RE: [gmx-users] force=nan in frame 0
Dear Mark, The installation works for other systems. The error happens in either EM or MD. When I turn off all interaction potentials, the forces between all particles should be zero, shouldn't they? Could you please tell me why the initial forces are NaN? Thanks! All the best! Dongsheng -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Mark Abraham Sent: Sunday, November 11, 2007 9:04 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] force=nan in frame 0 dongsheng zhang wrote: Dear Mark, Thank you for your reply. I have used gromacs before. In fact, I have built this FF before, and using it successfully. My old computer was crashed, so I need to do it again. The potential energies looked fine in the md.log. Even I turn off all potentials. I still get the initial foce = nan. Could you please give me any suggest about it? Can't tell. You still haven't told us what you were trying to do when it crashed. EM, MD? Did you minimize and/or equilibrate? Does this installation run other systems? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] force=nan in frame 0
Dear Yang Ye, Thank you very much for your reply. You are very helpful in my experience. I turned off the nb interaction by c6=0, c12 = 0. If you need my force field, I can give you the package for testing. All the best! Dongsheng - Original Message From: Yang Ye [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, November 12, 2007 2:33:38 PM Subject: Re: [gmx-users] force=nan in frame 0 how do you turn off the interactions? e.g. setting rvdw=0 doesn't mean turning of vdw interactions. Regards, Yang Ye On 11/13/2007 12:55 AM, dongsheng zhang wrote: Dear Mark, The installation works for other systems. The error happens in either EM or MD. When I turn off all interaction potentials, the forces between all particles should be zero, shouldn't they? Could you please tell me why the initial forces are NaN? Thanks! All the best! Dongsheng -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Mark Abraham Sent: Sunday, November 11, 2007 9:04 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] force=nan in frame 0 dongsheng zhang wrote: Dear Mark, Thank you for your reply. I have used gromacs before. In fact, I have built this FF before, and using it successfully. My old computer was crashed, so I need to do it again. The potential energies looked fine in the md.log. Even I turn off all potentials. I still get the initial foce = nan. Could you please give me any suggest about it? Can't tell. You still haven't told us what you were trying to do when it crashed. EM, MD? Did you minimize and/or equilibrate? Does this installation run other systems? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users 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 __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ 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] (no subject)
Hello, I have build my own FF for a copolomer. When I ran the program, I got KE is NaN. I checked the output file trr. I found the initial forces of all particles at frame 0 are infinite. Could anyone tell me why this happened? Where I might make a mistake? Thank you in advance! Dongsheng ___ 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] force=nan in frame 0
Dear Mark, Thank you for your reply. I have used gromacs before. In fact, I have built this FF before, and using it successfully. My old computer was crashed, so I need to do it again. The potential energies looked fine in the md.log. Even I turn off all potentials. I still get the initial foce = nan. Could you please give me any suggest about it? Thanks! Dongsheng -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Mark Abraham Sent: Sunday, November 11, 2007 8:40 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] (no subject) dongsheng zhang wrote: Hello, I have build my own FF for a copolomer. When I ran the program, I got KE is NaN. I checked the output file trr. I found the initial forces of all particles at frame 0 are infinite. Could anyone tell me why this happened? Where I might make a mistake? Thank you in advance! You could have made a mistake at every step. You should do some tutorial material, and get used to the mechanics *before* you attempt to define and use your own forcefields. Learn to walk before trying to run. Check out most of the wiki at http://wiki.gromacs.org Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] segmentation fault
Dear GMX users, I am studying adsorption of polymers on a surface. I want to enforce all polymers to be adsorbed, so I increase 10 times of the LJ interaction between polymers and the surface, then I got segmentation fault. Without increasing, the program ran fine (some polymers are not adsorbed). I have attached the log file at the end. From the log file, the second last step shows everything is fine, but the KE suddenly increases a lot in the last step. My question is why the KE increases so much if there is no bad contact in the second last step. Could someone shine a light on it? Thank you very much! Step Time Lambda 55715 111.430010.0 Energies (kJ/mol) Bond Angle G96Angle Ryckaert-Bell. LJ-14 1.02536e+043.21677e+032.50169e+047.22574e+032.65433e +02 Coulomb-14LJ (SR) Coulomb (SR) PotentialKinetic En. 3.13204e+00 -3.84609e+040.0e+007.52075e+032.04250e +04 Total EnergyTemperature Pressure (bar) 2.79458e+043.26040e+027.59950e-02 Step Time Lambda 55716 111.432010.0 Energies (kJ/mol) Bond Angle G96Angle Ryckaert-Bell. LJ-14 1.02167e+043.21698e+032.50005e+047.23403e+032.64875e +02 Coulomb-14LJ (SR) Coulomb (SR) PotentialKinetic En. 3.12067e+00 -3.84684e+040.0e+007.46781e+031.46039e +13 Total EnergyTemperature Pressure (bar) 1.46039e+132.33119e+113.81713e+08 All the best! Dongsheng ___ 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] mdrun hangs on nodes of P655+ aix 5.2
Dear Erik, Thank you. My gmx is 3.3.1. Maybe that's the reason there is no difference except documentation part. To my understanding to your email, gmx 3.3.1 has solved that problem. I don't know why I still encounter it. In fact, there is no COUL term in my coarse-grained FF. I don't know what is the cause in my case. If you need more information, please let me know. All the best! Dongsheng On Mon, 2006-08-07 at 07:45 +0200, Erik Lindahl wrote: Hi, I'm certainly seeing lots of differences between 1.5 and 1.5.4.1 when I run diff in my cvs tree. However, I think we made the 3.3.1 release after march 9, in which case it is included there. Cheers, Erik On Aug 5, 2006, at 12:05 AM, Dongsheng Zhang wrote: Dear Erik, I had the same problem as Arthur Roberts. So I downloaded your new version of gmx_system_xdr.h and gmx_system_xdr.c from http://bugzilla.gromacs.org/show_bug.cgi?id=55 Before I recompile gromacs, I checked the difference between your new version and the old one. The result is as follows: diff gmx_system_xdr.c gmx_system_xdr-n.c 2c2 * $Id: gmx_system_xdr.c,v 1.5.4.1 2006/03/09 08:12:16 lindahl Exp $ --- * $Id: gmx_system_xdr.c,v 1.5 2004/01/23 17:23:13 lindahl Exp $ diff gmx_system_xdr.h gmx_system_xdr-n.h 2c2 * $Id: gmx_system_xdr.h,v 1.3.4.1 2006/03/09 08:12:09 lindahl Exp $ --- * $Id: gmx_system_xdr.h,v 1.3 2003/11/17 21:50:40 spoel Exp $ Both differences are in documentation. I am confused how your modification can solve the problem. I had the same problem and posted in the mailing list before ( http://www.gromacs.org/pipermail/gmx-users/2006-June/022493.html ) I also found Jason O'Young had asked the similar question at http://www.gromacs.org/pipermail/gmx-users/2006-May/021605.html I think this problem sounds common, could you please investigate what's wrong? Thank you very much for your help! By the way, I can continue the simulation by tpbconv, but hangs soon without any error message. The top command shows the programs is running, but no more output data. All the best! Dongsheng On Mon, 2006-07-31 at 08:36 +0200, Erik Lindahl wrote: Hi, It _might_ be solved by the fix attachment at http://bugzilla.gromacs.org/show_bug.cgi?id=55 (also in CVS) Cheers, Erik On Jul 31, 2006, at 8:11 AM, Arthur Roberts wrote: Hi, all, I am trying to run Gromacs on a P655+ with Aix 5.2. Initially, mdrun appears to work, but always hangs. Eventually, I get timed out from the supercomputer with no data to show for it. Below is a link detailing the problem: http://cetus.mchem.washington.edu/pub/supercomputer/Mdrun-hangs- without-showing-steps.html I appreciate your input. Your previous suggestions have been very helpful. Best wishes, Art ___ 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 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 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] mdrun hangs on nodes of P655+ aix 5.2
Dear Erik, I had the same problem as Arthur Roberts. So I downloaded your new version of gmx_system_xdr.h and gmx_system_xdr.c from http://bugzilla.gromacs.org/show_bug.cgi?id=55 Before I recompile gromacs, I checked the difference between your new version and the old one. The result is as follows: diff gmx_system_xdr.c gmx_system_xdr-n.c 2c2 * $Id: gmx_system_xdr.c,v 1.5.4.1 2006/03/09 08:12:16 lindahl Exp $ --- * $Id: gmx_system_xdr.c,v 1.5 2004/01/23 17:23:13 lindahl Exp $ diff gmx_system_xdr.h gmx_system_xdr-n.h 2c2 * $Id: gmx_system_xdr.h,v 1.3.4.1 2006/03/09 08:12:09 lindahl Exp $ --- * $Id: gmx_system_xdr.h,v 1.3 2003/11/17 21:50:40 spoel Exp $ Both differences are in documentation. I am confused how your modification can solve the problem. I had the same problem and posted in the mailing list before ( http://www.gromacs.org/pipermail/gmx-users/2006-June/022493.html ) I also found Jason O'Young had asked the similar question at http://www.gromacs.org/pipermail/gmx-users/2006-May/021605.html I think this problem sounds common, could you please investigate what's wrong? Thank you very much for your help! By the way, I can continue the simulation by tpbconv, but hangs soon without any error message. The top command shows the programs is running, but no more output data. All the best! Dongsheng On Mon, 2006-07-31 at 08:36 +0200, Erik Lindahl wrote: Hi, It _might_ be solved by the fix attachment at http://bugzilla.gromacs.org/show_bug.cgi?id=55 (also in CVS) Cheers, Erik On Jul 31, 2006, at 8:11 AM, Arthur Roberts wrote: Hi, all, I am trying to run Gromacs on a P655+ with Aix 5.2. Initially, mdrun appears to work, but always hangs. Eventually, I get timed out from the supercomputer with no data to show for it. Below is a link detailing the problem: http://cetus.mchem.washington.edu/pub/supercomputer/Mdrun-hangs- without-showing-steps.html I appreciate your input. Your previous suggestions have been very helpful. Best wishes, Art ___ 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 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] Langevin dynamics ( Large VCM )
If you want to use BD, the friction coefficient has to be large. Please check the manual. If you change your bd-fric to 5000, it might help. On Wed, 2006-08-02 at 23:24 +0800, PAUL NEWMAN wrote: Hi: Thanks to everybody who helped me out with my last email. But now I have another problem and I hope you can help me. As i told you I'm doing a simulation of polyelectrolyte chain consisting of 50 charged beads (-1) with 50 charged counterions(+1). My box simulation is 400 nm x 400 nm x 400 nm and the polyelectrolyte length is 100 nm. My problem is when I chage the intregator md to bd (position langevin dynamics), it gives me Large VCM (group System) in the md.log file and after some time it crashes at some point. When i take a look at the energy file and plot the temperature I realized that the temperature is far from the desired temperature. Please take a look at my mdp file and help me figure out what i'm doing wrong. My last question how can I choose the rlist, Vdw and coulomb cut-off when I'm using PME and , for example my case in 400 nm x 400 nm x 400 nm and 100 atoms with fourierspacing = 20 (is it ok?). Thanks in advance. ; By user: pcl ; VARIOUS PREPROCESSING OPTIONS title= Yo cpp = /lib/cpp include = define = ; RUN CONTROL PARAMETERS integrator = bd ; Start time and timestep in ps tinit= 0 dt = 0.0001 nsteps = 1 comm-mode= Linear nstcomm = 1 comm-grps= System ; LANGEVIN DYNAMICS OPTIONS ; Friction coefficient (amu/ps) and random seed bd-fric = 0.05 ld_seed = 1993 ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 10 ; ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz (default), no (vacuum)or full (infinite systems only) pbc = xyz ; nblist cut-off rlist= 100 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME ;rcoulomb-switch = 0 rcoulomb = 100 fourierspacing = 20 optimize_fft = yes ; Relative dielectric constant for the medium and the reaction field epsilon_r= 13.89354; ; Method for doing Van der Waals vdw-type = Cut-off rvdw-switch = 0 rvdw = 100 ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling Tcoupl = Berendsen ; Groups to couple separately tc-grps = NA POL ; Time constant (ps) and reference temperature (K) tau_t= 0.01 0.01 ref_t= 120.2717 120.2717; ; Pressure coupling Pcoupl = no ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = no ; OPTIONS FOR BONDS constraints = none -- Cheers, Paul National Tsing Hua University (清A大W) xx你的兔 I appreciate your help. Thanks! Os agradezco la ayuda. Gracias! ___ 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] g_bond
Dear David, Thank you four reply. Since g_bond can read gro file as input. I amde the following test. I made a short gro file test.gro as: e100p64e100.pdb 8 1PEO C11 4.069 2.093 1.068 0.1450 0.0605 -0.1344 1PEO C22 3.829 2.253 0.932 -0.0153 -0.1263 0.2339 1PEO C33 3.758 2.298 0.621 0.0345 -0.0676 0.0808 1PEO C44 3.597 2.147 0.396 0.3742 0.2042 -0.2398 2PEO C15 3.332 2.252 0.360 -0.1458 -0.0531 -0.3600 2PEO C26 3.243 2.412 0.104 -0.0849 0.1382 0.1444 2PEO C37 2.984 2.456 -0.060 -0.1546 0.3956 -0.0143 2PEO C48 3.080 2.278 -0.316 0.1942 -0.1982 0.3747 5.64027 3.42476 11.12249 My index file bond.ndx is : [bond] 1 2 2 3 3 4 Then I tried to use: g_bond -f test.gro -n bond.ndx I got the error message: Fatal error: No distribution... (i0 = 999, i1 = 1)? ? ! ! ? ! Could you please tell me where is the error? Thank you! Dongsheng On Wed, 2006-07-19 at 08:40 +0200, David van der Spoel wrote: Dongsheng Zhang wrote: Hello, GMX users, When I tried to use g_bond -f *xtc -n *.ndx to get a bond length, I got an error message as follows: Fatal error: No distribution... (i0 = 999, i1 = 1)? ? ! ! ? ! You probably have given the program an empty index file. All bonds have length 0 anyway. Could someone tell me what that means? Thank you in advance! Dongsheng ___ 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] segmentation fault
Dear GMX users, My system is PEO-PPO-PEO triblock polymers with a coarse grained force field. The nonbonded interactions are tabulated. The interaction range in my tables in 5 nm. The cutoff is 1.4 nm. The table extention is 2 nm. If I simulation only one chain, it works fine. However, the program gave me Segmentation fault when I simulated 30 chains. The log file seems fine, as follows: Step Time Lambda 5000 10.00.0 Energies (kJ/mol) Bond Angle LJ-14 Coulomb-14LJ (SR) 1.10604e+042.16255e+043.01743e+026.81742e+01 -1.29044e +05 Coulomb (SR) PotentialKinetic En. Total Energy Temperature 0.0e+00 -9.59881e+042.95806e+04 -6.64076e+042.99508e +02 Pressure (bar) 8.75619e+00 Step Time Lambda 6000 12.00.0 Energies (kJ/mol) Bond Angle LJ-14 Coulomb-14LJ (SR) 1.17095e+042.20613e+042.40772e+026.78325e+01 -1.31923e +05 Coulomb (SR) PotentialKinetic En. Total Energy Temperature 0.0e+00 -9.78433e+042.96119e+04 -6.82314e+042.99825e +02 Pressure (bar) 4.47005e+00 The program stopped at step 6990 without any error message. When I ran the program with -debug, I got a different log file, as follows: PLEASE READ AND CITE THE FOLLOWING REFERENCE H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak Molecular dynamics with coupling to an external bath J. Chem. Phys. 81 (1984) pp. 3684-3690 --- Thank You --- Large VCM(group rest): -0.0, -0.0, 0.0, ekin-cm: 3.11775e-21 Energies (kJ/mol) Bond Angle LJ-14 Coulomb-14LJ (SR) 1.00042e+041.01454e+041.36360e+036.50650e+00 -2.68845e +04 Coulomb (SR) PotentialKinetic En. Total Energy Temperature 0.0e+00 -5.36480e+032.96549e+042.42901e+043.00260e +02 Pressure (bar) -2.46133e+01 Large VCM(group rest): -0.0, -0.0, 0.0, ekin-cm: 2.79878e-21 The program stopped at step 3600, and there is no output for step 1000, 2000 3000 even though I set nstlog = 1000 in my mdp file. With -debug, I got three of ctab.xvg dtab.xvg, rtab.xvg, and one of ctab14.xvg dtab14.xvg, rtab14.xvg. In table_*_*.xvg, I only use C6 term, three dtab.xvg matches my input table_*_*.xvg. ctab.xvg and rtab.xvg should be zeros, but I find some large negative values in the last several line as follows: #ctab.xvg.1 (for PEO-PEO COUL term) 3.398953e+00 -2.5368847225e+15 -5.3233641970e+22 3.3984000953e+00 -4.4703197993e+22 -2.2346273246e+26 3.3988000953e+00 -1.7877019745e+23 -4.4687222761e+26 3.3992000953e+00 -4.0220100090e+23 -6.7028177811e+26 3.3996000954e+00 -7.1499560834e+23 -8.9369125481e+26 #rtab.xvg.1 (for PEO-PEO C12 term) 3.398953e+00 -3.0786326528e+10 9.1349993896e+02 3.3984000953e+00 -3.0786326528e+10 1.0232022095e+03 3.3988000953e+00 -3.0786326527e+10 1.3522044678e+03 3.3992000953e+00 -3.0786326527e+10 1.9005067139e+03 3.3996000954e+00 -3.0786326526e+10 2.6681091309e+03 These are the only things I find specious. Could you please help me to found what causes segmentation fault? All the best! Dongsheng ___ 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_bond
Hello, GMX users, When I tried to use g_bond -f *xtc -n *.ndx to get a bond length, I got an error message as follows: Fatal error: No distribution... (i0 = 999, i1 = 1)? ? ! ! ? ! Could someone tell me what that means? Thank you in advance! Dongsheng ___ 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] program crashes when -table option used
Berk, Thank you very much for your suggestion. After I extend the table extension to 2.0nm, the program works fine now. Initially the cut_off is 1.4 nm, the table extension is 1.0nm, so my table is for the interactions whose distance is within 2.5nm. I thought it is long enough. Could you please explain to me why gromacs compares the distance between 1 and 4 to the table extension parameter, not the whole table length (cut-off + table extension)? I need to use multiple tables for pair interaction (1-4 interaction) calculations. Currently gromacs can only read one table for pair interactions. I am thinking to take advantage of the COUL term in table.xvg because there is no COUL interaction in my coarse-grained model. The only thing I need to modify in the source code is to switch the calculation of pair interaction to the calculation of COUL term. If you think this is a good approach, could you please tell me how to modify it? All the best! Dongsheng On Fri, 2006-07-14 at 10:23 +0200, Berk Hess wrote: From: Dongsheng Zhang [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] program crashes when -table option used Date: Fri, 14 Jul 2006 02:13:54 -0400 Yang Ye, I just can't understand why the program ran fine in one way, but crashed in another way. If the two coordinates file are the same, how come did the second run give me large value of LJ_14? If it is possible, I can give you my two tpr file, you can do the test. The large LJ_14 value could mean that a 1-4 interaction pair went beyond the table length. Did you get warnings about this? What is your cut-off and table-extension? I used a coarse grained model, dt = 0.002. I don't think it is too large for a monomer. By the way, it seems David has not told us how to input multiple tablep.xvg files, right? You can not have multiple tablep.xvg files. You can only use one, which is applied to all 1-4 interactions. Berk. ___ 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] program crashes when -table option used
Dear GMX users, I have a coarse-grained model whose nonbonded potentials are tabulated, so I have to use user defined potential in gromacs. With Yang Ye's great help, I can implement the new force field. However, the program always crashed because of Large VCM(group rest). I have done a test by run the program in two different ways. My new force field uses gromos FF format, so I used c6 and c12 parameters. First I ran the program in a normal way, which means I use LJ for regular VDWs and 1-4 interactions. The program ran fine. Second I copied table6-12.xvg to my working directory and rename it to a proper name, then I used this table as my user-defined potential for VDWs and 1-4 interactions. I expect the above two ways give me very similar results. This is true for the first 51 steps. In step 52, the second run suddenly crashed because of Large VCM(group rest). The details are as following: The differences in two mdp files: 59c59 vdw-type = user ;cut-off --- vdw-type = cut-off; user ;cut-off The information from two log files: full2.log (first run): Step Time Lambda 510.102000.0 Energies (kJ/mol) Bond Angle LJ-14 Coulomb-14LJ (SR) 3.02207e+023.7e+02 -3.73112e+010.0e+00 -2.27638e +02 Coulomb (SR) PotentialKinetic En. Total Energy Temperature 0.0e+003.37264e+021.01670e+031.35397e+033.09963e +02 Pressure (bar) 4.78614e+00 Step Time Lambda 520.104000.0 Energies (kJ/mol) Bond Angle LJ-14 Coulomb-14LJ (SR) 3.00485e+022.99534e+02 -3.73372e+010.0e+00 -2.27861e +02 Coulomb (SR) PotentialKinetic En. Total Energy Temperature 0.0e+003.34820e+021.01849e+031.35331e+033.10508e +02 Pressure (bar) 4.73457e+00 Step Time Lambda 530.106000.0 Energies (kJ/mol) Bond Angle LJ-14 Coulomb-14LJ (SR) 2.98871e+022.99071e+02 -3.73627e+010.0e+00 -2.28077e +02 Coulomb (SR) PotentialKinetic En. Total Energy Temperature 0.0e+003.32503e+021.02011e+031.35262e+033.11004e +02 Pressure (bar) 4.67219e+00 full.log (second run): Step Time Lambda 510.102000.0 Energies (kJ/mol) Bond Angle LJ-14 Coulomb-14LJ (SR) 3.02206e+023.7e+02 -3.73112e+010.0e+00 -2.27636e +02 Coulomb (SR) PotentialKinetic En. Total Energy Temperature 0.0e+003.37266e+021.01670e+031.35397e+033.09963e +02 Pressure (bar) 4.78604e+00 Step Time Lambda 520.104000.0 Large VCM(group rest): -362781422043267072.0, 46998104838242304.0, -95810352322707456.0, ekin-cm: inf Energies (kJ/mol) Bond Angle LJ-14 Coulomb-14LJ (SR) 3.00484e+022.99534e+02 -9.09769e+310.0e+00 -2.27860e +02 Coulomb (SR) PotentialKinetic En. Total Energy Temperature 0.0e+00 -9.09769e+31infinf inf Pressure (bar) inf Step Time Lambda 530.106000.0 Compare step 51 in two cases, every item has very similar value. In step 52, the second run give me very large value of LJ14. This causes the problem. However I compare the output xtc files at step 52 i those twp runs. They are identical. It really surprises me that LJ-14 is so large in the second run. Any suggest to find what's wrong will be highly appreciated. If you need more information, please let me know. All the best! Dongsheng ___ 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] coarse-grained model
Yang Ye,
Thank you for your help! I can use the table without any complaint, but
I get all zeros for LJ and LJ14. I believe something is wrong.
The following is from my log file:
Table routines are used for coulomb: FALSE
Table routines are used for vdw: TRUE
Cut-off's: NS: 1.4 Coulomb: 1.4 LJ: 1.4
System total charge: 0.000
Read user tables from table_EO_EO.xvg with 1251 data points.
Tabscale = 500 points/nm
Generated table with 1200 data points for COUL.
Tabscale = 500 points/nm
Read user tables from table_EO_PO.xvg with 1251 data points.
Tabscale = 500 points/nm
Generated table with 1200 data points for COUL.
Tabscale = 500 points/nm
Read user tables from table_PO_PO.xvg with 1251 data points.
Tabscale = 500 points/nm
Generated table with 1200 data points for COUL.
Tabscale = 500 points/nm
Read user tables from tablep_EO_EO.xvg with 1251 data points.
Tabscale = 500 points/nm
Generated table with 500 data points for 1-4 COUL.
Energies (kJ/mol)
Bond Angle LJ-14 Coulomb-14LJ
(SR)
2.88200e+023.30111e+020.0e+000.0e+000.0e
+00
Coulomb (SR) PotentialKinetic En. Total Energy
Temperature
0.0e+006.18310e+021.01226e+031.63057e+033.08610e
+02
Pressure (bar)
8.14486e+00
Step Time Lambda
10002.00.0
I have also input tablep_PO_PO.xvg and tablep_EO_PO.xvg, but it seems
that gromacs can only recognize the first tablep***.xvg file, which is
tablep_EO_EO.xvg.
The following is from my mdp file:
energygrps = EO PO
energygrp_table = EO EO PO PO EO PO
coulombtype = Cut-off; PME;
vdw-type = user ;cut-off
The command I used is :
mpirun -np 2 mdrun_mpi -s full -o full -c full -g full -e full -x full
-v -table table.xvg -tablep tablep_EO_EO.xvg tablep_PO_PO.xvg
tablep_EO_PO.xvg full.job
Could you please help me to find what's wrong?
All the best!
Dongsheng
On Wed, 2006-07-12 at 13:37 +0800, Yang Ye wrote:
Dongsheng Zhang wrote:
Yang Ye,
I am sorry to tell you I am not clear yet. Do you think I need to
specify energygrps and corresponding energygrp_table?
If so, then I got any error message. gp1 includes atom A, and gp3
includes atom A and B. Gromacs will complain that atoma has been in two
groups. Each group uses it own different table, but the group members
are overlapping bwteen some groups. How can I fix it?
You don't need to define 1-4 group again. with -table and -tablep for
mdrun, between energy group A and B, 1-2 interaction will be looked up
from table_A_B.xvg and 1-4 interaction will be looked up from
tablep_A_B.xvg.
And also, energygrps shall corresponds to energygrp_table.
So, instead to have
energygrps = gp1 gp2 gp3 gp4 gp5 gp6 ... gp12
energygrp_table = A A B B C C A B A C B C A14 A14 B14 B14 C14 C14 A14
B14 A14 C14 B14 C14
You shall have
energygrps = A B C ...
energygrp_table = A A B B C C A B A C B C
If not, I really have concern how gromacs knows to look for
table_A_A.xvg when it calculates A-A nonbonded interaction and look for
table_A14_A14.xvg when it calculates 1-4 interaction between A and A
monomers.
Could you please give me more instruction? Thank you for your help!
Dongsheng
On Wed, 2006-07-12 at 11:18 +0800, Yang Ye wrote:
Don't worry about that.
mdrun -tablep {tablep} will follow the scheme {tablep}_A_A.xvg,
{tablep}_B_B.xvg ...
{tablep} may be replaced by your own filename.
Yang Ye
Dongsheng Zhang wrote:
Yang ye,
Thank you very much.
I have three different monomers in my system, so I have 6 different
regular VMDs and 6 different 1-4 interactions. Could you please tell me
how to organize those table.xvg files?
energygrps = gp1 gp2 gp3 gp4 gp5 gp6 ... gp12
energygrp_table = A A B B C C A B A C B C A14 A14 B14 B14 C14 C14 A14
B14 A14 C14 B14 C14
If I set as the above, I wonder how gromacs know the last 6 table is for
1-4 interaction.
All the best!
Dongsheng
On Wed, 2006-07-12 at 09:54 +0800, Yang Ye wrote:
mdrun -tablep
Dongsheng Zhang wrote:
Hello, GMX users,
I have a coarse-grained model. Both 1-4 and regular vdw interaction are
tabulated, but no electrostatic interaction. Since there is no entry for
1-4 interaction in energy_table. I am thinking to fool gromacs by
treating 1-4 interactions as electrostatic interactions, in other words,
every time when 1-4 interaction energy needed, I will ask gromacs to
calculate COUL energy by reading energy_table. Does anyone know where
1-4 interaction is calculated and how I can switch it to calculate COUL
energy in the source code? Any help will be highly appreciated!
All the best!
Dongsheng
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Re: [gmx-users] proper dihedrals
Those parameters should be in **bond.itp file, and you can use four atoms to define a dihedral angle. You can check ffoplsaabon.itp. I am confused by that note as well. On Tue, 2006-07-11 at 13:14 -0400, ARGYRIOS KARATRANTOS wrote: Hi all, according to the manual the proper dihedrals are set, using in the topology file(top file) the inner two atoms of the dihedral. But how i can set the two following dihedrals, which have the same inner atoms C-O-C-H C-O-C-C but different external atoms, and of course different K values(KJ/mol) Argyris Karatrantos ___ 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] coarse-grained model
Yang ye, Thank you very much. I have three different monomers in my system, so I have 6 different regular VMDs and 6 different 1-4 interactions. Could you please tell me how to organize those table.xvg files? energygrps = gp1 gp2 gp3 gp4 gp5 gp6 ... gp12 energygrp_table = A A B B C C A B A C B C A14 A14 B14 B14 C14 C14 A14 B14 A14 C14 B14 C14 If I set as the above, I wonder how gromacs know the last 6 table is for 1-4 interaction. All the best! Dongsheng On Wed, 2006-07-12 at 09:54 +0800, Yang Ye wrote: mdrun -tablep Dongsheng Zhang wrote: Hello, GMX users, I have a coarse-grained model. Both 1-4 and regular vdw interaction are tabulated, but no electrostatic interaction. Since there is no entry for 1-4 interaction in energy_table. I am thinking to fool gromacs by treating 1-4 interactions as electrostatic interactions, in other words, every time when 1-4 interaction energy needed, I will ask gromacs to calculate COUL energy by reading energy_table. Does anyone know where 1-4 interaction is calculated and how I can switch it to calculate COUL energy in the source code? Any help will be highly appreciated! All the best! Dongsheng ___ 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 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] how to interpretate a tpr file
On Mon, 2006-07-10 at 13:58 +0800, Yang Ye wrote:
Dongsheng Zhang wrote:
Yang Ye,
Thank you very much for your help. I still have some questions:
On Mon, 2006-07-10 at 11:35 +0800, Yang Ye wrote:
Dongsheng Zhang wrote:
Dear GMX users:
Could someone help me to understand these information from a position
restrained tpr file?
1. excl[0][0..17]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 13, 14, 15,
16, 18, 26, 28}
Exclusion group 0, there are total 17 exclusions in this group. between
0 (the first one) and remaining 17 atoms.
Is this exclusion for nonbonded interactions, including 1-2, 1-3
interactions? If so, I don't understand why there are 17 atoms to be
excluded for atom 0. It is a capped carbon nanotube. Each C has three
single covalent bond, so the total exluded atoms for each atom should be
6.
This is next term for exlusion:
excl[1][18..35]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,
13, 14, 15, 20, 22}
Why are there two different exclusions for atom 0?
Please check your top file, including those files included into it.
Remove/Change some and compare the dump.
2. blocks[CGS][0][0..19]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11,
12, 13, 14, 15, 16, 17, 18, 19}
3. blocks[MOLS][2][1802..1805]={1802, 1803, 1804, 1805}
Both are useful for dividing the atoms for parallel processing (before
domain decomposition arrives in gmx 4.0 :-).
CGS means charge group. MOLS means molecules. Division shall not break
one charge group or a molecule (hope that I am not wrong here).
4. blocks[SBLOCKS][0][0..1039]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9,
10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23,
24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37,
38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51,
52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64,
65, ... 1039}
Not sure...
Anyone can help me for this one? Thanks!
5. functype[0]=LJ_SR, c6= 5.72640402e-03, c12= 1.86486031e-05
I know this is for the parameters of LJ potential. My question is where
is the information that tells gromacs to use these parameters for the
interaction between two specific atoms.
see atoms: section; type there refers to the functype here. Any functype
number for LJ_SR beyond the atom number there will not be used.
I am sorry I am not clear here. I know C6 and C12 is for the LJ
interaction between C and C in nanotube by looking at **nb.itp file. How
can gromacs know it in tpr file (I believe all information should be in
tpr file)? Let me give you an example. In tpr file, type=81 (ANGLES)
1041 1040 1042 shows that the angle bending parameters for atoms 1041
1040 1042 are from functype[81], but I can't find any information which
says the LJ parameters for C and C are from functype[0].
mdrun will associate functype[i] with atom type. check gmx source code
if you are still not sure.
my questions is how gromacs makes the association, especially for the LJ
potential between two different atoms. Do you mean atom type in:
atom[ 0]={type= 0, typeB= 0, ptype=Atom, m= 1.20110e+01, q=
0.0e+00, mB= 1.20110e+01, qB= 0.0e+00, resnr=0} grpnrs=[ 1 1
0 0 0 0 0 0 0 0 ]}
The number 0 in type= 0 is an index number for different atoms in the
top file. It doesn't match with i in functype[i] .
If you want me to check the source code, could please tell which portion
of the source code can answer my question? I have checked sim_util.c,
but haven't found the answer.
Thank you for your help!
As someone has suggested, if gromacs website can offer the
interpretation for each file, I believe many people will highly
appreciate it.
All the best!
Dongsheng
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[gmx-users] how to interpretate a tpr file
Dear GMX users:
Could someone help me to understand these information from a position
restrained tpr file?
1. excl[0][0..17]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 13, 14, 15,
16, 18, 26, 28}
2. blocks[CGS][0][0..19]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11,
12, 13, 14, 15, 16, 17, 18, 19}
3. blocks[MOLS][2][1802..1805]={1802, 1803, 1804, 1805}
4. blocks[SBLOCKS][0][0..1039]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9,
10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23,
24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37,
38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51,
52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64,
65, ... 1039}
5. functype[0]=LJ_SR, c6= 5.72640402e-03, c12= 1.86486031e-05
I know this is for the parameters of LJ potential. My question is where
is the information that tells gromacs to use these parameters for the
interaction between two specific atoms.
As someone has suggested, if gromacs website can offer the
interpretation for each file, I believe many people will highly
appreciate it.
All the best!
Dongsheng
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[gmx-users] use both LJ and buckingham potential for nonbonded potential
Dear gmx users, I find a force field that uses both LJ and Buckingham potential for different nonbonded potentials. I would like to use it in gromacs. I have try it, gromacs gave me a fatal error: ERROR 1 [file ffpolymernb.itp, line 49]: Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR) Does gromacs have any reason to prevent using two different forms for nonbonded potential? if not, please tell me how to remove the error message. Thank you very much! Dongsheng ___ 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] how to interpretate a tpr file
Yang Ye,
Thank you very much for your help. I still have some questions:
On Mon, 2006-07-10 at 11:35 +0800, Yang Ye wrote:
Dongsheng Zhang wrote:
Dear GMX users:
Could someone help me to understand these information from a position
restrained tpr file?
1. excl[0][0..17]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 13, 14, 15,
16, 18, 26, 28}
Exclusion group 0, there are total 17 exclusions in this group. between
0 (the first one) and remaining 17 atoms.
Is this exclusion for nonbonded interactions, including 1-2, 1-3
interactions? If so, I don't understand why there are 17 atoms to be
excluded for atom 0. It is a capped carbon nanotube. Each C has three
single covalent bond, so the total exluded atoms for each atom should be
6.
This is next term for exlusion:
excl[1][18..35]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,
13, 14, 15, 20, 22}
Why are there two different exclusions for atom 0?
2. blocks[CGS][0][0..19]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11,
12, 13, 14, 15, 16, 17, 18, 19}
3. blocks[MOLS][2][1802..1805]={1802, 1803, 1804, 1805}
Both are useful for dividing the atoms for parallel processing (before
domain decomposition arrives in gmx 4.0 :-).
CGS means charge group. MOLS means molecules. Division shall not break
one charge group or a molecule (hope that I am not wrong here).
4. blocks[SBLOCKS][0][0..1039]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9,
10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23,
24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37,
38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51,
52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64,
65, ... 1039}
Not sure...
Anyone can help me for this one? Thanks!
5. functype[0]=LJ_SR, c6= 5.72640402e-03, c12= 1.86486031e-05
I know this is for the parameters of LJ potential. My question is where
is the information that tells gromacs to use these parameters for the
interaction between two specific atoms.
see atoms: section; type there refers to the functype here. Any functype
number for LJ_SR beyond the atom number there will not be used.
I am sorry I am not clear here. I know C6 and C12 is for the LJ
interaction between C and C in nanotube by looking at **nb.itp file. How
can gromacs know it in tpr file (I believe all information should be in
tpr file)? Let me give you an example. In tpr file, type=81 (ANGLES)
1041 1040 1042 shows that the angle bending parameters for atoms 1041
1040 1042 are from functype[81], but I can't find any information which
says the LJ parameters for C and C are from functype[0].
As someone has suggested, if gromacs website can offer the
interpretation for each file, I believe many people will highly
appreciate it.
All the best!
Dongsheng
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Re: [gmx-users] high initial temperature with low ref_T
Dear Mark, Do you have any idea what's wrong with my simulation? You can find the mdp file and the description how I set up my system at the bottom of this email. All the best! Dongsheng On Thu, 2006-07-06 at 19:16 -0400, Dongsheng Zhang wrote: Mark, Thank you very much for your reply. On Fri, 2006-07-07 at 08:51 +1000, Mark Abraham wrote: Hello, GMX users, My system exploded very soon after mdrun. So I outputted the log file every step. I found the initial temperature is about 800 K even though I set ref_T = 300. Why does this happen? First please tell us you've done energy minimization and checked the structure and resulting trajectory visually to see that things look reasonable there. The following is the mdp file: ; VARIOUS PREPROCESSING OPTIONS title= nanotube_polymer - z T300 cpp = /lib/cpp -traditional include = define = ; RUN CONTROL PARAMETERS integrator = md tinit= 0 ; Start time and timestep in ps ;constraints = hbonds ; constrain bonds involving H. dt = 0.002 nsteps = 100 ;2 ns comm-mode= ANGULAR ;Linear nstcomm = 1 comm-grps= ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) ; this affects file traj.trr nstxout = 5 nstvout = 5 nstfout = 5 ; Checkpointing helps you continue after crashes nstcheckpoint= 1000 ; Output frequency for energies to log file and energy file nstlog = 1 nstenergy= 1 energygrps = CNT polymer ; Output frequency and precision for xtc file (for the movie) nstxtcout= 1 xtc-precision= 1000 ; NEIGHBORSEARCHING PARAMETERS nstlist = 5; nblist update frequency ns_type = simple; ns algorithm (simple or grid) pbc = no rlist= 0 ; nblist cut-off ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics: Cut-off, coulombtype = Cut-off fourierspacing = 0.12 pme_order= 4 rcoulomb = 0 optimize_fft = yes ;This saves a few percent for long simulations ;rcoulomb_switch = 0.95 ; Dielectric constant (DC) for cut-off or DC of reaction field ;epsilon-r= 1.0 ; for reaction field ; Method for doing Van der Waals vdw-type = cut-off ; cut-off lengths rvdw = 0 ;rvdw_switch = 0.95 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = no; EnerPres ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling Tcoupl = berendsen ; nose-hoover ;berendsen ; Groups to couple separately tc-grps = polymer CNT ; Time constant (ps) and reference temperature (K) tau_t= 0.1 0.1 ref_t= 300 300 ; Pressure coupling Pcoupl = no; berendsen ;Parrinello-Rahman ;berendsen Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p= 0.5 compressibility = 4.5e-5 ref_p= 1.0 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = yes gen_temp = 300 gen_seed = 1223188 ;Electric fields ;E_z = 1 40 1 My system is a carbone nanotube with a polymer. The polymer has 80 units. After I generated the polymer chain, I have relaxed the polymer alone in vacuum for 200 ps. Then I added CNT to the system, and made sure there was no overlap by VMD. Then I did EM in vacuum. I used the above mdp to generate a tpr file. When I ran it, the polymer exploded. However, If I simulate the polymer alone in vacuum, it works fine with the same force field. This problem sounds strange to me. How do you think? Best Wishes! Dongsheng If so, and there are still problems you'll need to supply a full .mdp and describe the simulation you're trying to run. 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 mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests
[gmx-users] program crash
Dear GMX users, My program crashed very soon after it started. I had done EM, and the conformation looked fine in VMD. When I investigated what's wrong, I outputted the coordinates, forces, velocities and log file in every step. I set some parameters in mdp file as follows: gen_vel = no; yes gen_temp = 100 gen_seed = 1223 ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling Tcoupl = berendsen ; nose-hoover ;berendsen ; Groups to couple separately tc-grps = protein ; Time constant (ps) and reference temperature (K) tau_t= 0.1 ref_t= 100 ; Pressure coupling Pcoupl = no; The following is from my log file: There are 1802 atoms in your xtc output selection PLEASE READ AND CITE THE FOLLOWING REFERENCE H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak Molecular dynamics with coupling to an external bath J. Chem. Phys. 81 (1984) pp. 3684-3690 --- Thank You --- Energies (kJ/mol) Bond Angle G96Angle Ryckaert-Bell. LJ-14 2.23601e+033.10376e+029.73565e+024.90946e+033.92667e +04 Coulomb-14LJ (SR) Coulomb (SR) PotentialKinetic En. 3.73370e+03 -3.85288e+03 -3.22634e+034.43506e+041.21982e +04 Total EnergyTemperature Pressure (bar) 5.65488e+045.43368e+020.0e+00 Step Time Lambda 10.002000.0 This is the first run after EM. I set gen_vel = no on purpose. When I checked the trr file, the initial velocities were zeros, so that's right. However, the log file showed that the initial KE and T were not zeros. This confuses me. How does gromacs calculate KE and T? Another strange thing is that the initial temperature is 500K, not 100K even though I set ref_t =100. Any help will be highly appreciated! All the best! Dongsheng ___ 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] tpr file
Dear GMX users,
The following message is from a tpr file by gmxdump command:
atom[ ]={type= 4, typeB= 4, ptype=Atom, m= 1.20110e+01,
q=-5.29400e-01, mB= 1.20110e+01, qB=-5.29400e-01, resnr= 32}
grpnrs=[ 0 0 0 0 0 0 0 0 0 0 ]}
Could anyone tell me what does type= 4 mean? I have checked the
manual and mailing list, but no fortune to get the answer. Thank you for
your help!
Dongsheng
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[gmx-users] high initial temperature with low ref_T
Hello, GMX users,
My system exploded very soon after mdrun. So I outputted the log file
every step. I found the initial temperature is about 800 K even though I
set ref_T = 300. Why does this happen?
The following is from my mdp file:
tau_t= 0.1 0.1
ref_t= 300 300
gen_vel = yes
gen_temp = 300
The following is from my log file:
Group rest with mass 1.71792e+04, Ekrot 2.03838e+00 Det(I) = 2.78698e
+12
COM: -0.44251 -0.27562 3.39794
P: -0.14897 -0.02236 0.01592
V: -0.1 -0.0 0.0
J: 444.35214-180.86247 -18.52021
w:0.00820 -0.00216 -0.00236
Inertia tensor (3x3):
Inertia tensor[0]={ 1.29701e+04, 5.56416e+03, -4.20521e+03}
Inertia tensor[1]={ 5.56416e+03, 7.12549e+03, -2.55740e+03}
Inertia tensor[2]={-4.20521e+03, -2.55740e+03, 4.68307e+04}
Energies (kJ/mol)
Bond Angle G96Angle Ryckaert-Bell.
LJ-14
2.23601e+033.10376e+029.73565e+024.90946e+033.92667e
+04
Coulomb-14LJ (SR) Coulomb (SR) PotentialKinetic
En.
3.73370e+03 -3.85288e+03 -3.22634e+034.43506e+041.88193e
+04
Total EnergyTemperature Pressure (bar)
6.31699e+048.38307e+020.0e+00
Step Time Lambda
10.002000.0
thank you for your help!
Dongsheng
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Re: [gmx-users] high initial temperature with low ref_T
Mark, Thank you very much for your reply. On Fri, 2006-07-07 at 08:51 +1000, Mark Abraham wrote: Hello, GMX users, My system exploded very soon after mdrun. So I outputted the log file every step. I found the initial temperature is about 800 K even though I set ref_T = 300. Why does this happen? First please tell us you've done energy minimization and checked the structure and resulting trajectory visually to see that things look reasonable there. The following is the mdp file: ; VARIOUS PREPROCESSING OPTIONS title= nanotube_polymer - z T300 cpp = /lib/cpp -traditional include = define = ; RUN CONTROL PARAMETERS integrator = md tinit= 0 ; Start time and timestep in ps ;constraints = hbonds ; constrain bonds involving H. dt = 0.002 nsteps = 100 ;2 ns comm-mode= ANGULAR ;Linear nstcomm = 1 comm-grps= ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) ; this affects file traj.trr nstxout = 5 nstvout = 5 nstfout = 5 ; Checkpointing helps you continue after crashes nstcheckpoint= 1000 ; Output frequency for energies to log file and energy file nstlog = 1 nstenergy= 1 energygrps = CNT polymer ; Output frequency and precision for xtc file (for the movie) nstxtcout= 1 xtc-precision= 1000 ; NEIGHBORSEARCHING PARAMETERS nstlist = 5; nblist update frequency ns_type = simple; ns algorithm (simple or grid) pbc = no rlist= 0 ; nblist cut-off ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics: Cut-off, coulombtype = Cut-off fourierspacing = 0.12 pme_order= 4 rcoulomb = 0 optimize_fft = yes ;This saves a few percent for long simulations ;rcoulomb_switch = 0.95 ; Dielectric constant (DC) for cut-off or DC of reaction field ;epsilon-r= 1.0 ; for reaction field ; Method for doing Van der Waals vdw-type = cut-off ; cut-off lengths rvdw = 0 ;rvdw_switch = 0.95 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = no; EnerPres ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling Tcoupl = berendsen ; nose-hoover ;berendsen ; Groups to couple separately tc-grps = polymer CNT ; Time constant (ps) and reference temperature (K) tau_t= 0.1 0.1 ref_t= 300 300 ; Pressure coupling Pcoupl = no; berendsen ;Parrinello-Rahman ;berendsen Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p= 0.5 compressibility = 4.5e-5 ref_p= 1.0 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = yes gen_temp = 300 gen_seed = 1223188 ;Electric fields ;E_z = 1 40 1 My system is a carbone nanotube with a polymer. The polymer has 80 units. After I generated the polymer chain, I have relaxed the polymer alone in vacuum for 200 ps. Then I added CNT to the system, and made sure there was no overlap by VMD. Then I did EM in vacuum. I used the above mdp to generate a tpr file. When I ran it, the polymer exploded. However, If I simulate the polymer alone in vacuum, it works fine with the same force field. This problem sounds strange to me. How do you think? Best Wishes! Dongsheng If so, and there are still problems you'll need to supply a full .mdp and describe the simulation you're trying to run. 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 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] high initial temperature with low ref_T
On Fri, 2006-07-07 at 09:02 +1000, Dallas B. Warren wrote: My system exploded very soon after mdrun. So I outputted the log file every step. I found the initial temperature is about 800 K even though I set ref_T = 300. Why does this happen? What temperature did you specify when generating velocities with grompp? Or if this is a continuation from another run, what was the temperature at the end of that trajectory? This is the first run, so I set gen_vel = yes gen_temp = 300 tau_t= 0.1 0.1 ref_t= 300 300 Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacology Victorian College of Pharmacy, Monash University 381 Royal Parade, Parkville VIC 3010 [EMAIL PROTECTED] +61 3 9903 9524 - When the only tool you own is a hammer, every problem begins to resemble a nail. ___ 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] program crashed
Mark, I have written a new force field for my polymer. I have used this force field for polymer in water. It worked fine. When I tried to put polymer with nanotube in water, then I had this strange problem (My force field worked fine for nanotube alone). Anyway I will try to rerun it. Thank you for your help! Dongsheng On Wed, 2006-07-05 at 16:04 +1000, Mark Abraham wrote: On Wed, 2006-07-05 at 15:11 +1000, Mark Abraham wrote: Mark, Thank you for your reply. When I checked step38885.pdb, I found a polymer chain in my system fall apart (bond broken). If I visualize the trajectory. it is fine till step38000 (last frame in my trr file). OK... bonds don't just break in MD simulations. Bonded potentials don't allow for it, and often bond-length constraint algorithms are being used anyway. That is what I expect. However I find some atoms are far away from others from step38885.pdb even though I have used all-bonds constraint. Do you have any idea what's going on? Thank you for your help! I don't have many further ideas. You have a bunch of atoms that appear to have moved around messily. If your visual check of the trajectory is valid then there shouldn't be anything wrong with your topology, but it might be worth checking. Maybe try re-running the calculation keeping lots of velocities and positions so you can do restarts close to the problem area and get more info... 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 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] program crashed
Dear GMX users, After I edit vdwradii.dat and run genbox, my program still crashes when I run position restrained MD with heating the system from 100K to 300K. When I check the log file. I find the kinetic energy doubles (step 38880 compare to step 38870, by the way, the re_t is the same in these two steps) when the constraint problem starts to take place. Does anyone know why KE doubles? The following message is from my log file: Step Time Lambda 38870 77.740010.0 Rel. Constraint Deviation: Maxbetween atoms RMS Before LINCS 0.029985 1381 1382 0.004488 After LINCS 0.002836360390 0.002298 Current ref_t for group Protein:269.4 Current ref_t for group SOL:269.4 Energies (kJ/mol) Angle G96Angle Ryckaert-Bell. LJ-14 Coulomb-14 1.86369e+038.21120e+023.90504e+039.13784e+041.63718e +03 LJ (SR) Coulomb (SR) Position Rest. PotentialKinetic En. 2.63152e+04 -2.08977e+051.31793e+03 -8.17386e+043.00352e +04 Total EnergyTemperature Pressure (bar) -5.17034e+042.67248e+021.12117e+02 Step Time Lambda 38880 77.760000.0 Rel. Constraint Deviation: Maxbetween atoms RMS Before LINCS 8.028940 1182 1184 0.184534 After LINCS 6.697157 1182 1184 0.153625 Step 38880, time 77.76 (ps) LINCS WARNING relative constraint deviation after LINCS: max 6.697157 (between atoms 1182 and 1184) rms 0.153625 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 1182 1184 90.00.1090 0.8390 0.1090 1182 1185 50.40.1090 0.1093 0.1090 Constraint error in algorithm Lincs at step 38880 Current ref_t for group Protein:269.4 Current ref_t for group SOL:269.4 Energies (kJ/mol) Angle G96Angle Ryckaert-Bell. LJ-14 Coulomb-14 1.92677e+038.35797e+023.89187e+039.12880e+041.63733e +03 LJ (SR) Coulomb (SR) Position Rest. PotentialKinetic En. 3.17595e+04 -2.09746e+051.31354e+03 -7.70932e+048.35900e +04 Total EnergyTemperature Pressure (bar) 6.49684e+037.43768e+024.87090e+03 Step 38881, time 77.762 (ps) LINCS WARNING relative constraint deviation after LINCS: max 0.385035 (between atoms 1182 and 1184) rms 0.009398 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 1182 1183 35.10.1078 0.1122 0.1090 1182 1184 89.90.8390 0.1510 0.1090 1182 1185 57.30.1093 0.1129 0.1090 1242 1245 61.10.1090 0.1092 0.1090 Thank you for your help! Dongsheng On Tue, 2006-07-04 at 09:52 -0400, Dongsheng Zhang wrote: mark, That is a good idea. Thank you very much! Dongsheng On Tue, 2006-07-04 at 15:38 +1000, Mark Abraham wrote: Dongsheng Zhang wrote: Mark, Thank you for your reply. EM works fine before position-restrained MD. Do you have any other suggestion besides to reduce the number of water inside the nanotube? Thanks! You could edit vdwradii.dat in the gromacs/share/top directory to give either the water atoms or nanotube atoms more bulk for genbox - see man genbox for a few details. 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 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] program crashed
Mark, Thank you for your reply. When I checked step38885.pdb, I found a polymer chain in my system fall apart (bond broken). If I visualize the trajectory. it is fine till step38000 (last frame in my trr file). I don't understand why the bond breaks after 76 ps simulation and why KE doubles suddenly. Do you have any idea what's wrong? All the best! Dongsheng On Wed, 2006-07-05 at 13:54 +1000, Mark Abraham wrote: Dear GMX users, After I edit vdwradii.dat and run genbox, my program still crashes when I run position restrained MD with heating the system from 100K to 300K. When I check the log file. I find the kinetic energy doubles (step 38880 compare to step 38870, by the way, the re_t is the same in these two steps) when the constraint problem starts to take place. Does anyone know why KE doubles? Have you visualized the trajectory to see where things start 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 ___ 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] program crashed
On Wed, 2006-07-05 at 15:11 +1000, Mark Abraham wrote: Mark, Thank you for your reply. When I checked step38885.pdb, I found a polymer chain in my system fall apart (bond broken). If I visualize the trajectory. it is fine till step38000 (last frame in my trr file). OK... bonds don't just break in MD simulations. Bonded potentials don't allow for it, and often bond-length constraint algorithms are being used anyway. That is what I expect. However I find some atoms are far away from others from step38885.pdb even though I have used all-bonds constraint. Do you have any idea what's going on? Thank you for your help! The following is part of my pdb file: ATOM 1183 HH31 PPO B 40 -63.880 12.235 23.304 1.00 0.00 ATOM 1184 HH32 PPO B 40 -69.011 3.629 46.672 1.00 0.00 ATOM 1185 HH33 PPO B 40-144.627 84.477 51.559 1.00 0.00 ATOM 1186 CH PPO B 40 -51.713 0.381 2.039 1.00 0.00 ATOM 1187 HH PPO B 40-110.463 36.603 -0.242 1.00 0.00 ATOM 1188 CH2 PPO B 40 -38.759 29.954 26.664 1.00 0.00 ATOM 1189 HH21 PPO B 40 -28.084 28.831 32.811 1.00 0.00 ATOM 1190 HH22 PPO B 40 -28.802 16.898 37.557 1.00 0.00 ATOM 1191 O PPO B 40 -32.030 16.986 38.515 1.00 0.00 Dongsheng If you're not using such algorithms, it might be helpful to look at the time evolution of the bond length of the bond that breaks. I have heard of weird cases where some resonance got established in the system eventually leading to some catastrophic failure (think Tacoma Narrows Suspension Bridge!) - if so then the time evolution should show such behaviour. I can't explain the KE doubling though... 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 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] program crashed
Dear GMX users, I am studying a system of a capped nanotube with a polymer in water. When I use genbox, some water will be inside of the nanotube. This might cause bad contact of water molecules inside of nanotube. Does anyone know how to control the total number of water molecules inside the nanotube? In general, could someone give me suggestion how to prevent the program crash because of bad contacts? I am having this problem now. I have tried to use position constraint to relax water and heat the system from 100K. It doesn't help. Any suggestion will be highly appreciated. All the best! Dongsheng ___ 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] oplsaa force field
Dear GMX users, I'd like to use oplsaa FF format to build my own force field for my project. After I finished it, I can use pdb2gmx. but not grompp. The problem is from my **nb.itp file. I have specified some unusual (not follow the combination rule) nonbonded interaction parameters after [ atomtypes ] section as follows: [ nonbond_params ] ; ij func sigma epsilon CTCT 13.8e-01 2.09200e-01 When I run grompp, the program complains that atom type CT is not found. If I change CT to opls_182, then it works fine. However, when I check oplsaabon.itp, CT is used, but not opls_182. Could anyone tell me why I can't use atom type in *nb.itp? How can I fix it? If opls_182 is defined as atom type, then how does gromacs recognize CT is **bon.itp? By the way, my question relates to my previous question. Unfortunately, no one answered it. I really appreciate someone can help me. The following is my previous email: In ffoplsaanb.itp, there are 8 columns. ; name bond_typemasscharge ptype sigma epsilon opls_001 C 6 12.01100 0.500 A3.75000e-01 4.39320e-01 ; SIG In ffG53a5nb.itp, there are 7 columns. [ atomtypes ] ;name at.num mass charge ptype c6 c12 O8 0.000 0.000 A 0.0022619536 1e-06 Could anyone tell me how gromacs knows to read 8 columns for oplsaa FF, but 7 columns for gromos FF? Thanks! All the best! Dongsheng ___ 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] oplsaa force field
Dear GMX users, In ffoplsaanb.itp, there are 8 columns. ; name bond_typemasscharge ptype sigma epsilon opls_001 C 6 12.01100 0.500 A3.75000e-01 4.39320e-01 ; SIG In ffG53a5nb.itp, there are 7 columns. [ atomtypes ] ;name at.num mass charge ptype c6 c12 O8 0.000 0.000 A 0.0022619536 1e-06 Could anyone tell me how gromacs knows to read 8 columns for oplsaa FF, but 7 columns for gromos FF? Thanks! Have a nice weekend! Dongsheng ___ 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] no more output data from a simulation
Erik, Thank you for your reply. It seems no other jobs are running in my computer. The following message is the result of top command: PID USER PR NI VIRT RES SHR S %CPU %MEMTIME+ COMMAND 18230 dong 20 19 10468 9m 1924 R 54.0 1.1 2380:49 mdrun_mpi 18231 dong 19 19 7964 7676 1660 R 46.0 0.8 2284:11 mdrun_mpi 1 root 8 0 468 436 436 S 0.0 0.0 0:00.11 init 2 root 9 0 000 S 0.0 0.0 0:00.01 keventd 3 root 19 19 000 S 0.0 0.0 0:00.00 ksoftirqd_CPU0 4 root 9 0 000 S 0.0 0.0 0:02.98 kswapd 5 root 9 0 000 S 0.0 0.0 0:00.00 bdflush 6 root 9 0 000 S 0.0 0.0 0:00.06 kupdated My computer has two CPUs. Any other suggestion? Dongsheng On Tue, 2006-06-27 at 22:50 +0200, Erik Lindahl wrote: Hi, The serial version of mdrun defaults to nice 19, i.e. it only runs when nothing else wants the CPU. Check if something else is running! Cheers, Erik On Jun 27, 2006, at 8:12 PM, Dongsheng Zhang wrote: Dear GMX users, I have run a simulation several days ago. It supposed to finish on Sunday. However, the program seems stop in the middle. There is no more output. If I use command top to check the process, it shows the program is still running. And there is no error message in the log file either. Could anyone tell me what's going on? Thank you for your help! By the way, My computer has plenty of disk space. All the best! Dongsheng ___ 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 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] xyz to gdb
Hello, Jason, You can download babel program and use babel -ixyz old.xyz -opdb new.pdb to get a pdb file, then you can use gromacs now. Dongsheng On Mon, 2006-06-26 at 15:00 -0700, Jason Byrd wrote: Hello, I amd working with using the Siesta program in conjunction with gromacs, and I need to be able to read quasi xyz (quasi as in first collumn is atom type, the next 3 are xyz coordinates) coordinates into gromacs as either a gdb or gro file. Has any one else attepted this successfully? thanks for your feedback jason ___ 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] energy minimization
Hello, everyone, I have a system with a nanotube and a polymer chain. First I did EM for the system in vacuum. After that, I added some water to my system, and tried to do EM again. This time I got some large force on some atoms. The messages are as folllows: Step=0, Dmax= 5.0e-03 nm, Epot= -4.89150e+06 Fmax= 6.50095e+04, atom= 2463 Step=1, Dmax= 5.0e-03 nm, Epot= -4.91505e+06 Fmax= 3.30822e+04, atom= 2463 Step=2, Dmax= 6.0e-03 nm, Epot= -4.96938e+06 Fmax= 1.72511e+04, atom= 2463 Step=3, Dmax= 7.2e-03 nm, Epot= -5.09757e+06 Fmax= 1.02066e+04, atom= 11109 Step=4, Dmax= 8.6e-03 nm, Epot= -5.39186e+06 Fmax= 8.89407e+03, atom= 11109 Step=5, Dmax= 1.0e-02 nm, Epot= -5.92594e+06 Fmax= 1.27715e+04, atom= 2464 Step=6, Dmax= 1.2e-02 nm, Epot= -6.59458e+06 Fmax= 3.53621e+04, atom= 10534 Step=7, Dmax= 1.5e-02 nm, Epot= -7.04583e+06 Fmax= 9.01766e+05, atom= 10534 Step=8, Dmax= 1.8e-02 nm, Epot= -7.12198e+06 Fmax= 6.09737e+07, atom= 2464 Step= 14, Dmax= 6.7e-04 nm, Epot= -7.17427e+06 Fmax= 2.34996e+08, atom= 2463 Step= 16, Dmax= 4.0e-04 nm, Epot= -7.20472e+06 Fmax= 3.88459e+08, atom= 2464 Step= 18, Dmax= 2.4e-04 nm, Epot= -7.43615e+06 Fmax= 2.80954e+09, atom= 2463 Step= 21, Dmax= 7.3e-05 nm, Epot= -1.05082e+07 Fmax= 2.44979e+11, atom= 2464 Step= 25, Dmax= 1.1e-05 nm, Epot= -1.33633e+07 Fmax= 8.20246e+11, atom= 2463 Step= 27, Dmax= 6.5e-06 nm, Epot= -1.60347e+07 Fmax= 1.66408e+12, atom= 2463 Step= 29, Dmax= 3.9e-06 nm, Epot= -2.73531e+07 Fmax= 8.51628e+12, atom= 2463 Step= 32, Dmax= 1.2e-06 nm, Epot= -3.69604e+08 Fmax= 2.72010e+15, atom= 2463 Step= 33, Dmax= 1.4e-06 nm, Epot= -2.43314e+07 Fmax= 6.16803e+12, atom= 2463 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 I believe something is wrong here. Could anyone give me a hand how to fix it? Thank you very much! Have a nice weekend! Dongsheng ___ 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 minimization
Hi, David, Thank you for your help. I have fix it now. Have a nice weekend! Dongsheng On Sat, 2006-06-24 at 21:53 +0200, David van der Spoel wrote: Dongsheng Zhang wrote: Hello, everyone, I have a system with a nanotube and a polymer chain. First I did EM for the system in vacuum. After that, I added some water to my system, and tried to do EM again. This time I got some large force on some atoms. The messages are as folllows: Step=0, Dmax= 5.0e-03 nm, Epot= -4.89150e+06 Fmax= 6.50095e+04, atom= 2463 Step=1, Dmax= 5.0e-03 nm, Epot= -4.91505e+06 Fmax= 3.30822e+04, atom= 2463 Step=2, Dmax= 6.0e-03 nm, Epot= -4.96938e+06 Fmax= 1.72511e+04, atom= 2463 Step=3, Dmax= 7.2e-03 nm, Epot= -5.09757e+06 Fmax= 1.02066e+04, atom= 11109 Step=4, Dmax= 8.6e-03 nm, Epot= -5.39186e+06 Fmax= 8.89407e+03, atom= 11109 Step=5, Dmax= 1.0e-02 nm, Epot= -5.92594e+06 Fmax= 1.27715e+04, atom= 2464 Step=6, Dmax= 1.2e-02 nm, Epot= -6.59458e+06 Fmax= 3.53621e+04, atom= 10534 Step=7, Dmax= 1.5e-02 nm, Epot= -7.04583e+06 Fmax= 9.01766e+05, atom= 10534 Step=8, Dmax= 1.8e-02 nm, Epot= -7.12198e+06 Fmax= 6.09737e+07, atom= 2464 Step= 14, Dmax= 6.7e-04 nm, Epot= -7.17427e+06 Fmax= 2.34996e+08, atom= 2463 Step= 16, Dmax= 4.0e-04 nm, Epot= -7.20472e+06 Fmax= 3.88459e+08, atom= 2464 Step= 18, Dmax= 2.4e-04 nm, Epot= -7.43615e+06 Fmax= 2.80954e+09, atom= 2463 Step= 21, Dmax= 7.3e-05 nm, Epot= -1.05082e+07 Fmax= 2.44979e+11, atom= 2464 Step= 25, Dmax= 1.1e-05 nm, Epot= -1.33633e+07 Fmax= 8.20246e+11, atom= 2463 Step= 27, Dmax= 6.5e-06 nm, Epot= -1.60347e+07 Fmax= 1.66408e+12, atom= 2463 Step= 29, Dmax= 3.9e-06 nm, Epot= -2.73531e+07 Fmax= 8.51628e+12, atom= 2463 Step= 32, Dmax= 1.2e-06 nm, Epot= -3.69604e+08 Fmax= 2.72010e+15, atom= 2463 Step= 33, Dmax= 1.4e-06 nm, Epot= -2.43314e+07 Fmax= 6.16803e+12, atom= 2463 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 topology is wrong. check atom 2463 I believe something is wrong here. Could anyone give me a hand how to fix it? Thank you very much! Have a nice weekend! Dongsheng ___ 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] make_ndx
Hello, gmx users: In make_ndx, I would like to keep two groups, for instance, group 4 and group 5. I have try it in two ways, namely, keep 4 keep 5 and keep 4 | keep 5. However both ways only keep group 4. Anyway to accomplish my task is to delete other groups one by one, but it is not so convenient. Could anyone tell me what is the trick? Thanks! Dongsheng ___ 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] make_ndx
Hello, Manuel, Thank you very much for your trick. It is neat. Have a nice weekend! Dongsheng On Sun, 2006-06-25 at 02:58 +0200, Manuel Prinz wrote: Hello Dongsheng! Am Samstag, den 24.06.2006, 17:26 -0400 schrieb Dongsheng Zhang: In make_ndx, I would like to keep two groups, for instance, group 4 and group 5. I have try it in two ways, namely, keep 4 keep 5 and keep 4 | keep 5. However both ways only keep group 4. Anyway to accomplish my task is to delete other groups one by one, but it is not so convenient. Could anyone tell me what is the trick? Thanks! I don't think this can be done directly. Nevertheless, a quite simple solution is to first copy the selections you would like to keep (by just giving the number of the group you want to copy) and then deleting all default groups (del 0-13). Your session might look like this: 4 [Enter] Copied index group 4 'Backbone' 14 Backbone:39 atoms 5 [Enter] Copied index group 5 'MainChain' 15 MainChain :53 atoms del 0-13 [Enter] Removed group 0 'System' Removed group 1 'Protein' Removed group 2 'Protein-H' Removed group 3 'C-alpha' Removed group 4 'Backbone' Removed group 5 'MainChain' Removed group 6 'MainChain+Cb' Removed group 7 'MainChain+H' Removed group 8 'SideChain' Removed group 9 'SideChain-H' Removed group 10 'Prot-Masses' Removed group 11 'Non-Protein' Removed group 12 'SOL' Removed group 13 'Other' [Enter] 0 Backbone:39 atoms 1 MainChain :53 atoms nr : group ! 'name' nr name 'splitch' nrEnter: list groups 'a': atom 'del' nr 'splitres' nr 'l': list residues 't': atom type | 'keep' nr'splitat' nr'h': help 'r': residue 'res' nr 'chain' char name: group'case': case sensitive 'q': save and quit q [Enter] The resulting index.ndx contains the desired groups. HTH Manuel ___ 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] a strange behavior in editconf -rotate
Dear Tsjerk, Thank you very much for your reply. You are right. After I specify pbc=no in mdp file, EM works fine for test2.pdb now. All the best! Dongsheng On Fri, 2006-06-23 at 08:19 +0200, Tsjerk Wassenaar wrote: Hi Dongsheng Zhang, Rotating the system with editconf does not change the box. It is likely that you rotated your molecule with respect to the box, such that you have caused severe overlaps. Glancing at your coordinates (notably z) and the box vectors supports this. Try creating a new box for the rotated molecule. Cheers, Tsjerk On 6/22/06, Dongsheng Zhang [EMAIL PROTECTED] wrote: Dear GMX users, I have generated a pdb file (test1.pdb) for a PPO chain. I can do energy minimization for this chain using oplsaa FF. However, if I rotate the chain by editconf -f test1.pdb -rotate 9 -9 0 -o test2.pdb then I can't do EM for test2.pdb. Could anyone tell me why the rotation of a molecule can affect EM? Thank you in advance! If you want to test my case, please add PPO to aminoacids.dat, and [PPO] building block to ffoplsaa.rtp By the way, is it possible to add one more function of genconf to extend a chain by translation? The detailed information is as follows: test1.pdb TITLE 15PPO.pdb REMARKTHIS IS A SIMULATION BOX CRYST1 19.900 12.630 11.640 90.00 90.00 90.00 P 1 1 MODEL1 ATOM 1 CH3 PPO 1 -8.740 0.260 -77.460 1.00 0.00 ATOM 2 HH31 PPO 1 -8.400 -0.180 -76.540 1.00 0.00 ATOM 3 HH32 PPO 1 -7.990 0.040 -78.190 1.00 0.00 ATOM 4 HH33 PPO 1 -8.800 1.330 -77.320 1.00 0.00 ATOM 5 CH PPO 1 -10.000 -0.360 -77.990 1.00 0.00 ATOM 6 HH PPO 1 -9.960 -1.430 -77.960 1.00 0.00 ATOM 7 CH2 PPO 1 -10.150 0.020 -79.440 1.00 0.00 ATOM 8 HH21 PPO 1 -10.610 0.990 -79.570 1.00 0.00 ATOM 9 HH22 PPO 1 -9.140 0.110 -79.800 1.00 0.00 ATOM 10 O PPO 1 -10.740 -1.000 -80.240 1.00 0.00 ATOM 11 CH3 PPO 2 -10.550 -3.410 -80.440 1.00 0.00 ATOM 12 HH31 PPO 2 -11.510 -3.460 -80.940 1.00 0.00 ATOM 13 HH32 PPO 2 -10.710 -3.610 -79.380 1.00 0.00 ATOM 14 HH33 PPO 2 -9.980 -4.250 -80.790 1.00 0.00 ATOM 15 CH PPO 2 -9.850 -2.050 -80.630 1.00 0.00 ATOM 16 HH PPO 2 -9.180 -2.070 -79.800 1.00 0.00 ATOM 17 CH2 PPO 2 -8.670 -1.940 -81.680 1.00 0.00 ATOM 18 HH21 PPO 2 -8.620 -2.970 -81.800 1.00 0.00 ATOM 19 HH22 PPO 2 -7.800 -1.670 -81.100 1.00 0.00 ATOM 20 O PPO 2 -8.540 -1.320 -83.030 1.00 0.00 ATOM 21 CH3 PPO 3 -8.300 -3.490 -84.140 1.00 0.00 ATOM 22 HH31 PPO 3 -7.310 -3.850 -84.160 1.00 0.00 ATOM 23 HH32 PPO 3 -8.960 -3.880 -84.890 1.00 0.00 ATOM 24 HH33 PPO 3 -8.670 -4.020 -83.290 1.00 0.00 ATOM 25 CH PPO 3 -8.200 -1.980 -84.280 1.00 0.00 ATOM 26 HH PPO 3 -7.240 -1.550 -84.240 1.00 0.00 ATOM 27 CH2 PPO 3 -7.980 -1.490 -85.770 1.00 0.00 ATOM 28 HH21 PPO 3 -8.230 -0.480 -85.940 1.00 0.00 ATOM 29 HH22 PPO 3 -6.950 -1.520 -86.120 1.00 0.00 ATOM 30 O PPO 3 -8.620 -2.430 -86.580 1.00 0.00 ATOM 31 CH3 PPO 4 -9.510 -3.830 -87.970 1.00 0.00 ATOM 32 HH31 PPO 4 -10.320 -3.720 -88.690 1.00 0.00 ATOM 33 HH32 PPO 4 -9.890 -4.010 -86.980 1.00 0.00 ATOM 34 HH33 PPO 4 -8.960 -4.710 -88.190 1.00 0.00 ATOM 35 CH PPO 4 -8.580 -2.670 -88.000 1.00 0.00 ATOM 36 HH PPO 4 -7.570 -2.820 -87.700 1.00 0.00 ATOM 37 CH2 PPO 4 -7.740 -2.850 -89.270 1.00 0.00 ATOM 38 HH21 PPO 4 -7.150 -1.990 -89.580 1.00 0.00 ATOM 39 HH22 PPO 4 -8.470 -3.050 -90.020 1.00 0.00 ATOM 40 O PPO 4 -7.080 -4.090 -89.380 1.00 0.00 ATOM 41 CH3 PPO 5 -5.570 -5.590 -90.290 1.00 0.00 ATOM 42 HH31 PPO 5 -5.430 -6.280 -91.110 1.00 0.00 ATOM 43 HH32 PPO 5 -5.850 -6.150 -89.440 1.00 0.00 ATOM 44 HH33 PPO 5 -4.550 -5.380 -90.170 1.00 0.00 ATOM 45 CH PPO 5 -6.280 -4.220 -90.540 1.00 0.00 ATOM 46 HH PPO 5 -5.670 -3.390 -90.260 1.00 0.00 ATOM 47 CH2 PPO 5 -6.900 -4.060 -92.030 1.00 0.00 ATOM 48 HH21 PPO 5 -7.960 -4.120 -91.940 1.00 0.00 ATOM 49 HH22 PPO 5 -6.770 -5.070 -92.320 1.00 0.00 ATOM 50 O PPO 5 -6.510 -3.440 -93.380 1.00 0.00 ATOM 51 CH3 PPO 6 -5.210 -1.190 -93.590 1.00 0.00 ATOM 52 HH31 PPO 6 -4.210 -1.160 -93.270 1.00 0.00
[gmx-users] a strange behavior in editconf -rotate
Dear GMX users, I have generated a pdb file (test1.pdb) for a PPO chain. I can do energy minimization for this chain using oplsaa FF. However, if I rotate the chain by editconf -f test1.pdb -rotate 9 -9 0 -o test2.pdb then I can't do EM for test2.pdb. Could anyone tell me why the rotation of a molecule can affect EM? Thank you in advance! If you want to test my case, please add PPO to aminoacids.dat, and [PPO] building block to ffoplsaa.rtp By the way, is it possible to add one more function of genconf to extend a chain by translation? The detailed information is as follows: test1.pdb TITLE 15PPO.pdb REMARKTHIS IS A SIMULATION BOX CRYST1 19.900 12.630 11.640 90.00 90.00 90.00 P 1 1 MODEL1 ATOM 1 CH3 PPO 1 -8.740 0.260 -77.460 1.00 0.00 ATOM 2 HH31 PPO 1 -8.400 -0.180 -76.540 1.00 0.00 ATOM 3 HH32 PPO 1 -7.990 0.040 -78.190 1.00 0.00 ATOM 4 HH33 PPO 1 -8.800 1.330 -77.320 1.00 0.00 ATOM 5 CH PPO 1 -10.000 -0.360 -77.990 1.00 0.00 ATOM 6 HH PPO 1 -9.960 -1.430 -77.960 1.00 0.00 ATOM 7 CH2 PPO 1 -10.150 0.020 -79.440 1.00 0.00 ATOM 8 HH21 PPO 1 -10.610 0.990 -79.570 1.00 0.00 ATOM 9 HH22 PPO 1 -9.140 0.110 -79.800 1.00 0.00 ATOM 10 O PPO 1 -10.740 -1.000 -80.240 1.00 0.00 ATOM 11 CH3 PPO 2 -10.550 -3.410 -80.440 1.00 0.00 ATOM 12 HH31 PPO 2 -11.510 -3.460 -80.940 1.00 0.00 ATOM 13 HH32 PPO 2 -10.710 -3.610 -79.380 1.00 0.00 ATOM 14 HH33 PPO 2 -9.980 -4.250 -80.790 1.00 0.00 ATOM 15 CH PPO 2 -9.850 -2.050 -80.630 1.00 0.00 ATOM 16 HH PPO 2 -9.180 -2.070 -79.800 1.00 0.00 ATOM 17 CH2 PPO 2 -8.670 -1.940 -81.680 1.00 0.00 ATOM 18 HH21 PPO 2 -8.620 -2.970 -81.800 1.00 0.00 ATOM 19 HH22 PPO 2 -7.800 -1.670 -81.100 1.00 0.00 ATOM 20 O PPO 2 -8.540 -1.320 -83.030 1.00 0.00 ATOM 21 CH3 PPO 3 -8.300 -3.490 -84.140 1.00 0.00 ATOM 22 HH31 PPO 3 -7.310 -3.850 -84.160 1.00 0.00 ATOM 23 HH32 PPO 3 -8.960 -3.880 -84.890 1.00 0.00 ATOM 24 HH33 PPO 3 -8.670 -4.020 -83.290 1.00 0.00 ATOM 25 CH PPO 3 -8.200 -1.980 -84.280 1.00 0.00 ATOM 26 HH PPO 3 -7.240 -1.550 -84.240 1.00 0.00 ATOM 27 CH2 PPO 3 -7.980 -1.490 -85.770 1.00 0.00 ATOM 28 HH21 PPO 3 -8.230 -0.480 -85.940 1.00 0.00 ATOM 29 HH22 PPO 3 -6.950 -1.520 -86.120 1.00 0.00 ATOM 30 O PPO 3 -8.620 -2.430 -86.580 1.00 0.00 ATOM 31 CH3 PPO 4 -9.510 -3.830 -87.970 1.00 0.00 ATOM 32 HH31 PPO 4 -10.320 -3.720 -88.690 1.00 0.00 ATOM 33 HH32 PPO 4 -9.890 -4.010 -86.980 1.00 0.00 ATOM 34 HH33 PPO 4 -8.960 -4.710 -88.190 1.00 0.00 ATOM 35 CH PPO 4 -8.580 -2.670 -88.000 1.00 0.00 ATOM 36 HH PPO 4 -7.570 -2.820 -87.700 1.00 0.00 ATOM 37 CH2 PPO 4 -7.740 -2.850 -89.270 1.00 0.00 ATOM 38 HH21 PPO 4 -7.150 -1.990 -89.580 1.00 0.00 ATOM 39 HH22 PPO 4 -8.470 -3.050 -90.020 1.00 0.00 ATOM 40 O PPO 4 -7.080 -4.090 -89.380 1.00 0.00 ATOM 41 CH3 PPO 5 -5.570 -5.590 -90.290 1.00 0.00 ATOM 42 HH31 PPO 5 -5.430 -6.280 -91.110 1.00 0.00 ATOM 43 HH32 PPO 5 -5.850 -6.150 -89.440 1.00 0.00 ATOM 44 HH33 PPO 5 -4.550 -5.380 -90.170 1.00 0.00 ATOM 45 CH PPO 5 -6.280 -4.220 -90.540 1.00 0.00 ATOM 46 HH PPO 5 -5.670 -3.390 -90.260 1.00 0.00 ATOM 47 CH2 PPO 5 -6.900 -4.060 -92.030 1.00 0.00 ATOM 48 HH21 PPO 5 -7.960 -4.120 -91.940 1.00 0.00 ATOM 49 HH22 PPO 5 -6.770 -5.070 -92.320 1.00 0.00 ATOM 50 O PPO 5 -6.510 -3.440 -93.380 1.00 0.00 ATOM 51 CH3 PPO 6 -5.210 -1.190 -93.590 1.00 0.00 ATOM 52 HH31 PPO 6 -4.210 -1.160 -93.270 1.00 0.00 ATOM 53 HH32 PPO 6 -5.790 -1.000 -92.710 1.00 0.00 ATOM 54 HH33 PPO 6 -5.300 -0.320 -94.220 1.00 0.00 ATOM 55 CH PPO 6 -5.540 -2.590 -94.170 1.00 0.00 ATOM 56 HH PPO 6 -6.380 -2.030 -94.370 1.00 0.00 ATOM 57 CH2 PPO 6 -5.030 -2.910 -95.730 1.00 0.00 ATOM 58 HH21 PPO 6 -5.630 -2.520 -96.520 1.00 0.00 ATOM 59 HH22 PPO 6 -4.290 -2.120 -95.780 1.00 0.00 ATOM 60 O PPO 6 -4.050 -3.870 -96.340 1.00 0.00 ATOM 61 CH3 PPO 7 -4.000 -6.800 -96.280 1.00 0.00 ATOM 62 HH31 PPO 7 -3.560 -6.990 -95.330 1.00 0.00 ATOM 63 HH32 PPO 7 -3.540 -7.460 -97.010 1.00 0.00 ATOM 64 HH33 PPO 7
Re: [gmx-users] unexpected result from mdrun
Dear GMX users,
I have two EXACTLY identical tpr files at two different directories on
the SAME machine. When I try to use these two tpr files. One works fine.
Another one gives me bad result, the molecule explodes. Could anyone
tell me why this happens? Thank you in advance!
Dongsheng
On Mon, 2006-06-19 at 14:52 -0400, Dongsheng Zhang wrote:
Dear GMX users,
I am studying the interaction between a polymer chain and a nanotube in
vacuum. After I set up my system, I use vmd to visualize my gro file. It
looks fine. The polymer chain is a little far away from the nanotube.
There is no overlap. However, after I do mdrun, I can't get edr file
(empty). The log file is as follows:
There are 1008 atoms in your xtc output selection
PLEASE READ AND CITE THE FOLLOWING REFERENCE
H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak
Molecular dynamics with coupling to an external bath
J. Chem. Phys. 81 (1984) pp. 3684-3690
--- Thank You ---
Energies (kJ/mol)
Bond Angle G96Angle Ryckaert-Bell.
LJ-14
9.09629e+024.91326e+022.36889e+012.32269e+033.46380e
+04
Coulomb-14LJ (SR) Coulomb (SR) PotentialKinetic
En.
9.42152e+023.60034e+03 -1.16196e+034.17659e+043.97332e
+05
Total EnergyTemperature Pressure (bar)
4.39097e+053.16685e+040.0e+00
Large VCM(group rest): -0.07615, 0.03311, 0.00164,
ekin-cm: 3.72526e+01
Group rest with mass 1.08005e+04, Ekrot 6.72960e+03 Det(I) = 1.33951e
+29
COM: 0.07250 0.17529 1.86474
P: -822.48108 357.63647 17.73926
V: -0.07615 0.03311 0.00164
J: -1438767104.0 -38931256.0 -906993664.0
w:0.4 -0.4 -0.7
Inertia tensor (3x3):
Inertia tensor[0]={ 5.38545e+13, -4.65369e+13, -8.34326e+13}
Inertia tensor[1]={-4.65369e+13, 4.02137e+13, 7.20962e+13}
Inertia tensor[2]={-8.34326e+13, 7.20962e+13, 1.29256e+14}
Large VCM(group rest): 0.01199, -0.09814, 0.04721,
ekin-cm: 6.48211e+01
Group rest with mass 1.08005e+04, Ekrot 6.62037e+04 Det(I) = 5.30238e
+28
COM: 0.07266 0.17504 1.86508
P: 129.52625 -1059.92761 509.88013
V:0.01199 -0.09814 0.04721
J: -4924144128.0 220606032.0 -3301491456.0
w:0.00072 -0.00064 -0.00116
Inertia tensor (3x3):
Inertia tensor[0]={ 5.54846e+13, -4.79487e+13, -8.59614e+13}
Inertia tensor[1]={-4.79487e+13, 4.14364e+13, 7.42863e+13}
Inertia tensor[2]={-8.59614e+13, 7.42863e+13, 1.33179e+14}
Large VCM(group rest): 0.06178, -0.00576, 0.03008,
ekin-cm: 2.56742e+01
Group rest with mass 1.08005e+04, Ekrot 3.70064e+03 Det(I) = -4.14226e
+27
COM: 0.07271 0.17515 1.86534
P: 667.20703 -62.18475 324.89392
V:0.06178 -0.00576 0.03008
J: -564741376.0 -1195921280.0 302564480.0
w:0.00016 -0.00015 -0.00026
I have seen that LJ (SR) is positive. I believe something is wrong here.
Could anyone give me a hint what's happening? Thank you very much.
All the best!
Dongsheng
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Re: [gmx-users] unexpected result from mdrun
Dear David,
yes. I have try it. Even I try to give two different name for two tpr
file, then COPY them to those directories. Both tpr files in one
directory works fine, In the other directory none works.
Dongsheng
On Mon, 2006-06-19 at 13:39 -0700, David Mobley wrote:
Maybe they're not exactly identical? Did you try gmxdump and then diff
the output?
David
On 6/19/06, Dongsheng Zhang [EMAIL PROTECTED] wrote:
Dear GMX users,
I have two EXACTLY identical tpr files at two different directories on
the SAME machine. When I try to use these two tpr files. One works fine.
Another one gives me bad result, the molecule explodes. Could anyone
tell me why this happens? Thank you in advance!
Dongsheng
On Mon, 2006-06-19 at 14:52 -0400, Dongsheng Zhang wrote:
Dear GMX users,
I am studying the interaction between a polymer chain and a nanotube in
vacuum. After I set up my system, I use vmd to visualize my gro file. It
looks fine. The polymer chain is a little far away from the nanotube.
There is no overlap. However, after I do mdrun, I can't get edr file
(empty). The log file is as follows:
There are 1008 atoms in your xtc output selection
PLEASE READ AND CITE THE FOLLOWING REFERENCE
H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak
Molecular dynamics with coupling to an external bath
J. Chem. Phys. 81 (1984) pp. 3684-3690
--- Thank You ---
Energies (kJ/mol)
Bond Angle G96Angle Ryckaert-Bell.
LJ-14
9.09629e+024.91326e+022.36889e+012.32269e+033.46380e
+04
Coulomb-14LJ (SR) Coulomb (SR) PotentialKinetic
En.
9.42152e+023.60034e+03 -1.16196e+034.17659e+043.97332e
+05
Total EnergyTemperature Pressure (bar)
4.39097e+053.16685e+040.0e+00
Large VCM(group rest): -0.07615, 0.03311, 0.00164,
ekin-cm: 3.72526e+01
Group rest with mass 1.08005e+04, Ekrot 6.72960e+03 Det(I) = 1.33951e
+29
COM: 0.07250 0.17529 1.86474
P: -822.48108 357.63647 17.73926
V: -0.07615 0.03311 0.00164
J: -1438767104.0 -38931256.0 -906993664.0
w:0.4 -0.4 -0.7
Inertia tensor (3x3):
Inertia tensor[0]={ 5.38545e+13, -4.65369e+13, -8.34326e+13}
Inertia tensor[1]={-4.65369e+13, 4.02137e+13, 7.20962e+13}
Inertia tensor[2]={-8.34326e+13, 7.20962e+13, 1.29256e+14}
Large VCM(group rest): 0.01199, -0.09814, 0.04721,
ekin-cm: 6.48211e+01
Group rest with mass 1.08005e+04, Ekrot 6.62037e+04 Det(I) = 5.30238e
+28
COM: 0.07266 0.17504 1.86508
P: 129.52625 -1059.92761 509.88013
V:0.01199 -0.09814 0.04721
J: -4924144128.0 220606032.0 -3301491456.0
w:0.00072 -0.00064 -0.00116
Inertia tensor (3x3):
Inertia tensor[0]={ 5.54846e+13, -4.79487e+13, -8.59614e+13}
Inertia tensor[1]={-4.79487e+13, 4.14364e+13, 7.42863e+13}
Inertia tensor[2]={-8.59614e+13, 7.42863e+13, 1.33179e+14}
Large VCM(group rest): 0.06178, -0.00576, 0.03008,
ekin-cm: 2.56742e+01
Group rest with mass 1.08005e+04, Ekrot 3.70064e+03 Det(I) = -4.14226e
+27
COM: 0.07271 0.17515 1.86534
P: 667.20703 -62.18475 324.89392
V:0.06178 -0.00576 0.03008
J: -564741376.0 -1195921280.0 302564480.0
w:0.00016 -0.00015 -0.00026
I have seen that LJ (SR) is positive. I believe something is wrong here.
Could anyone give me a hint what's happening? Thank you very much.
All the best!
Dongsheng
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Re: [gmx-users] grompp error:Invalid order for directive defaults
Dear David,
Thank you very much for your reply. I am sorry to tell you that I get
the same error mesasge after I try your suggestion. Any other
suggestion?
I think the question is if we can put two sets of force field parameters
in two itp files which will be included in one topology file. From the
source code (topio.c line 381 - 390):
if (DS_Check_Order (DS,newd)) {
DS_Push (DS,newd);
d = newd;
}
else {
/* we should print here which directives should have
been present, and which actually are */
gmx_fatal(FARGS,Invalid order for directive %s, file \%s\, line
%d,dirstr,curfile,curline);
/* d = d_invalid; */
}
It seems gromacs does check if a same directive has been present. Is it
correct?
Best Wishes!
Dongsheng
On Mon, 2006-06-12 at 09:35 +0200, David van der Spoel wrote:
Dongsheng Zhang wrote:
Dear GMX users,
I'd like to study the interaction between carbon nanotube and a polymer
chain. I have made cnt.itp for the nanotube and poly.itp. Both itp files
contains force field parameters (such as [ defaults ], [ atomtypes],
[ bondtypes ]), in this way, I don't need to include any force field in
my topology file (but it will include *.itp) and it is much easier to
modify the parameters. For use nanotube or polymer alone as my system, I
can use grompp to process .gro, .itp, .top to get .tpr file. If I use
nanotube and polymer together as my system, grompp give me the following
error message:
Invalid order for directive defaults, file poly.itp, line 16
divide your itp files into two, force field and molecule description
then in your .top file you include all four. chapter 5 in the manual
line 16 is [ defaults ], so I am thinking maybe I can't have
[ defaults ] in each of two itp files. If I delete [ defaults ] in the
second itp file. It will complain [ atomtypes] in the second itp file.
It seems I can't put force field parameters in two itp files which will
be included in one topology file. Could anyone tell me if my guessing is
correct? If so, why does gromacs prevent it?
Thank you in advance! If you need more information, I will be more than
happy to provide it.
Best wishes!
Dongsheng
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Re: [gmx-users] special molecule
I think you can use editconf to convert your original pdb to a gro file. On Mon, 2006-06-12 at 13:48 +, Tamas Horvath wrote: As I understand, if there are special molecules in a pdb file, pdb2gmx cannot convert it. However, PRODRG can create an *.itp file for that molecule, so that I can include it in the generated topology file. But how can I place the molecule in it's original position? Or even better, how can I convert the original (full) .pdb file for gromacs? ___ 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] special molecule
Sear Mark, Since PRODRG server only generates a itp file by using gromos type force field, do I have to use gromos force field for my whole protein-ligand system if my ligand force field parameters are got from PRODRG? In another word, can I mix two different force field (one for protein, one for ligand) in one system? Thanks! Best Wishes! Dongsheng On Tue, 2006-06-13 at 01:16 +1000, Mark Abraham wrote: Tamas Horvath wrote: As I understand, if there are special molecules in a pdb file, pdb2gmx cannot convert it. However, PRODRG can create an *.itp file for that molecule, so that I can include it in the generated topology file. But how can I place the molecule in it's original position? Or even better, how can I convert the original (full) .pdb file for gromacs? Where's the problem? pdb2gmx makes a .top file for your non-special system, you #include the .itp file for your special part. There's nothing about atomic positions yet have a look at a .top file. Now grompp takes the .top and some file with atomic positions and makes a .tpr file. Same general procedure as normal. 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 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:Invalid order for directive defaults
Dear David,
Thank you for your help. It makes sense now. However, it leads me to ask
you another question:
My poly.itp is got from PRODRG server. It has gromos type force field
paramters. Do you think my cnt.itp has to be gromos type force field
format as well (atomtype, bondtype etc)? In fact I used oplsaa to get my
cnt.itp, that's the reason I need two defaults sections.
Best Wishes!
Dongsheng
On Mon, 2006-06-12 at 17:20 +0200, David van der Spoel wrote:
Dongsheng Zhang wrote:
Dear David,
Thank you very much for your reply. I am sorry to tell you that I get
the same error mesasge after I try your suggestion. Any other
suggestion?
check the manual, check the archives.
you can not have two defaults sections.
I think the question is if we can put two sets of force field parameters
in two itp files which will be included in one topology file. From the
source code (topio.c line 381 - 390):
if (DS_Check_Order (DS,newd)) {
DS_Push (DS,newd);
d = newd;
}
else {
/* we should print here which directives should have
been present, and which actually are */
gmx_fatal(FARGS,Invalid order for directive %s, file \%s\, line
%d,dirstr,curfile,curline);
/* d = d_invalid; */
}
It seems gromacs does check if a same directive has been present. Is it
correct?
Best Wishes!
Dongsheng
On Mon, 2006-06-12 at 09:35 +0200, David van der Spoel wrote:
Dongsheng Zhang wrote:
Dear GMX users,
I'd like to study the interaction between carbon nanotube and a polymer
chain. I have made cnt.itp for the nanotube and poly.itp. Both itp files
contains force field parameters (such as [ defaults ], [ atomtypes],
[ bondtypes ]), in this way, I don't need to include any force field in
my topology file (but it will include *.itp) and it is much easier to
modify the parameters. For use nanotube or polymer alone as my system, I
can use grompp to process .gro, .itp, .top to get .tpr file. If I use
nanotube and polymer together as my system, grompp give me the following
error message:
Invalid order for directive defaults, file poly.itp, line 16
divide your itp files into two, force field and molecule description
then in your .top file you include all four. chapter 5 in the manual
line 16 is [ defaults ], so I am thinking maybe I can't have
[ defaults ] in each of two itp files. If I delete [ defaults ] in the
second itp file. It will complain [ atomtypes] in the second itp file.
It seems I can't put force field parameters in two itp files which will
be included in one topology file. Could anyone tell me if my guessing is
correct? If so, why does gromacs prevent it?
Thank you in advance! If you need more information, I will be more than
happy to provide it.
Best wishes!
Dongsheng
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[gmx-users] grompp error:Invalid order for directive defaults
Dear GMX users, I'd like to study the interaction between carbon nanotube and a polymer chain. I have made cnt.itp for the nanotube and poly.itp. Both itp files contains force field parameters (such as [ defaults ], [ atomtypes], [ bondtypes ]), in this way, I don't need to include any force field in my topology file (but it will include *.itp) and it is much easier to modify the parameters. For use nanotube or polymer alone as my system, I can use grompp to process .gro, .itp, .top to get .tpr file. If I use nanotube and polymer together as my system, grompp give me the following error message: Invalid order for directive defaults, file poly.itp, line 16 line 16 is [ defaults ], so I am thinking maybe I can't have [ defaults ] in each of two itp files. If I delete [ defaults ] in the second itp file. It will complain [ atomtypes] in the second itp file. It seems I can't put force field parameters in two itp files which will be included in one topology file. Could anyone tell me if my guessing is correct? If so, why does gromacs prevent it? Thank you in advance! If you need more information, I will be more than happy to provide it. Best wishes! Dongsheng ___ 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] REMD in one nodes with two processors
David, Thank you for your reply. I have provided replica0.tpr and replica1.tpr, but the program looks for replica.tpr. It surprises me. I have also tried to run /home/brasilia/dong/mdrun_mpi -np 2 -replex 500 -reseed -1 -multi -s replica0 replica1 -deffnm replica -N 2 -v zevel It doesn't work either (complains only one replica: Nothing to exchange with only one replica). it seems the program does not recognize the -multi option. Best wishes! Dongsheng On Thu, 2006-05-04 at 18:11 +0200, David van der Spoel wrote: Dongsheng Zhang wrote: Dear gmx users, I have trouble to run REMD on one node with two processors. The command I used is /home/brasilia/dong/mdrun_mpi -np 2 -replex 500 -reseed -1 -multi -s replica -deffnm replica -N 2 -v zevel the error message is: Can not open file: replica.tpr you need replica0 and replica1.tpr This error message looks strange to me. Because I have used -multi, the program should look for replica0.tpr and replica1.tpr. Could anyone point out what's wrong in my command? Thank you in advance! Dongsheng ___ 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] REMD in one nodes with two processors
Marcus, Thank you for your suggestion. I try it. The computer gives me the same error message. The problem is that the program always looks for replica.tpr instead of replica0.tpr and replica1.tpr. I don't know why. Best wishes! Dongsheng On Thu, 2006-05-04 at 18:38 +0200, Marcus Kubitzki wrote: If you use the -deffnm option, you do not need -s, b/c it is already accounted for with the -deffnm. Marcus Dongsheng Zhang wrote: David, Thank you for your reply. I have provided replica0.tpr and replica1.tpr, but the program looks for replica.tpr. It surprises me. I have also tried to run /home/brasilia/dong/mdrun_mpi -np 2 -replex 500 -reseed -1 -multi -s replica0 replica1 -deffnm replica -N 2 -v zevel It doesn't work either (complains only one replica: Nothing to exchange with only one replica). it seems the program does not recognize the -multi option. Best wishes! Dongsheng On Thu, 2006-05-04 at 18:11 +0200, David van der Spoel wrote: Dongsheng Zhang wrote: Dear gmx users, I have trouble to run REMD on one node with two processors. The command I used is /home/brasilia/dong/mdrun_mpi -np 2 -replex 500 -reseed -1 -multi -s replica -deffnm replica -N 2 -v zevel the error message is: Can not open file: replica.tpr you need replica0 and replica1.tpr This error message looks strange to me. Because I have used -multi, the program should look for replica0.tpr and replica1.tpr. Could anyone point out what's wrong in my command? Thank you in advance! Dongsheng ___ 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 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] REMD in one nodes with two processors
Dear David, I had tried mpirun before, it didn't work either. the command was: mpirun -np 2 n1 /home/brasilia/dong/mdrun_mpi_MC -replex 500 -reseed -1 -multi -s replica -deffnm replica -N 2 -v zevel Because the two processors are in one node, so I changed my command to ( and go to the local node n1 to submit the job): /home/brasilia/dong/mdrun_mpi -np 2 -replex 500 -reseed -1 -multi -s replica -deffnm replica -N 2 -v zevel Could you please tell me if there is any way to check if the program can recognize -multi option? Thank you! Dongsheng On Thu, 2006-05-04 at 19:13 +0200, David van der Spoel wrote: Dongsheng Zhang wrote: Marcus, Thank you for your suggestion. I try it. The computer gives me the same error message. The problem is that the program always looks for replica.tpr instead of replica0.tpr and replica1.tpr. I don't know why. use mpirun search mailinglist Best wishes! Dongsheng On Thu, 2006-05-04 at 18:38 +0200, Marcus Kubitzki wrote: If you use the -deffnm option, you do not need -s, b/c it is already accounted for with the -deffnm. Marcus Dongsheng Zhang wrote: David, Thank you for your reply. I have provided replica0.tpr and replica1.tpr, but the program looks for replica.tpr. It surprises me. I have also tried to run /home/brasilia/dong/mdrun_mpi -np 2 -replex 500 -reseed -1 -multi -s replica0 replica1 -deffnm replica -N 2 -v zevel It doesn't work either (complains only one replica: Nothing to exchange with only one replica). it seems the program does not recognize the -multi option. Best wishes! Dongsheng On Thu, 2006-05-04 at 18:11 +0200, David van der Spoel wrote: Dongsheng Zhang wrote: Dear gmx users, I have trouble to run REMD on one node with two processors. The command I used is /home/brasilia/dong/mdrun_mpi -np 2 -replex 500 -reseed -1 -multi -s replica -deffnm replica -N 2 -v zevel the error message is: Can not open file: replica.tpr you need replica0 and replica1.tpr This error message looks strange to me. Because I have used -multi, the program should look for replica0.tpr and replica1.tpr. Could anyone point out what's wrong in my command? Thank you in advance! Dongsheng ___ 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 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] REMD
Dear David, The commands I used are as following: grompp -f replica0.mdp -c confout.gro -p topol.top -o replica0 to get replica0.tpr grompp -f replica1.mdp -c confout.gro -p topol.top -o replica1 to get replica1.tpr the script I used is: #PBS -S /bin/ksh -q sp_large ### CPU number #PBS -l nodes=2:ppn=1 ### -lwalltime=0:05:0 would be five minutes. #PBS -lwalltime=24:00:00 ###Job name #PBS -N remd . /etc/profile module load gromacs cd $PBS_O_WORKDIR mdrun_mpi -np 2 -multi -replex 500 -reseed -1 -s replica -deffnm replica -v -N 2 I have done several tests: 1. ran replica0.tpr and replica1.tpr seperately. Both worked fine 2. used grompp -np 2 -sort -shuffle -f replica0.mdp -c confout.gro -p topol.top -o replica0 to get replica0.tpr. I ran replica0.tpr. It worked fine. I also tried to use replica1.mdp to get replica1.tpr in the same way. replica1.tpr worked fine as well. If you need more information, please let me know. Thank you very much for your help! Best Wishes! Dongsheng On Thu, 2006-04-13 at 09:52 +0200, David van der Spoel wrote: Dongsheng Zhang wrote: dear Mark, Thank you very much for your prompt reply. I try to use parallel computing. It works fine. for example: grompp -f -c -p -o replica0 -np 2 -sort -shuffle to get replica0.tpr then, mdrun_mpi -np 2 -s replica0.tpr please give EXACT command line and do use mpirun The error message mentioned in the previous email looks very strange to me. MPI works fine, and individual tpr runs fine. The error message comes out before replica exchange. replica0 stops at step 500, replica1 stops at step 400, even the output informatio can't be complted. The last lines in replica1.log is Step Time Lambda 4000.80.0 Rel. Constraint Deviation: Maxbetween atoms RMS I hope these further information can help you to figure out what's the problem. Best Wishes! Dongsheng On Thu, 2006-04-13 at 15:17 +1000, Mark Abraham wrote: Dear gmx users: I am trying to run REMD with two replicas (for testing). I used grompp -f -c -p -o replica0 to get replica0.tpr grompp -f -c -p -o replica1 to get replica1.tpr then used mdrun_mpi -np 2 -multi -replex 500 -reseed -1 -s replica -deffnm replica -v -N 2 to run it. mdrun doesn't take '-N 2' but I'm not sure this is the problem. Otherwise, looks fine to me. I got an error message Segmentation fault from my script output, but no error message in both log files. When I tried to run individual tpr file, it worked fine. Could someone can comment why I got Segmentation fault? Thank you for your help! Your MPI setup might require you use a command like mpirun -N 2 mdrun_mpi ... to make it work - the segfault might be a gromacs-MPI interaction problem. If you can run an MPI process from the command line you may get more helpful feedback. 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 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] REMD
Dear David, I forgot one more information. The computer administrator told me I did not need to use mpirun. As I told you in the previous email, I have done tests for parallel computing. It worked fine. Dongsheng On Thu, 2006-04-13 at 09:52 +0200, David van der Spoel wrote: Dongsheng Zhang wrote: dear Mark, Thank you very much for your prompt reply. I try to use parallel computing. It works fine. for example: grompp -f -c -p -o replica0 -np 2 -sort -shuffle to get replica0.tpr then, mdrun_mpi -np 2 -s replica0.tpr please give EXACT command line and do use mpirun The error message mentioned in the previous email looks very strange to me. MPI works fine, and individual tpr runs fine. The error message comes out before replica exchange. replica0 stops at step 500, replica1 stops at step 400, even the output informatio can't be complted. The last lines in replica1.log is Step Time Lambda 4000.80.0 Rel. Constraint Deviation: Maxbetween atoms RMS I hope these further information can help you to figure out what's the problem. Best Wishes! Dongsheng On Thu, 2006-04-13 at 15:17 +1000, Mark Abraham wrote: Dear gmx users: I am trying to run REMD with two replicas (for testing). I used grompp -f -c -p -o replica0 to get replica0.tpr grompp -f -c -p -o replica1 to get replica1.tpr then used mdrun_mpi -np 2 -multi -replex 500 -reseed -1 -s replica -deffnm replica -v -N 2 to run it. mdrun doesn't take '-N 2' but I'm not sure this is the problem. Otherwise, looks fine to me. I got an error message Segmentation fault from my script output, but no error message in both log files. When I tried to run individual tpr file, it worked fine. Could someone can comment why I got Segmentation fault? Thank you for your help! Your MPI setup might require you use a command like mpirun -N 2 mdrun_mpi ... to make it work - the segfault might be a gromacs-MPI interaction problem. If you can run an MPI process from the command line you may get more helpful feedback. 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 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] REMD
Dear David,
I believe it runs in two processors because I can get two log files. I
tried to use mpirun, the computer complains that command mpirun (or
mpi_run) not found.
Replica1.log stops at:
Rel. Constraint Deviation: Maxbetween atoms RMS
Then I search where those messages are from in the source code. I found
they are in mdlib/clincs.c, as following:
if (do_per_step(step,ir-nstlog) || (step 0)) {
fprintf(stdlog, Rel. Constraint Deviation: Maxbetween
atoms RMS\n);
fprintf(stdlog, Before LINCS %.6f %6d %6d %.6f
\n,
p_max,lincsd-bla[2*p_imax]+1,lincsd-bla[2*p_imax+1]+1,p_rms);
cconerr(p_max,p_rms,p_imax,xprime,pbc_null,
lincsd-nc,lincsd-bla,lincsd-bllen);
fprintf(stdlog,After LINCS %.6f %6d %6d %.6f\n
\n,
p_max,lincsd-bla[2*p_imax]+1,lincsd-bla[2*p_imax+1]+1,p_rms);
}
I have a question about these codes, why does the output process stop in
the middle? (Disk space is very large, not full)
thank you for your help!
Dongsheng
On Thu, 2006-04-13 at 16:13 +0200, David van der Spoel wrote:
Dongsheng Zhang wrote:
Dear David,
I forgot one more information. The computer administrator told me I did
not need to use mpirun. As I told you in the previous email, I have done
tests for parallel computing. It worked fine.
try it with mpirun anyway.
I suspect you are just running a single process which crashes as soon as
it needs to do REMD communication.
Dongsheng
On Thu, 2006-04-13 at 09:52 +0200, David van der Spoel wrote:
Dongsheng Zhang wrote:
dear Mark,
Thank you very much for your prompt reply. I try to use parallel
computing. It works fine.
for example: grompp -f -c -p -o replica0 -np 2 -sort -shuffle
to get replica0.tpr
then, mdrun_mpi -np 2 -s replica0.tpr
please give EXACT command line and do use mpirun
The error message mentioned in the previous email looks very strange to
me. MPI works fine, and individual tpr runs fine. The error message
comes out before replica exchange. replica0 stops at step 500, replica1
stops at step 400, even the output informatio can't be complted. The
last lines in replica1.log is
Step Time Lambda
4000.80.0
Rel. Constraint Deviation: Maxbetween atoms RMS
I hope these further information can help you to figure out what's the
problem.
Best Wishes!
Dongsheng
On Thu, 2006-04-13 at 15:17 +1000, Mark Abraham wrote:
Dear gmx users:
I am trying to run REMD with two replicas (for testing). I used
grompp -f -c -p -o replica0 to get replica0.tpr
grompp -f -c -p -o replica1 to get replica1.tpr
then used
mdrun_mpi -np 2 -multi -replex 500 -reseed -1 -s replica -deffnm replica
-v -N 2
to run it.
mdrun doesn't take '-N 2' but I'm not sure this is the problem.
Otherwise,
looks fine to me.
I got an error message Segmentation fault from my script output, but
no error message in both log files. When I tried to run individual tpr
file, it worked fine.
Could someone can comment why I got Segmentation fault? Thank you for
your help!
Your MPI setup might require you use a command like mpirun -N 2
mdrun_mpi
... to make it work - the segfault might be a gromacs-MPI interaction
problem. If you can run an MPI process from the command line you may get
more helpful feedback.
Mark
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--
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] REMD
Dear gmx users: I am trying to run REMD with two replicas (for testing). I used grompp -f -c -p -o replica0 to get replica0.tpr grompp -f -c -p -o replica1 to get replica1.tpr then used mdrun_mpi -np 2 -multi -replex 500 -reseed -1 -s replica -deffnm replica -v -N 2 to run it. I got an error message Segmentation fault from my script output, but no error message in both log files. When I tried to run individual tpr file, it worked fine. Could someone can comment why I got Segmentation fault? Thank you for your help! Dongsheng ___ 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] pdb2gmx illegal instruction (core dumped)
Dear David, Thank you very much for your quick reply. The machine is IBM. Then, could you please tell me how to fix it? Thanks again. Best Wishes! Dongsheng On Tue, 2006-03-21 at 17:00 +0100, David van der Spoel wrote: Dongsheng Zhang wrote: Dear All, I want to use gromacs in research computing center in my school. When I used pdb2gmx as pdb2gmx -f Ace5AlaNac -o Ace5AlaNac -p Ace5AlaNac -ignh -ter it gave me an error message as follows, illegal instruction (core dumped) what kind of computer? this kind of stuff usually happens on IBM boxes. Could anyone give me a clue what is wrong? Thank you in advance! Dongsheng ___ 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] pdb2gmx illegal instruction
Dear Tom, Thank you for your reply. Unfortunately, mpirun is not available. I can only find mdrun_mpi which is related with mpi. Best wishes! Dongsheng On Tue, 2006-03-21 at 21:02 -0500, Tom Joseph wrote: Certainly you should consult your documentation, but one possibility is: mpirun -np 8 mdrun_mpi -np 8 -s pr -o pr -c after_pr -e pr -g pr -v - N 8 --Tom On Mar 21, 2006, at 6:48 PM, Erik Lindahl wrote: mdrun_mpi -np 8 mdrun -np 8 -s pr -o pr -c after_pr -e pr -g pr - v -N 8 This won't work. You should start mdrun_mpi, using the program (mpirun or something) specified by your MPI library. There is no standard for this, so consult the documentation for your MPI implementation. Cheers, Erik ___ 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 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 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
