index group by merging the groups SOL and NA+ (or negating prot+pep+mg. Hope it helps, Tsjerk On 10/18/06, Yang Ye [EMAIL PROTECTED] wrote: On 10/18/2006 8:10 AM, Aline Rossi wrote: Hi list, Im dealing with a problem when trying to monitoring energygrps. When I run the grompp i receive this output: creating statusfile for 1 node... Back Off! I just backed up mdout.mdp to ./#mdout.mdp.16# checking input for internal consistency... calling /lib/cpp... processing topology... Generated 279 of the 1225 non-bonded parameter combinations Excluding 3 bonded neighbours for Protein_A 1 Excluding 3 bonded neighbours for Protein_B 1 Excluding 3 bonded neighbours for Protein_C 1 Excluding 2 bonded neighbours for SOL 30314 Excluding 1 bonded neighbours for NA+ 2 processing coordinates... double-checking input for internal consistency... Velocities were taken from a Maxwell distribution at 312 K renumbering atomtypes... converting bonded parameters... # G96BONDS: 6825 # G96ANGLES: 9964 # PDIHS: 3583 # IDIHS: 3430 # LJ14: 10944 # SETTLE: 30314 initialising group options... processing index file... Making dummy/rest group for T-Coupling containing 90944 elements --- Program grompp, VERSION 3.3 Source code file: readir.c, line: 1131 Fatal error: Not enough ref_t and tau_t values! my index file is: 0 System : 96772 atoms 1 Protein : 6694 atoms 2 Protein-H : 5213 atoms 3 C-alpha : 666 atoms 4 Backbone: 1998 atoms 5 MainChain : 2667 atoms 6 MainChain+Cb: 3268 atoms 7 MainChain+H : 3306 atoms 8 SideChain : 3388 atoms 9 SideChain-H : 2546 atoms 10 Prot-Masses : 6694 atoms 11 Non-Protein : 90078 atoms 12 Mg : 7 atoms 13 SOL : 90069 atoms 14 NA+ : 2 atoms 15 Other : 90078 atoms 16 alphabeta : 6648 atoms 17 his159 :12 atoms 18 arg157 :17 atoms 19 ecdw:51 atoms 20 glu1:12 atoms 21 cys2: 8 atoms 22 asp3: 9 atoms 23 trp4:22 atoms 24 tyr458 :18 atoms 25 ala585 : 6 atoms 26 prot+pep: 6703 atoms 27 prot+pep+mg : 6706 atoms 28 alpha : 4453 atoms 29 beta: 2202 atoms 30 pep :51 atoms title = PEP MD cpp = /lib/cpp constraints = none integrator = md dt = 0.0015; ps ! nsteps = 1000; total 500 ps. nstcomm = 3000 nstxout = 3000 nstvout = 5000 nstfout = 3000 nstlog = 1500 nstenergy = 3000 nstlist = 5 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb= 0.9 rvdw= 0.9 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes unconstrained-start = yes ; Berendsen temperature coupling is off in two groups Tcoupl = berendsen tc-grps= alpha beta pep tau_t = 0.1 0.1 0.1 ref_t = 312 312 312 ; Energy monitoring energygrps = alphabetapep beside the proteins, solvent also needs t-coupl. Try this tc-grps= alpha beta pep rest tau_t = 0.1 0.1 0.10.1 ref_t = 312 312 312 312 ; Energy monitoring energygrps = alphabetapep rest ; Isotropic 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 312 K. gen_vel = yes gen_temp= 312.0 gen_seed= 173529 What should be wrong with my imputs?? Thanks for help and my .mdp file is:
Re: [gmx-users] what to do if CU1+ warning appears after grompp?
Hi Stefan, Guessing that you're using GMX3.3.1, you probably overlooked the automatic inclusion of ions.itp in the .top file, which wasn't there in previous versions. Have a look in the .top file for two lines reading #include ions.itp and remove one of them. In general, if you read the term redefined, something's been added twice, in relation to ions, it is likely it has to do with ions.itp, so no need to try a newer version at that point. Best, Tsjerk On 10/18/06, David van der Spoel [EMAIL PROTECTED] wrote: Stefan Schöbel wrote: Hi, I installed the latest gromacs version but after the grompp command i got this warning that CU1+ is redifined. I tried a new ions.itp that I found in the mailing list but I didn't succeeded. How to solve this problem? Thanks in advance Stefan more info please. which force field? did you edit force field files? -- 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 -- Tsjerk A. Wassenaar, Ph.D. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands +31 50 363 4336 ___ 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] PCA multiple outputs from g_anaeig
Hello, g_anaeig analyzes the eigen vectors from eigenvec.trr and eigenval.xvg generated by g_covar and writes the proj.xvg, 2d_proj.xvg, 3d_proj.xvg, filtered.xvg. etc. My question is., For a single run of g_anaeig only a specific 2d_proj.xvg (say between eigenvec 1 and 8), 3d_proj.xvg. etc could be written. But one may want to study the projections between 1 and 2, 1 and 3, 2 and 3. etc. Is there any way to simultaneously write all the desired projections and filtered trajectories from a single run of g_anaeig, since all the required information will be already read once by the program. Any contributors for this? Thanks in advance. sridhar ___ 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] g_hbond error Your computational box has shrunk too much
Hi all, I'm beginning to analyze my trajectories, everything works fine with (g_rmsf, g_saltbr ...) but when i try to use g_hbond I receive this error: -- Program g_hbond, VERSION 3.3.1 Source code file: gmx_hbond.c, line: 631 Fatal error: Your computational box has shrunk too much. g_hbond can not handle this situation, sorry. --- Is this a bug or a problme with my system? Is there the possibility to avoid this problem in some way? THANKS Andrea ___ 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] New version of dock.pl
Hi everybody, I've submitted a new version of my script dock.pl. You can find the new version in the contributed software of the Gromacs website. This version fix some bugs and add new functionality like growing the ligand at the binding site of a protein. Please, read the documentation for more details about the new features. By the way, I haven't received any feedback about this script. So, if you are a user, I would appreciate if you can send me any comments about it. Thanks in advance, César.- ---Cesar Araujo, Lic. of ChemistryResearch Center for Molecular EndocrinologyP.O. Box 5000, FIN-90014 University of OuluFinland phone: +358 8 3155632e-mail: [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] Re: g_hbond error Your computational box has shrunk too much
andrea carotti wrote: Is it correct? Did you plot the box volume as a function of time? You can use g_hbond for different stretches of the trajectory and combine the results manually. -- Thanks for the fast reply. I'm only trying to monitor the hbond formation with the basic command g_hbond -f m93_newtraj.trr -s topol.tpr -n and giving to the groups selection two different parts of my protein (i've made an index file)..and then the programs suddenly stop. the default output (-num) should be the total number of hbond per frame. Please help me again Andrea you haven't answered my question, and haven't read my advice either. ___ 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
Re: [gmx-users] Re: g_hbond error Your computational box has shrunk too much
andrea carotti wrote: The problem is that i don't have an energy file cause this time I'm using gromacs only for analyze my trajs...so I don't know how to make the plot you suggested. Now perhaps I've found a workaroud using trjconv with the option -box 1 1 1 set, but I' don't know if this could be correct. make it a realistic size, maybe 3 3 3 (I've checked the ouput traj in VMD and seems fine, and with it g_hbond is working) Best Andrea -- ___ 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
Re: [gmx-users] dg/dl at lambda = 1
Hi, Dear gromacs users, I am trying to use FEP method for the calculation of relative binding free energy of peptide-protein complex. I am using gmx-3.3.1. As per previous discussions on the mailing list, i learnt that i need to do two different sets of simulations for my case. first set will be for modification of electrostatics and second one for vdw. The second set should be started with a structure from the last simulation of first set. And every simulation in each set should be run independent of each other with em and water-equilibration at each lambda value. following are the values for peptide only (not in complex) simulation in SPC216 water-box... lambda dg/dl (avg) error 0.0 55.777174 0.586923 0.015 57.524631 0.808737 0.0354.648669 1.03151 0.0554.833890 1.08532 0.1 52.990600 1.70822 0.2 50.377182 1.74758 0.3546.725657 0.683906 0.5 37.016530 0.826907 0.6533.239827 2.03776 0.7527.867797 0.300761 0.8515.989920 1.66024 0.9 1.5912180.924152 0.95 -32.877432 1.58611 0.99 -259.656906 9.28882 I assume this is for a calculation where you're inserting/deleting one or more particles? Are you using soft core? This sort of behavior is typical when you're doing insertion/deletion without soft core (I would expect the problem to be near lambda=1 if you are doing deletion without soft core). You can of course also have similar problems if you are using soft core but are using non-ideal parameters for soft core (i.e. the soft core parameters listed in my tutorial are very carefully chosen). David error is calculated by using g_analyze with -ee option i am getting very huge values at lambda = 1.0. as can be seen from the values, the steepness of the graph has increased a lot towards end. for l=1, dg/dl values go till ~ -2 x 10^11. what can be wrong? I have used the same version of gmx for the tutorial provided by Dill group. In that case, i am not getting any problem I am completely clueless here... please help.. thanks bharat ___ 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] PCA multiple outputs from g_anaeig
Hello, Not sure if you have already recieved the answer but you can use the option -first and -last with g_anaeig to get the required correlation plots. Hope this helps, -Original Message- From: [EMAIL PROTECTED] on behalf of Sridhar Acharya Sent: Wed 10/18/2006 6:51 AM To: gmx-users@gromacs.org Subject: [gmx-users] PCA multiple outputs from g_anaeig Hello, g_anaeig analyzes the eigen vectors from eigenvec.trr and eigenval.xvg generated by g_covar and writes the proj.xvg, 2d_proj.xvg, 3d_proj.xvg, filtered.xvg. etc. My question is., For a single run of g_anaeig only a specific 2d_proj.xvg (say between eigenvec 1 and 8), 3d_proj.xvg. etc could be written. But one may want to study the projections between 1 and 2, 1 and 3, 2 and 3. etc. Is there any way to simultaneously write all the desired projections and filtered trajectories from a single run of g_anaeig, since all the required information will be already read once by the program. Any contributors for this? Thanks in advance. sridhar ___ 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 winmail.dat___ 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: New version of dock.pl (Cesar Araujo)
Link is not working.. -- == Dr. JORGE HERNANDEZ FERNANDEZ == == Center of Applied Toxinology == = CAT-CEPID - Instituto Butantan = == Ave Vital Brasil, 1500 S.P. == Tel: 055 11 3726 7222 r.2042 Fax: 055 11 3721 6605 S.B.I.- EMBRAPA - BioInformatica C.p. 6041 Cidade Universitária Zeferino Vaz = Barão Geraldo Campinas S.P. === 13080-970 Tel: 055 19-37895828 Cell: 055 11-97126104 The information contained in this e-mail and any files tr Date: Wed, 18 Oct 2006 13:16:26 -0700 From: Cesar Araujo [EMAIL PROTECTED] Subject: [gmx-users] New version of dock.pl To: gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=iso-8859-1 Hi everybody, I've submitted a new version of my script dock.pl. You can find the new version in the contributed software of the Gromacs website. This version fix some bugs and add new functionality like growing the ligand at the binding site of a protein. Please, read the documentation for more details about the new features. By the way, I haven't received any feedback about this script. So, if you are a user, I would appreciate if you can send me any comments about it. Thanks in advance, César.- --- Cesar Araujo, Lic. of Chemistry Research Center for Molecular Endocrinology P.O. Box 5000, FIN-90014 University of Oulu Finland phone: +358 8 3155632 e-mail: [EMAIL PROTECTED] -- next part -- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx- users/attachments/20061018/f3b32605/attachment-0001.html -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please 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] Range checking error: ci barely out of bounds.
I am attempting to solve my range checking errors where ci is just barely out of bounds. This particular run is on 4cpus. I have reposted because now I have noticed that a0.log differs from the other log files with respect to the reported cells in the grid and that this may be important. Any help is greatly appreciated. My error message is: Variable ci has value 1625. It should have been within [ 0 .. 1584 ] And I notice that 12 x 12 x 11 = 1584, but 13 x 12 x 11 = 1716 (which would put ci=1625 in bounds). grep 'Grid:' a0.log | wc -l = 24 lines grep 'Grid:' (a1.log or a2.log or a3.log) | wc -l = 25 lines The straight grep 'Grid:' output is: ... Grid: 12 x 12 x 11 cells Grid: 13 x 12 x 11 cells (a0.log does not contain this line) The same pattern tends to occur for different jobs. For another example, Grid: 13 x 13 x 10 cells -- Grid: 13 x 13 x 11 cells (not on a0.log) and ci = 1721. It should have been within [ 0 .. 1690 ] (But 13 x 13 x 11 = 1859 putting 1721 in bounds). Can the grid sizes be different for the different processors or is this an output artifact? Here is my MDP file: title = seriousMD cpp = /home/cneale/exe/cpp integrator = md nsteps = 35 tinit = 0 dt = 0.002 comm_mode = linear nstcomm = 1 comm_grps = System nstxout = 5 nstvout = 5 nstfout = 5 nstlog = 1000 nstlist = 10 nstenergy = 5000 nstxtcout = 5000 ns_type = grid pbc = xyz coulombtype = PME rcoulomb= 0.9 fourierspacing = 0.12 pme_order = 4 vdwtype = cut-off rvdw_switch = 0 rvdw= 1.4 rlist = 0.9 DispCorr= no Pcoupl = Berendsen pcoupltype = semiisotropic compressibility = 4.5e-5 4.5e-5 ref_p = 1. 1. tau_p = 4.04.0 tcoupl = Berendsen tc_grps = Protein LDA_POPE_DMPE SOL_NA+ tau_t = 0.1 0.1 0.1 ref_t = 300.300. 300. annealing = no gen_vel = yes unconstrained-start = no gen_temp= 300. gen_seed= 9896 constraints = all-bonds constraint_algorithm= lincs lincs-iter = 1 lincs-order = 4 There is more background information and run data here: http://www.gromacs.org/pipermail/gmx-users/2006-October/024154.html http://www.gromacs.org/pipermail/gmx-users/2006-September/024003.html ___ 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] what to do if CU1+ warning appears after grompp?
thanks!! it's working now! Stefan -- GMX DSL-Flatrate 0,- Euro* - Überall, wo DSL verfügbar ist! NEU: Jetzt bis zu 16.000 kBit/s! http://www.gmx.net/de/go/dsl ___ 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
