Re: [gmx-users] mdrun error
On 7/21/13 12:18 AM, Collins Nganou wrote: Dear Users, when trying to run the following command: mdrun -v -deffnm protein-EM-solvated -c protein-EM-solvated.pdb I have received the error below. Reading file dna-EM-solvated.tpr, VERSION 4.5.5 (single precision) Starting 2 threads --- Program mdrun, VERSION 4.5.5 Source code file: /build/buildd/gromacs-4.5.5/src/mdlib/domdec.c, line: 6005 Fatal error: Domain decomposition does not support simple neighbor searching, use grid searching or use particle decomposition For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I am looking any suggestion that can help me to overcome this error. Not all combinations of options are compatible, and mdrun already told you exactly what to do. If you want to use DD, you can't use nstype = simple, so you have to invoke mdrun -pd in this case or otherwise switch to nstype = grid. How you proceed depends on what you're trying to achieve with your .mdp settings. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] mdrun error
Dear Users, when trying to run the following command: mdrun -v -deffnm protein-EM-solvated -c protein-EM-solvated.pdb I have received the error below. Reading file dna-EM-solvated.tpr, VERSION 4.5.5 (single precision) Starting 2 threads --- Program mdrun, VERSION 4.5.5 Source code file: /build/buildd/gromacs-4.5.5/src/mdlib/domdec.c, line: 6005 Fatal error: Domain decomposition does not support simple neighbor searching, use grid searching or use particle decomposition For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I am looking any suggestion that can help me to overcome this error. Best regards Albert Collins -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] mdrun error
Dear gmx users, Would be this error (as you see here) a symptom of blowing up of a system? Or just .mdp options should be changed? Fatal error: 1 of the 16625 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (0.817695 nm) or the two-body cut-off distance (1 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Thanks for your suggestions. Sincerely, Shima -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] mdrun error
On 8/9/12 1:40 PM, Shima Arasteh wrote: Dear gmx users, Would be this error (as you see here) a symptom of blowing up of a system? Or just .mdp options should be changed? Fatal error: 1 of the 16625 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (0.817695 nm) or the two-body cut-off distance (1 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Any time something moves too far, it's a case of blowing up. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] mdrun : error
Hello, I am trying to do equilibration for my system (solvent + solute). I am geting the following error. If I run solvent and solute molecules separately, its run well. For mixture I am getting following error. What this error means. Fatal error: 1 of the 22334 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (0.8 nm) or the two-body cut-off distance (1 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck NIlesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] mdrun : error
Nilesh Dhumal wrote: Hello, I am trying to do equilibration for my system (solvent + solute). I am geting the following error. If I run solvent and solute molecules separately, its run well. For mixture I am getting following error. What this error means. Fatal error: 1 of the 22334 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (0.8 nm) or the two-body cut-off distance (1 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck Search the list archive. This has been asked and answered several times, so you'll likely find something useful. Also, take mdrun's advice and read about the options it's telling you. -Justin NIlesh -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Mdrun error
Hello Justin, I used Gromacs 4.0.5 and the error was gone. Thank you. But now I have another problem when using mdrun_d. I gave the comand: mdrun_d -s dppc.tpr -o dppc128.trr -c dppc128.gro -g dppc.log And first I got a lot of output on the shell window and I think it is strange. This output should be on a file or not? And after a few seconds I got an error which says: t = 0.052 ps: Water molecule starting at atom 17276 can not be settled. Check for bad contacts and/or reduce the timestep. Back Off! I just backed up step26b.pdb to ./#step26b.pdb.2# Back Off! I just backed up step26c.pdb to ./#step26c.pdb.2# Wrote pdb files with previous and current coordinates MPI process rank 0 (n0, p23764) caught a SIGSEGV. Can you help me? Thank you Cíntia C. Vequi-Suplicy Biophysics Group Physics Institute São Paulo University Justin A. Lemkul wrote: Cíntia C. Vequi-Suplicy wrote: Hello, I am trying to simulate a lipid membrane with Gromacs. I am trying to generate the *.tpr file o run the simulation, but every time I use the command grompp I got the following error: checking input for internal consistency... ...ling /usr/bin/cpp : No such file or directory cpp exit code: 32512 dppc128.top gromppzJXISa'cpp ' command is defined in the .mdp file * * Important: if you do not have a c-preprocessor installed, * * you MUST run grompp with the -pp command line option* * in place of the -p option. * * processing topology... processing coordinates... --- Program grompp, VERSION 3.3.3 Source code file: ../../../../src/kernel/grompp.c, line: 469 Fatal error: number of coordinates in coordinate file (dppc128.gro, 17365) does not match topology (dppc128.top, 0) --- One Cross Each (Monty Python) I don´t where the problem is, I've already checked the cpp compiler and it installed in the /usr/bin/cpp, as I put in the .mdp file. In the topology file I have the following lines: Have you tried the advice from grompp to use -pp instead of -p? General advice for this problem can be found here: http://oldwiki.gromacs.org/index.php/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology Also an option is to upgrade to the most recent version of Gromacs (4.0.5), which does not require cpp. -Justin ; ;File 'dppc128.top' was generated ;By user: onbekend (0) ;On host: onbekend ;At date: Tue Aug 18 10:02:52 2009 ; ;This is your topology file ;Pure DPPC bilayer with 128 lipids and 3655 water molecules ; ; The force field files to be include #include ffoplsaa.itp ; Include DPPC topology #include dppc.itp #include lipid.itp #include spc.itp [ molecules ] ; Compound #mol DPP 128 SOL 3655 If anyone can help It will be very nice, Thank you very much so far, Cíntia C. Vequi-Suplicy Biophysics Group Physics Institute São Paulo University ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Mdrun error
Cíntia C. Vequi-Suplicy wrote: Hello Justin, I used Gromacs 4.0.5 and the error was gone. Thank you. But now I have another problem when using mdrun_d. I gave the comand: mdrun_d -s dppc.tpr -o dppc128.trr -c dppc128.gro -g dppc.log And first I got a lot of output on the shell window and I think it is strange. This output should be on a file or not? No, this output to stdout is normal. 3.3.3 does that too. Roughly the same content got written to the .log file. It sounds like you should do some tutorial material to get used to the GROMACS workflow. And after a few seconds I got an error which says: t = 0.052 ps: Water molecule starting at atom 17276 can not be settled. Check for bad contacts and/or reduce the timestep. Back Off! I just backed up step26b.pdb to ./#step26b.pdb.2# Back Off! I just backed up step26c.pdb to ./#step26c.pdb.2# Wrote pdb files with previous and current coordinates MPI process rank 0 (n0, p23764) caught a SIGSEGV. See http://oldwiki.gromacs.org/index.php/Errors#LINCS.2FSETTLE.2FSHAKE_warnings You should do some searching on the wiki/web to help diagnose your own problems before asking here :-) You'll learn more about problems you've solved yourself :-) Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] mdrun error
I am trying to run the simulation of protein ligand complex. But after running the mdrun by giving command-grompp –f md. mdp –c pr.gro –p trp.top –o md.tpr and then nohup mdrun –deffnm md the md.log file is showing the following message- Step 11 Warning: pressure scaling more than 1%, mu: 1.01684 1.01684 1.01684 Step 13 Warning: pressure scaling more than 1%, mu: 0.947161 0.947161 0.947161 Step 14 Warning: pressure scaling more than 1%, mu: 1.01207 1.01207 1.01207 Step 15 Warning: pressure scaling more than 1%, mu: 1.18248 1.18248 1.18248 Step 16 Warning: pressure scaling more than 1%, mu: 0.867467 0.867467 0.867467 Step 16, time 0.032 (ps) LINCS WARNING relative constraint deviation after LINCS: max 0.099556 (between atoms 1396 and 1398) rms 0.028595 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 21 23 30.80.1740 0.1569 0.1470 38 40 32.00.1740 0.1583 0.1470 54 56 33.00.1740 0.1588 0.1470 56 57 30.60.1810 0.1623 0.1530 67 69 31.40.1740 0.1568 0.1470 104106 32.60.1740 0.1588 0.1470 106107 31.10.1811 0.1632 0.1530 216218 31.80.1741 0.1584 0.1470 I am attaching my md.mdp file.Please help me in this regard. -- Sheetal Arora M.Tech(Biotechnology Medical Engg) NIT Rourkela md.mdp Description: Binary data ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] mdrun error
Pawan Kumar wrote: probably a bad starting structure... check this website for pressure scaling warning : http://wiki.gromacs.org/index.php/Errors Also, compressibility = 4.575e-4 is of the wrong magnitude for water. Should be e-5. -Justin regards, pawan On Mon, Apr 27, 2009 at 5:21 PM, Sheetal Arora sheetal.aror...@gmail.com mailto:sheetal.aror...@gmail.com wrote: I am trying to run the simulation of protein ligand complex. But after running the mdrun by giving command-grompp –f md. mdp –c pr.gro –p trp.top –o md.tpr and then nohup mdrun –deffnm md the md.log file is showing the following message- Step 11 Warning: pressure scaling more than 1%, mu: 1.01684 1.01684 1.01684 Step 13 Warning: pressure scaling more than 1%, mu: 0.947161 0.947161 0.947161 Step 14 Warning: pressure scaling more than 1%, mu: 1.01207 1.01207 1.01207 Step 15 Warning: pressure scaling more than 1%, mu: 1.18248 1.18248 1.18248 Step 16 Warning: pressure scaling more than 1%, mu: 0.867467 0.867467 0.867467 Step 16, time 0.032 (ps) LINCS WARNING relative constraint deviation after LINCS: max 0.099556 (between atoms 1396 and 1398) rms 0.028595 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 21 23 30.80.1740 0.1569 0.1470 38 40 32.00.1740 0.1583 0.1470 54 56 33.00.1740 0.1588 0.1470 56 57 30.60.1810 0.1623 0.1530 67 69 31.40.1740 0.1568 0.1470 104106 32.60.1740 0.1588 0.1470 106107 31.10.1811 0.1632 0.1530 216218 31.80.1741 0.1584 0.1470 I am attaching my md.mdp file.Please help me in this regard. -- Sheetal Arora M.Tech(Biotechnology Medical Engg) NIT Rourkela ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] mdrun error
Dear all, I am doing a protein simulation for 20ns in single processor machine. after 11.1ns when I am trying to rerun mdrun its coming out with the following error. -- Inner product between old and new vector = 0.0! constraint #0 atoms 1 and 2 Warning: 1-4 interaction between 1 and 7 at distance inf which is larger than the 1-4 table size 2.400 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size MPI process rank 0 (n0, p20175) caught a SIGSEGV. - Can anybody please give me some clue to solve this? Thanks in advance Supti Mukhopadhyay ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] mdrun error
hi i tried to run the simulation with single alamethicin molecule but i am getting the same error as i was getting earlier. Warning: 1-4 interaction between 164 and 169 at distance 3.430 which is larger than the 1-4 table size 1.000 nm. I used the command $ genbox -cp alamethicin.gro -cs popc.gro -o system.gro my pdb file at 164 to 169 is: ATOM 164 CZ PHL 21 44.000 52.840 35.170 1.00 0.00 ATOM 165 HZ PHL 21 44.990 53.260 35.090 1.00 0.00 ATOM 166 CX PHL 21 38.140 50.450 37.160 1.00 0.00 ATOM 167 OY PHL 21 37.940 49.350 38.060 1.00 0.00 ATOM 168 HY PHL 21 37.040 48.940 37.950 1.00 0.00 ATOM 169 CA ACE 22 53.840 44.410 66.930 1.00 0.00. This is occuring at the start of equillibration step . I have not done any simulation as yet. I also tried pre-equillibrating the protein and directly simulating by restrain but that also is not working. I cannot figure out the problem. Please help at Windows Live Ideas—so new they haven’t even been officially released yet. http://www.msnspecials.in/windowslive/___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php = Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ = ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ Call friends with PC-to-PC calling -- FREE http://get.live.com/messenger/overview = Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ = ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ Windows Live Spaces is here! It’s easy to create your own personal Web site. http://spaces.live.com/?mkt=en-in = Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ = = Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ = ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ Windows Live Spaces is here! It’s easy to create your own personal Web site. http://spaces.live.com/?mkt=en-in___ 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] mdrun error
Date: Fri, 9 Nov 2007 09:01:48 -0500 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: Re: [gmx-users] mdrun error Check out the wiki at: http://wiki.gromacs.org/index.php/Errors#LINCS_warnings Alternatively, search the list for some of my posts from around a year ago - NVT and minimization of a lipid bilayer (or search for my name, they should come up as well). I suspect you have bad contacts in your starting structure. -Justin Quoting pragya chohan : hi i am trying to run mdrun for protein in membrane system. When i run mdrun i get a warning Step -2, time -0.002 (ps) LINCS WARNING relative constraint deviation after LINCS: max 2.144082 (between atoms 12433 and 12434) rms 0.216090 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 11761 11762 90.0 0.1633 0.2387 0.1000 11929 11930 31.7 0.1633 0.1000 0.1000 12097 12098 90.0 0.1632 0.1041 0.1000 12265 12266 90.0 0.1633 0.2266 0.1000 12433 12434 90.0 0.1633 0.3144 0.1000 starting mdrun 'alamethicin in popc' 500 steps, 0.5 ps. Warning: 1-4 interaction between 115 and 136 at distance 1.144 which is larger t han the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max inf (between atoms 12007 and 12008) rms inf bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 11619 11620 90.0 0.1000 0.1411 0.1000 11633 11634 90.0 0.1000 13155507200. 0.1000 11640 11641 90.0 0.1000 0.1214 0.1000 . 12619 12620 90.0 0.1080 0.1447 0.1080 Wrote pdb files with previous and current coordinates step 0Segmentation fault I am using shake in my mdp file. I want to restrain water. my mdp file is: title = popc128a integrator = md define = -DFLEX_SPC dt = 0.001 nsteps = 500 nstxout = 500 ns_type = grid pbc = xyz constraints = hbonds constraints_algorithm= shake coulombtype = PME vdwtype = cut-off rcoloumb = 1.0 nstlist = 10.0 Tcoupl = no pcoupl = no compressibility = 4.5e-5 gen_temp = 300 gen_vel = no Please help. Thanks in advance. _ Check out some new online services at Windows Live Ideas—so new they haven’t even been officially released yet. http://www.msnspecials.in/windowslive/___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php = Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ = ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Thanks for your help. I figured the problem out but am getting an error again. I have alamethicin in popc and water. Since alamethicin has some non standard residue i made topology file in text editor and ran mdrun with only alamethicin. It went fine. But when i am tring to minimize alamethicin in popc mdrum probably does not recognize the starting of second chain and gives me following error: Warning: 1-4 interaction between 164 and 169 at distance 3.430 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file Step=1, Dmax= 1.0e-02 nm, Epot= 3.25524e+09 Fmax= 1.00321e+09, atom= 2441 Step=2, Dmax= 1.2e-02 nm, Epot= 2.21743e+09 Fmax= 1.82388e+08, atom= 12852 Step=3, Dmax= 1.4e-02 nm, Epot= 1.95672e+09 Fmax= 7.44135e+07, atom= 262 Step=4, Dmax= 1.7e-02 nm, Epot= 1.88109e+09 Fmax= 4.32188e+07, atom= 260 Step=5, Dmax= 2.1e-02 nm, Epot= 1.84989e+09 Fmax= 2.77292e+07, atom= 262 Step=6, Dmax= 2.5e-02 nm, Epot= 1.83083e+09 Fmax= 1.89783e+07, atom= 258 Step=7, Dmax= 3.0e-02 nm, Epot= 1.81606e+09 Fmax= 9.97167e+06, atom= 253 Step=8, Dmax= 3.6e-02 nm, Epot= 1.79660e+09 Fmax= 2.09557e+07, atom= 258 Step=9, Dmax= 4.3e-02 nm, Epot= 1.78793e+09 Fmax= 1.63547e+07, atom= 259 Step= 10, Dmax= 5.2e
RE: [gmx-users] mdrun error
Since alamethicin works on its own, it suggests to me that the introduction of alamethicin into POPC is what's causing the problem, and judging by the enormous potential energies and forces, it appears to be bad contacts/atomic overlap (at least, that's been the cause of problems in my experience). How are you generating your starting structure? -Justin Thanks for your help. I figured the problem out but am getting an error again. I have alamethicin in popc and water. Since alamethicin has some non standard residue i made topology file in text editor and ran mdrun with only alamethicin. It went fine. But when i am tring to minimize alamethicin in popc mdrum probably does not recognize the starting of second chain and gives me following error: Warning: 1-4 interaction between 164 and 169 at distance 3.430 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file Step=1, Dmax= 1.0e-02 nm, Epot= 3.25524e+09 Fmax= 1.00321e+09, atom= 2441 Step=2, Dmax= 1.2e-02 nm, Epot= 2.21743e+09 Fmax= 1.82388e+08, atom= 12852 Step=3, Dmax= 1.4e-02 nm, Epot= 1.95672e+09 Fmax= 7.44135e+07, atom= 262 Step=4, Dmax= 1.7e-02 nm, Epot= 1.88109e+09 Fmax= 4.32188e+07, atom= 260 Step=5, Dmax= 2.1e-02 nm, Epot= 1.84989e+09 Fmax= 2.77292e+07, atom= 262 Step=6, Dmax= 2.5e-02 nm, Epot= 1.83083e+09 Fmax= 1.89783e+07, atom= 258 Step=7, Dmax= 3.0e-02 nm, Epot= 1.81606e+09 Fmax= 9.97167e+06, atom= 253 Step=8, Dmax= 3.6e-02 nm, Epot= 1.79660e+09 Fmax= 2.09557e+07, atom= 258 Step=9, Dmax= 4.3e-02 nm, Epot= 1.78793e+09 Fmax= 1.63547e+07, atom= 259 Step= 10, Dmax= 5.2e-02 nm, Epot= 1.77532e+09 Fmax= 7.54157e+06, atom= 12539 Step= 11, Dmax= 6.2e-02 nm, Epot= 1.74488e+09 Fmax= 7.42417e+06, atom= 12539 Step= 12, Dmax= 7.4e-02 nm, Epot= 1.70998e+09 Fmax= 7.28331e+06, atom= 12539 Step= 13, Dmax= 8.9e-02 nm, Epot= 1.66920e+09 Fmax= 7.11508e+06, atom= 12539 Wrote pdb files with previous and current coordinates Back Off! I just backed up step13.pdb to ./#step13.pdb.1# Back Off! I just backed up step14.pdb to ./#step14.pdb.1# Wrote pdb files with previous and current coordinates my pdb file at 164 to 169 is: ATOM164 CZ PHL21 44.000 52.840 35.170 1.00 0.00 ATOM165 HZ PHL21 44.990 53.260 35.090 1.00 0.00 ATOM166 CX PHL21 38.140 50.450 37.160 1.00 0.00 ATOM167 OY PHL21 37.940 49.350 38.060 1.00 0.00 ATOM168 HY PHL21 37.040 48.940 37.950 1.00 0.00 ATOM169 CA ACE22 53.840 44.410 66.930 1.00 0.00 I think it is not recognising different chain. Am i right? Please help me. _ Check out some new online services at Windows Live Ideasso new they havent even been officially released yet. http://www.msnspecials.in/windowslive/___ 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 = Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ = ___ 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] mdrun error
Thanks Justin for your reply. I am generating the starting structure through genbox. I added popc as solvent around alamethicin after aligning alamethicin in a box and centering it in the box and followed same procedure for popc also. Do you have any better way? Date: Sat, 10 Nov 2007 10:22:45 -0500 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: RE: [gmx-users] mdrun error Since alamethicin works on its own, it suggests to me that the introduction of alamethicin into POPC is what's causing the problem, and judging by the enormous potential energies and forces, it appears to be bad contacts/atomic overlap (at least, that's been the cause of problems in my experience). How are you generating your starting structure? -JustinThanks for your help. I figured the problem out but am getting an error again. I have alamethicin in popc and water. Since alamethicin has some non standard residue i made topology file in text editor and ran mdrun with only alamethicin. It went fine. But when i am tring to minimize alamethicin in popc mdrum probably does not recognize the starting of second chain and gives me following error: Warning: 1-4 interaction between 164 and 169 at distance 3.430 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file Step= 1, Dmax= 1.0e-02 nm, Epot= 3.25524e+09 Fmax= 1.00321e+09, atom= 2441 Step= 2, Dmax= 1.2e-02 nm, Epot= 2.21743e+09 Fmax= 1.82388e+08, atom= 12852 Step= 3, Dmax= 1.4e-02 nm, Epot= 1.95672e+09 Fmax= 7.44135e+07, atom= 262 Step= 4, Dmax= 1.7e-02 nm, Epot= 1.88109e+09 Fmax= 4.32188e+07, atom= 260 Step= 5, Dmax= 2.1e-02 nm, Epot= 1.84989e+09 Fmax= 2.77292e+07, atom= 262 Step= 6, Dmax= 2.5e-02 nm, Epot= 1.83083e+09 Fmax= 1.89783e+07, atom= 258 Step= 7, Dmax= 3.0e-02 nm, Epot= 1.81606e+09 Fmax= 9.97167e+06, atom= 253 Step= 8, Dmax= 3.6e-02 nm, Epot= 1.79660e+09 Fmax= 2.09557e+07, atom= 258 Step= 9, Dmax= 4.3e-02 nm, Epot= 1.78793e+09 Fmax= 1.63547e+07, atom= 259 Step= 10, Dmax= 5.2e-02 nm, Epot= 1.77532e+09 Fmax= 7.54157e+06, atom= 12539 Step= 11, Dmax= 6.2e-02 nm, Epot= 1.74488e+09 Fmax= 7.42417e+06, atom= 12539 Step= 12, Dmax= 7.4e-02 nm, Epot= 1.70998e+09 Fmax= 7.28331e+06, atom= 12539 Step= 13, Dmax= 8.9e-02 nm, Epot= 1.66920e+09 Fmax= 7.11508e+06, atom= 12539 Wrote pdb files with previous and current coordinates Back Off! I just backed up step13.pdb to ./#step13.pdb.1# Back Off! I just backed up step14.pdb to ./#step14.pdb.1# Wrote pdb files with previous and current coordinates my pdb file at 164 to 169 is: ATOM 164 CZ PHL 21 44.000 52.840 35.170 1.00 0.00 ATOM 165 HZ PHL 21 44.990 53.260 35.090 1.00 0.00 ATOM 166 CX PHL 21 38.140 50.450 37.160 1.00 0.00 ATOM 167 OY PHL 21 37.940 49.350 38.060 1.00 0.00 ATOM 168 HY PHL 21 37.040 48.940 37.950 1.00 0.00 ATOM 169 CA ACE 22 53.840 44.410 66.930 1.00 0.00 I think it is not recognising different chain. Am i right? Please help me. _ Check out some new online services at Windows Live Ideas—so new they haven’t even been officially released yet. http://www.msnspecials.in/windowslive/___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php = Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ = ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ Call friends with PC-to-PC calling -- FREE http://get.live.com/messenger/overview___ 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
RE: [gmx-users] mdrun error
Quoting pragya chohan [EMAIL PROTECTED]: Thanks Justin for your reply. I am generating the starting structure through genbox. I added popc as solvent around alamethicin after aligning alamethicin in a box and centering it in the box and followed same procedure for popc also. Do you have any better way? In theory, that should work just fine, but I don't understand what you mean by followed the same procedure for popc. What did you do there? The first part should be all you need (alamethicin in the box, solvated with popc). Alternatively, you can use make_hole.pl or the inflategro script available through Peter Tieleman's site: http://moose.bio.ucalgary.ca/index.php?page=Translate_lipdis -Justin Date: Sat, 10 Nov 2007 10:22:45 -0500 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: RE: [gmx-users] mdrun error Since alamethicin works on its own, it suggests to me that the introduction of alamethicin into POPC is what's causing the problem, and judging by the enormous potential energies and forces, it appears to be bad contacts/atomic overlap (at least, that's been the cause of problems in my experience). How are you generating your starting structure? -JustinThanks for your help. I figured the problem out but am getting an error again. I have alamethicin in popc and water. Since alamethicin has some non standard residue i made topology file in text editor and ran mdrun with only alamethicin. It went fine. But when i am tring to minimize alamethicin in popc mdrum probably does not recognize the starting of second chain and gives me following error: Warning: 1-4 interaction between 164 and 169 at distance 3.430 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file Step= 1, Dmax= 1.0e-02 nm, Epot= 3.25524e+09 Fmax= 1.00321e+09, atom= 2441 Step= 2, Dmax= 1.2e-02 nm, Epot= 2.21743e+09 Fmax= 1.82388e+08, atom= 12852 Step= 3, Dmax= 1.4e-02 nm, Epot= 1.95672e+09 Fmax= 7.44135e+07, atom= 262 Step= 4, Dmax= 1.7e-02 nm, Epot= 1.88109e+09 Fmax= 4.32188e+07, atom= 260 Step= 5, Dmax= 2.1e-02 nm, Epot= 1.84989e+09 Fmax= 2.77292e+07, atom= 262 Step= 6, Dmax= 2.5e-02 nm, Epot= 1.83083e+09 Fmax= 1.89783e+07, atom= 258 Step= 7, Dmax= 3.0e-02 nm, Epot= 1.81606e+09 Fmax= 9.97167e+06, atom= 253 Step= 8, Dmax= 3.6e-02 nm, Epot= 1.79660e+09 Fmax= 2.09557e+07, atom= 258 Step= 9, Dmax= 4.3e-02 nm, Epot= 1.78793e+09 Fmax= 1.63547e+07, atom= 259 Step= 10, Dmax= 5.2e-02 nm, Epot= 1.77532e+09 Fmax= 7.54157e+06, atom= 12539 Step= 11, Dmax= 6.2e-02 nm, Epot= 1.74488e+09 Fmax= 7.42417e+06, atom= 12539 Step= 12, Dmax= 7.4e-02 nm, Epot= 1.70998e+09 Fmax= 7.28331e+06, atom= 12539 Step= 13, Dmax= 8.9e-02 nm, Epot= 1.66920e+09 Fmax= 7.11508e+06, atom= 12539 Wrote pdb files with previous and current coordinates Back Off! I just backed up step13.pdb to ./#step13.pdb.1# Back Off! I just backed up step14.pdb to ./#step14.pdb.1# Wrote pdb files with previous and current coordinates my pdb file at 164 to 169 is: ATOM 164 CZ PHL 21 44.000 52.840 35.170 1.00 0.00 ATOM 165 HZ PHL 21 44.990 53.260 35.090 1.00 0.00 ATOM 166 CX PHL 21 38.140 50.450 37.160 1.00 0.00 ATOM 167 OY PHL 21 37.940 49.350 38.060 1.00 0.00 ATOM 168 HY PHL 21 37.040 48.940 37.950 1.00 0.00 ATOM 169 CA ACE 22 53.840 44.410 66.930 1.00 0.00 I think it is not recognising different chain. Am i right? Please help me. _ Check out some new online services at Windows Live Ideasso new they havent even been officially released yet. http://www.msnspecials.in/windowslive/___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php = Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ = ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ Call friends with PC
RE: [gmx-users] mdrun error
Hi justin I placed POPC membrane in a box too of same dimension as the box of alamethicin and centred it too so that alamethicin is placed correctly in the membrane. I am attaching the pdb please have a look.Any help would be appreciated Pragya Date: Sat, 10 Nov 2007 12:42:01 -0500 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: RE: [gmx-users] mdrun error Quoting pragya chohan [EMAIL PROTECTED]: Thanks Justin for your reply. I am generating the starting structure through genbox. I added popc as solvent around alamethicin after aligning alamethicin in a box and centering it in the box and followed same procedure for popc also. Do you have any better way? In theory, that should work just fine, but I don't understand what you mean by followed the same procedure for popc. What did you do there? The first part should be all you need (alamethicin in the box, solvated with popc). Alternatively, you can use make_hole.pl or the inflategro script available through Peter Tieleman's site: http://moose.bio.ucalgary.ca/index.php?page=Translate_lipdis -Justin Date: Sat, 10 Nov 2007 10:22:45 -0500 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: RE: [gmx-users] mdrun error Since alamethicin works on its own, it suggests to me that the introduction of alamethicin into POPC is what's causing the problem, and judging by the enormous potential energies and forces, it appears to be bad contacts/atomic overlap (at least, that's been the cause of problems in my experience). How are you generating your starting structure? -JustinThanks for your help. I figured the problem out but am getting an error again. I have alamethicin in popc and water. Since alamethicin has some non standard residue i made topology file in text editor and ran mdrun with only alamethicin. It went fine. But when i am tring to minimize alamethicin in popc mdrum probably does not recognize the starting of second chain and gives me following error: Warning: 1-4 interaction between 164 and 169 at distance 3.430 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file Step= 1, Dmax= 1.0e-02 nm, Epot= 3.25524e+09 Fmax= 1.00321e+09, atom= 2441 Step= 2, Dmax= 1.2e-02 nm, Epot= 2.21743e+09 Fmax= 1.82388e+08, atom= 12852 Step= 3, Dmax= 1.4e-02 nm, Epot= 1.95672e+09 Fmax= 7.44135e+07, atom= 262 Step= 4, Dmax= 1.7e-02 nm, Epot= 1.88109e+09 Fmax= 4.32188e+07, atom= 260 Step= 5, Dmax= 2.1e-02 nm, Epot= 1.84989e+09 Fmax= 2.77292e+07, atom= 262 Step= 6, Dmax= 2.5e-02 nm, Epot= 1.83083e+09 Fmax= 1.89783e+07, atom= 258 Step= 7, Dmax= 3.0e-02 nm, Epot= 1.81606e+09 Fmax= 9.97167e+06, atom= 253 Step= 8, Dmax= 3.6e-02 nm, Epot= 1.79660e+09 Fmax= 2.09557e+07, atom= 258 Step= 9, Dmax= 4.3e-02 nm, Epot= 1.78793e+09 Fmax= 1.63547e+07, atom= 259 Step= 10, Dmax= 5.2e-02 nm, Epot= 1.77532e+09 Fmax= 7.54157e+06, atom= 12539 Step= 11, Dmax= 6.2e-02 nm, Epot= 1.74488e+09 Fmax= 7.42417e+06, atom= 12539 Step= 12, Dmax= 7.4e-02 nm, Epot= 1.70998e+09 Fmax= 7.28331e+06, atom= 12539 Step= 13, Dmax= 8.9e-02 nm, Epot= 1.66920e+09 Fmax= 7.11508e+06, atom= 12539 Wrote pdb files with previous and current coordinates Back Off! I just backed up step13.pdb to ./#step13.pdb.1# Back Off! I just backed up step14.pdb to ./#step14.pdb.1# Wrote pdb files with previous and current coordinates my pdb file at 164 to 169 is: ATOM 164 CZ PHL 21 44.000 52.840 35.170 1.00 0.00 ATOM 165 HZ PHL 21 44.990 53.260 35.090 1.00 0.00 ATOM 166 CX PHL 21 38.140 50.450 37.160 1.00 0.00 ATOM 167 OY PHL 21 37.940 49.350 38.060 1.00 0.00 ATOM 168 HY PHL 21 37.040 48.940 37.950 1.00 0.00 ATOM 169 CA ACE 22 53.840 44.410 66.930 1.00 0.00 I think it is not recognising different chain. Am i right? Please help me. _ Check out some new online services at Windows Live Ideas—so new they haven’t even been officially released yet. http://www.msnspecials.in/windowslive/___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php = Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
RE: [gmx-users] mdrun error
Quoting pragya chohan [EMAIL PROTECTED]: Hi justin I placed POPC membrane in a box too of same dimension as the box of alamethicin and centred it too so that alamethicin is placed correctly in the membrane. I am attaching the pdb please have a look.Any help would be appreciated Looks like the listserv ate the PDB file, but from your description it sounds like you've generated some severe atomic overlap. Simply pasting coordinates of a protein into a membrane is sure to cause bad contacts. The proper procedure would be to create a cavity within the membrane and place the protein in it (i.e., make_hole.pl, inflategro, as I previously suggested), or using genbox, which you originally said you did. Try this (assuming you have the box dimensions correct): $ genbox -cp alamethicin.gro -cs popc.gro -o system.gro -Justin Pragya Date: Sat, 10 Nov 2007 12:42:01 -0500 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: RE: [gmx-users] mdrun error Quoting pragya chohan [EMAIL PROTECTED]: Thanks Justin for your reply. I am generating the starting structure through genbox. I added popc as solvent around alamethicin after aligning alamethicin in a box and centering it in the box and followed same procedure for popc also. Do you have any better way? In theory, that should work just fine, but I don't understand what you mean by followed the same procedure for popc. What did you do there? The first part should be all you need (alamethicin in the box, solvated with popc). Alternatively, you can use make_hole.pl or the inflategro script available through Peter Tieleman's site: http://moose.bio.ucalgary.ca/index.php?page=Translate_lipdis -Justin Date: Sat, 10 Nov 2007 10:22:45 -0500 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: RE: [gmx-users] mdrun error Since alamethicin works on its own, it suggests to me that the introduction of alamethicin into POPC is what's causing the problem, and judging by the enormous potential energies and forces, it appears to be bad contacts/atomic overlap (at least, that's been the cause of problems in my experience). How are you generating your starting structure? -JustinThanks for your help. I figured the problem out but am getting an error again. I have alamethicin in popc and water. Since alamethicin has some non standard residue i made topology file in text editor and ran mdrun with only alamethicin. It went fine. But when i am tring to minimize alamethicin in popc mdrum probably does not recognize the starting of second chain and gives me following error: Warning: 1-4 interaction between 164 and 169 at distance 3.430 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file Step= 1, Dmax= 1.0e-02 nm, Epot= 3.25524e+09 Fmax= 1.00321e+09, atom= 2441 Step= 2, Dmax= 1.2e-02 nm, Epot= 2.21743e+09 Fmax= 1.82388e+08, atom= 12852 Step= 3, Dmax= 1.4e-02 nm, Epot= 1.95672e+09 Fmax= 7.44135e+07, atom= 262 Step= 4, Dmax= 1.7e-02 nm, Epot= 1.88109e+09 Fmax= 4.32188e+07, atom= 260 Step= 5, Dmax= 2.1e-02 nm, Epot= 1.84989e+09 Fmax= 2.77292e+07, atom= 262 Step= 6, Dmax= 2.5e-02 nm, Epot= 1.83083e+09 Fmax= 1.89783e+07, atom= 258 Step= 7, Dmax= 3.0e-02 nm, Epot= 1.81606e+09 Fmax= 9.97167e+06, atom= 253 Step= 8, Dmax= 3.6e-02 nm, Epot= 1.79660e+09 Fmax= 2.09557e+07, atom= 258 Step= 9, Dmax= 4.3e-02 nm, Epot= 1.78793e+09 Fmax= 1.63547e+07, atom= 259 Step= 10, Dmax= 5.2e-02 nm, Epot= 1.77532e+09 Fmax= 7.54157e+06, atom= 12539 Step= 11, Dmax= 6.2e-02 nm, Epot= 1.74488e+09 Fmax= 7.42417e+06, atom= 12539 Step= 12, Dmax= 7.4e-02 nm, Epot= 1.70998e+09 Fmax= 7.28331e+06, atom= 12539 Step= 13, Dmax= 8.9e-02 nm, Epot= 1.66920e+09 Fmax= 7.11508e+06, atom= 12539 Wrote pdb files with previous and current coordinates Back Off! I just backed up step13.pdb to ./#step13.pdb.1# Back Off! I just backed up step14.pdb to ./#step14.pdb.1# Wrote pdb files with previous and current coordinates my pdb file at 164 to 169 is: ATOM 164 CZ PHL 21 44.000 52.840 35.170 1.00 0.00 ATOM 165 HZ PHL 21 44.990 53.260 35.090 1.00 0.00 ATOM 166 CX PHL 21 38.140 50.450 37.160 1.00 0.00 ATOM 167 OY PHL 21 37.940 49.350 38.060 1.00 0.00 ATOM 168 HY PHL 21 37.040 48.940 37.950 1.00 0.00 ATOM 169 CA ACE 22 53.840 44.410 66.930 1.00 0.00 I think it is not recognising different chain. Am i right? Please help me. _ Check out some new online services at Windows Live Ideasso new they havent even been officially released yet. http://www.msnspecials.in/windowslive/___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive
RE: [gmx-users] mdrun error
Pragya, I just realized that I may have read your message incorrectly. If you'd like to send me your PDB file off-list, I'd be happy to have a look. -Justin Quoting Justin A. Lemkul [EMAIL PROTECTED]: Quoting pragya chohan [EMAIL PROTECTED]: Hi justin I placed POPC membrane in a box too of same dimension as the box of alamethicin and centred it too so that alamethicin is placed correctly in the membrane. I am attaching the pdb please have a look.Any help would be appreciated Looks like the listserv ate the PDB file, but from your description it sounds like you've generated some severe atomic overlap. Simply pasting coordinates of a protein into a membrane is sure to cause bad contacts. The proper procedure would be to create a cavity within the membrane and place the protein in it (i.e., make_hole.pl, inflategro, as I previously suggested), or using genbox, which you originally said you did. Try this (assuming you have the box dimensions correct): $ genbox -cp alamethicin.gro -cs popc.gro -o system.gro -Justin Pragya Date: Sat, 10 Nov 2007 12:42:01 -0500 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: RE: [gmx-users] mdrun error Quoting pragya chohan [EMAIL PROTECTED]: Thanks Justin for your reply. I am generating the starting structure through genbox. I added popc as solvent around alamethicin after aligning alamethicin in a box and centering it in the box and followed same procedure for popc also. Do you have any better way? In theory, that should work just fine, but I don't understand what you mean by followed the same procedure for popc. What did you do there? The first part should be all you need (alamethicin in the box, solvated with popc). Alternatively, you can use make_hole.pl or the inflategro script available through Peter Tieleman's site: http://moose.bio.ucalgary.ca/index.php?page=Translate_lipdis -Justin Date: Sat, 10 Nov 2007 10:22:45 -0500 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: RE: [gmx-users] mdrun error Since alamethicin works on its own, it suggests to me that the introduction of alamethicin into POPC is what's causing the problem, and judging by the enormous potential energies and forces, it appears to be bad contacts/atomic overlap (at least, that's been the cause of problems in my experience). How are you generating your starting structure? -JustinThanks for your help. I figured the problem out but am getting an error again. I have alamethicin in popc and water. Since alamethicin has some non standard residue i made topology file in text editor and ran mdrun with only alamethicin. It went fine. But when i am tring to minimize alamethicin in popc mdrum probably does not recognize the starting of second chain and gives me following error: Warning: 1-4 interaction between 164 and 169 at distance 3.430 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file Step= 1, Dmax= 1.0e-02 nm, Epot= 3.25524e+09 Fmax= 1.00321e+09, atom= 2441 Step= 2, Dmax= 1.2e-02 nm, Epot= 2.21743e+09 Fmax= 1.82388e+08, atom= 12852 Step= 3, Dmax= 1.4e-02 nm, Epot= 1.95672e+09 Fmax= 7.44135e+07, atom= 262 Step= 4, Dmax= 1.7e-02 nm, Epot= 1.88109e+09 Fmax= 4.32188e+07, atom= 260 Step= 5, Dmax= 2.1e-02 nm, Epot= 1.84989e+09 Fmax= 2.77292e+07, atom= 262 Step= 6, Dmax= 2.5e-02 nm, Epot= 1.83083e+09 Fmax= 1.89783e+07, atom= 258 Step= 7, Dmax= 3.0e-02 nm, Epot= 1.81606e+09 Fmax= 9.97167e+06, atom= 253 Step= 8, Dmax= 3.6e-02 nm, Epot= 1.79660e+09 Fmax= 2.09557e+07, atom= 258 Step= 9, Dmax= 4.3e-02 nm, Epot= 1.78793e+09 Fmax= 1.63547e+07, atom= 259 Step= 10, Dmax= 5.2e-02 nm, Epot= 1.77532e+09 Fmax= 7.54157e+06, atom= 12539 Step= 11, Dmax= 6.2e-02 nm, Epot= 1.74488e+09 Fmax= 7.42417e+06, atom= 12539 Step= 12, Dmax= 7.4e-02 nm, Epot= 1.70998e+09 Fmax= 7.28331e+06, atom= 12539 Step= 13, Dmax= 8.9e-02 nm, Epot= 1.66920e+09 Fmax= 7.11508e+06, atom= 12539 Wrote pdb files with previous and current coordinates Back Off! I just backed up step13.pdb to ./#step13.pdb.1# Back Off! I just backed up step14.pdb to ./#step14.pdb.1# Wrote pdb files with previous and current coordinates my pdb file at 164 to 169 is: ATOM 164 CZ PHL 21 44.000 52.840 35.170 1.00 0.00 ATOM 165 HZ PHL 21 44.990 53.260 35.090 1.00 0.00 ATOM 166 CX PHL 21 38.140 50.450 37.160 1.00 0.00 ATOM 167 OY PHL 21 37.940 49.350 38.060 1.00 0.00 ATOM 168 HY PHL 21 37.040 48.940 37.950 1.00 0.00 ATOM 169 CA ACE 22 53.840 44.410 66.930 1.00 0.00 I think it is not recognising different chain. Am i right? Please help me. _ Check out some new online
Re: [gmx-users] mdrun error
pragya chohan wrote: Hi justin I placed POPC membrane in a box too of same dimension as the box of alamethicin and centred it too so that alamethicin is placed correctly in the membrane. I am attaching the pdb please have a look. Any help would be appreciated Check out http://wiki.gromacs.org/index.php/Membrane_Simulations 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] mdrun error
hi i am trying to run mdrun for protein in membrane system. When i run mdrun i get a warning Step -2, time -0.002 (ps) LINCS WARNING relative constraint deviation after LINCS: max 2.144082 (between atoms 12433 and 12434) rms 0.216090 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 11761 11762 90.00.1633 0.2387 0.1000 11929 11930 31.70.1633 0.1000 0.1000 12097 12098 90.00.1632 0.1041 0.1000 12265 12266 90.00.1633 0.2266 0.1000 12433 12434 90.00.1633 0.3144 0.1000 starting mdrun 'alamethicin in popc' 500 steps, 0.5 ps. Warning: 1-4 interaction between 115 and 136 at distance 1.144 which is larger t han the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max inf (between atoms 12007 and 12008) rms inf bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 11619 11620 90.00.1000 0.1411 0.1000 11633 11634 90.00.1000 13155507200. 0.1000 11640 11641 90.00.1000 0.1214 0.1000 . 12619 12620 90.00.1080 0.1447 0.1080 Wrote pdb files with previous and current coordinates step 0Segmentation fault I am using shake in my mdp file. I want to restrain water. my mdp file is: title= popc128a integrator = md define = -DFLEX_SPC dt = 0.001 nsteps = 500 nstxout = 500 ns_type = grid pbc = xyz constraints = hbonds constraints_algorithm= shake coulombtype = PME vdwtype = cut-off rcoloumb = 1.0 nstlist = 10.0 Tcoupl = no pcoupl = no compressibility = 4.5e-5 gen_temp = 300 gen_vel = no Please help. Thanks in advance. _ Check out some new online services at Windows Live Ideas—so new they haven’t even been officially released yet. http://www.msnspecials.in/windowslive/___ 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] mdrun error
Check out the wiki at: http://wiki.gromacs.org/index.php/Errors#LINCS_warnings Alternatively, search the list for some of my posts from around a year ago - NVT and minimization of a lipid bilayer (or search for my name, they should come up as well). I suspect you have bad contacts in your starting structure. -Justin Quoting pragya chohan [EMAIL PROTECTED]: hi i am trying to run mdrun for protein in membrane system. When i run mdrun i get a warning Step -2, time -0.002 (ps) LINCS WARNING relative constraint deviation after LINCS: max 2.144082 (between atoms 12433 and 12434) rms 0.216090 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 11761 11762 90.00.1633 0.2387 0.1000 11929 11930 31.70.1633 0.1000 0.1000 12097 12098 90.00.1632 0.1041 0.1000 12265 12266 90.00.1633 0.2266 0.1000 12433 12434 90.00.1633 0.3144 0.1000 starting mdrun 'alamethicin in popc' 500 steps, 0.5 ps. Warning: 1-4 interaction between 115 and 136 at distance 1.144 which is larger t han the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max inf (between atoms 12007 and 12008) rms inf bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 11619 11620 90.00.1000 0.1411 0.1000 11633 11634 90.00.1000 13155507200. 0.1000 11640 11641 90.00.1000 0.1214 0.1000 . 12619 12620 90.00.1080 0.1447 0.1080 Wrote pdb files with previous and current coordinates step 0Segmentation fault I am using shake in my mdp file. I want to restrain water. my mdp file is: title= popc128a integrator = md define = -DFLEX_SPC dt = 0.001 nsteps = 500 nstxout = 500 ns_type = grid pbc = xyz constraints = hbonds constraints_algorithm= shake coulombtype = PME vdwtype = cut-off rcoloumb = 1.0 nstlist = 10.0 Tcoupl = no pcoupl = no compressibility = 4.5e-5 gen_temp = 300 gen_vel = no Please help. Thanks in advance. _ Check out some new online services at Windows Live Ideasso new they havent even been officially released yet. http://www.msnspecials.in/windowslive/___ 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 = Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ = ___ 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] mdrun error
hi i am trying to run mdrun for protein in membrane system. When i run mdrun i get a warning Check out the wiki link Justin provided. Also read http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation and make sure your setup regime is reasonable. Also, when you run grompp, pay attention to the warning messages. You'll get at least one for this .mdp file. my mdp file is: title= popc128a integrator = md define = -DFLEX_SPC dt = 0.001 nsteps = 500 nstxout = 500 ns_type = grid pbc = xyz constraints = hbonds constraints_algorithm= shake coulombtype = PME vdwtype = cut-off rcoloumb = 1.0 nstlist = 10.0 Tcoupl = no pcoupl = no compressibility = 4.5e-5 gen_temp = 300 gen_vel = no Please help. Thanks in advance. 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
Re: [gmx-users] mdrun error after 2.6nS
Hello Mark and Tsjerk, Thanks a lot for your suggestions. I have gone through that web site and it doesn't say anything very specific, for example if the system is not minimized properly it should have complained at the beginning, but the problem arises after 2.6nS! I have searched in the archive, when somebody had similar problem with PR run David suggested to look for the "center-of-mass motion removal", to give POPC+Protein, but I dont have POPC in my system. In another case advised to reduce the time step, does it mean that I should reduce the time step from 0.002 to 0.001 and do the simulations from the beginning? Another suggestion was the computing power may not be sufficient, but I don't think this will be applicable for me, b'se I am running in 8 nodes each node is with 4 processors, and the unit cell size is ~96000 atoms in total.What could be the most appropriate way to solve this problem? Many thanks in advance!Kind Regards,BlaiseBlaiseMathiasCosta,PhDDepartmentofPharmacologyandExperimentalNeuroscienceUniversityofNebraskaMedicalCenterOmaha,NE68198-5800,USA.Tel:0014025597132[EMAIL PROTECTED] wrote: -To: Discussion list for GROMACS users gmx-users@gromacs.orgFrom: Mark Abraham [EMAIL PROTECTED]Sent by: [EMAIL PROTECTED]Date: 10/02/2007 12:29PMSubject: Re: [gmx-users] mdrun error after 2.6nSBlaise Mathias-Costa wrote: Hi all, The mdrun stopped after 2.6nS after writing this error: Step 1321571, time 2643.14 (ps) LINCS WARNINGSee http://wiki.gromacs.org/index.php/Errors#LINCS_warningsMark___gmx-users mailing list gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease search the archive at http://www.gromacs.org/searchbefore 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] mdrun error after 2.6nS
Hi Blaise, Check for the first occurrence of the error in the log file and match the atom numbers against your .gro file to see which residue is involved from the beginning. Also, do you have non-standard residues/metal ions? Tell more about the system and what you're trying to do. Best, Tsjerk On 10/3/07, Blaise Mathias-Costa [EMAIL PROTECTED] wrote: Hello Mark and Tsjerk, Thanks a lot for your suggestions. I have gone through that web site and it doesn't say anything very specific, for example if the system is not minimized properly it should have complained at the beginning, but the problem arises after 2.6nS! I have searched in the archive, when somebody had similar problem with PR run David suggested to look for the center-of-mass motion removal, to give POPC+Protein, but I dont have POPC in my system. In another case advised to reduce the time step, does it mean that I should reduce the time step from 0.002 to 0.001 and do the simulations from the beginning? Another suggestion was the computing power may not be sufficient, but I don't think this will be applicable for me, b'se I am running in 8 nodes each node is with 4 processors, and the unit cell size is ~96000 atoms in total. What could be the most appropriate way to solve this problem? Many thanks in advance! Kind Regards, Blaise Blaise Mathias Costa, PhD Department of Pharmacology and Experimental Neuroscience University of Nebraska Medical Center Omaha, NE 68198-5800, USA. Tel: 001 402 559 7132 [EMAIL PROTECTED] wrote: - To: Discussion list for GROMACS users gmx-users@gromacs.org From: Mark Abraham [EMAIL PROTECTED] Sent by: [EMAIL PROTECTED] Date: 10/02/2007 12:29PM Subject: Re: [gmx-users] mdrun error after 2.6nS Blaise Mathias-Costa wrote: Hi all, The mdrun stopped after 2.6nS after writing this error: Step 1321571, time 2643.14 (ps) LINCS WARNING See http://wiki.gromacs.org/index.php/Errors#LINCS_warnings 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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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] mdrun error after 2.6nS
Blaise Mathias-Costa wrote: Hello Mark and Tsjerk, Thanks a lot for your suggestions. I have gone through that web site and it doesn't say anything very specific, for example if the system is not minimized properly it should have complained at the beginning, but the problem arises after 2.6nS! No. The numerical equations are well-defined whether or not you minimize. Whether the system is numerically or physically stable is another matter, and things could fairly easily take many picoseconds to nanoseconds in a feedback loop to get bad enough to cause LINCS warnings. The website can't be more specific, because proper system preparation is a bit of dark art and system-dependent. I have searched in the archive, when somebody had similar problem with PR run David suggested to look for the center-of-mass motion removal, to give POPC+Protein, but I dont have POPC in my system. In another case advised to reduce the time step, does it mean that I should reduce the time step from 0.002 to 0.001 and do the simulations from the beginning? Yes. Making the integration time step smaller can help you relax away from bad numerical space into good ones... once equilibrated you can then try relaxing the time step back to 2fs. Another suggestion was the computing power may not be sufficient, but I don't think this will be applicable for me, b'se I am running in 8 nodes each node is with 4 processors, and the unit cell size is ~96000 atoms in total. What could be the most appropriate way to solve this problem? Many thanks in advance! Find a reasonable equilibration protocol in the literature for a system similar to yours, try it out, and experiment. 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] mdrun error after 2.6nS
Hi all,The mdrun stopped after 2.6nS after writing this error:Step 1321571, time 2643.14 (ps) LINCS WARNINGrelative constraint deviation after LINCS:max 2.814066 (between atoms 2742 and 2745) rms 0.041434bonds that rotated more than 30 degrees:atom 1 atom 2 angle previous, current, constraint length 2742 2743 90.1 0.1728 0.0946 0.1000 2742 2744 90.0 0.1010 0.2410 0.1000 2742 2745 90.0 0.1675 0.3814 0.1000like this for 100s of times..here is the md.mdp file:cpp = cppinclude = -I../topdefine =integrator= mddt= 0.002comm_grps= Proteinnstcomm= 1nsteps= 250nstxout = 5000nstvout = 5000nstlog = 5000nstenergy= 500nstxtcout = 250xtc_grps = Proteinenergygrps= Protein non-proteinnstlist = 10BlaiseMathiasCosta,PhDDepartmentofPharmacologyandExperimentalNeuroscienceUniversityofNebraskaMedicalCenterOmaha,NE68198-5800,USA.Tel:0014025597132___ 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] mdrun error after 2.6nS
Hi Blaise, You'd better look in the log file where this starts. I bet it's either Lys-NH3+ or phosphate (ATP?) spinning like crazy. Check the archive for solutions. Best, Tsjerk On 10/2/07, Blaise Mathias-Costa [EMAIL PROTECTED] wrote: Hi all, The mdrun stopped after 2.6nS after writing this error: Step 1321571, time 2643.14 (ps) LINCS WARNING relative constraint deviation after LINCS: max 2.814066 (between atoms 2742 and 2745) rms 0.041434 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2742 2743 90.10.1728 0.0946 0.1000 2742 2744 90.00.1010 0.2410 0.1000 2742 2745 90.00.1675 0.3814 0.1000 like this for 100s of times.. here is the md.mdp file: cpp = cpp include = -I../top define = integrator = md dt= 0.002 comm_grps= Protein nstcomm = 1 nsteps = 250 nstxout = 5000 nstvout = 5000 nstlog = 5000 nstenergy = 500 nstxtcout = 250 xtc_grps = Protein energygrps = Protein non-protein nstlist= 10 Blaise Mathias Costa, PhD Department of Pharmacology and Experimental Neuroscience University of Nebraska Medical Center Omaha, NE 68198-5800, USA. Tel: 001 402 559 7132 ___ 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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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] mdrun error during pr
Hello all, I have minimized the pdb file and wish to do mdrun for position restrain dynamics. For this when I run grompp programm, it is showing error as follows. I don't understand why it is showing this error: processing coordinates... double-checking input for internal consistency... Velocities were taken from a Maxwell distribution at 300 K Reading position restraint coords from 2HT1_b4pr.gro renumbering atomtypes... converting bonded parameters... # G96ANGLES: 9382 # PDIHS: 3544 # IDIHS: 2984 # LJ14: 10898 # POSRES: 5054 # CONSTR: 6472 # SETTLE: 25639 Walking down the molecule graph to make shake-blocks initialising group options... processing index file... Analysing residue names: Opening library file /users/soft/GromacsSingle/share/gromacs/top/aminoacids.dat There are: 25641 OTHER residues There are: 648PROTEIN residues There are: 0DNA residues Analysing Protein... Analysing Other... Making dummy/rest group for T-Coupling containing 10 elements --- Program grompp, VERSION 3.3 Source code file: readir.c, line: 1131 Fatal error: Not enough ref_t and tau_t values! --- I was detained, I was restrained (The Smiths) Please anybody tell me what is wrong here ? for the reference I have attached pr.mdp file Thanking you in advance.. -- Dhananjay pr.mdp Description: Binary data ___ 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 error during pr
Hi Dhananjay, Happy new year :) Just what it says: not enough ref_t and tau_t values. You use Protein and Sol as temperature coupling groups, but likely, you also have ions in your system, which are not coupled now. You may want to use Protein and Non-Protein in stead. In case you have some non standard groups (modified amino acid, ligands, cofactors), you need to use an index group. Do not think of giving a cofactor/ligand/small group of ions a private heat bath. Check the archives using Not enough ref_t and tau_t values as search string, or simply ref_t and tau_t. You should've done that before posting, really, because this issue has been dealt with several times already, including explanations of why not giving private heat baths. Cheers, Tsjerk On 1/2/07, Dhananjay [EMAIL PROTECTED] wrote: Hello all, I have minimized the pdb file and wish to do mdrun for position restrain dynamics. For this when I run grompp programm, it is showing error as follows. I don't understand why it is showing this error: processing coordinates... double-checking input for internal consistency... Velocities were taken from a Maxwell distribution at 300 K Reading position restraint coords from 2HT1_b4pr.gro renumbering atomtypes... converting bonded parameters... # G96ANGLES: 9382 # PDIHS: 3544 # IDIHS: 2984 # LJ14: 10898 # POSRES: 5054 # CONSTR: 6472 # SETTLE: 25639 Walking down the molecule graph to make shake-blocks initialising group options... processing index file... Analysing residue names: Opening library file /users/soft/GromacsSingle/share/gromacs/top/aminoacids.dat There are: 25641 OTHER residues There are: 648PROTEIN residues There are: 0DNA residues Analysing Protein... Analysing Other... Making dummy/rest group for T-Coupling containing 10 elements --- Program grompp, VERSION 3.3 Source code file: readir.c, line: 1131 Fatal error: Not enough ref_t and tau_t values! --- I was detained, I was restrained (The Smiths) Please anybody tell me what is wrong here ? for the reference I have attached pr.mdp file Thanking you in advance.. -- Dhananjay ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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] mdrun error
In God We Trust Hi Dr Biswas Thank you for your guids.Excuse me for many question. I am using a serial version of CPMD. I made cpmdmpi script and corrected the path of cpmd.x ( /root/CPMD-3.11.1/SOURCE/cpmd.x CPMD_inp.run.),but when I run rgmx script , mdrun says:GROMACS awaits QM-result for present step ==/root/CPMD-3.11.1/SOURCE/cpmd.x: error while loading shared libraries: libsvml.so: cannot open shared object file: No such file or directoryI attached my cpmdmpi to this mail .Would appreciate if you got any more ideas what went wrong. Thank you very much in advance for your kindness and your reply. Sincerely yoursKarim MahnamInstitute of Biochemistry and Biophysics (IBB)Tehran University P.O.box 13145-1384 Tehran Iran http://www.ibb.ut.ac.ir/ #! /bin/sh /root/CPMD-3.11.1/SOURCE/cpmd.x CPMD_inp.run ___ 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 error
Mahnam wrote: In God We Trust Hi Dr Biswas Thank you for your guids.Excuse me for many question. I am using a serial version of CPMD. I made cpmdmpi script and corrected the path of cpmd.x ( /root/CPMD-3.11.1/SOURCE/cpmd.x CPMD_inp.run.),but when I run rgmx script , mdrun says: GROMACS awaits QM-result for present step == /root/CPMD-3.11.1/SOURCE/cpmd.x: error while loading shared libraries: libsvml.so: cannot open shared object file: No such file or directory Locate this file libsvml.so on your machine and make sure it is the path for the linker (edit /etc/ld.so.conf and run ldconfig). You probably want to install the CPMD package somewhere more logical like /usr/local I attached my cpmdmpi to this mail .Would appreciate if you got any more ideas what went wrong. Thank you very much in advance for your kindness and your reply. Sincerely yours Karim Mahnam Institute of Biochemistry and Biophysics (IBB) Tehran University P.O.box 13145-1384 Tehran Iran http://www.ibb.ut.ac.ir/ #! /bin/sh /root/CPMD-3.11.1/SOURCE/cpmd.x CPMD_inp.run ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] mdrun error with QM/MM with Gromacs-CPMD
Hi Maham, You need to edit the script 'cpmdmpi' so that it does have the path to access the cpmd.x from your working folder. The error message is due to that; it is not being able to access cpmd.x. 1. If you are using a serial version of CPMD then create a script 'cpmdmpi' with the following line: /.../.../cpmd.x CPMD_inp.run where you must replace the .../../ with the proper path where you have your cpmd.x. 2. If you are using a parallel version of CPMD then edit the existing cpmdmpi script accordingly by replacing the paths like: /Users/biswas/host_file so that it refers to your host_file and ~/bin/cpmd_mpi.x so that it referes to the path og your cpmd.x (Note that here I renamed the mpi version of CPMD executable cpmd.x as cpmd_mpi.x; you do not need to do that; you can maintain cpmd.x). best wishes, pb -- Pradip K. Biswas, PhD. Research Associate, Department of Chemistry; Cleveland State University, Ohio-44115 Phone: 1-216-875-9723 http://comppsi.csuohio.edu/groups/people/biswas.html On Jun 14, 2006, at 10:29 AM, Mahnam wrote: In God We Trust Hello Dr Biswas Yes, our run created the output.pdb2gmx, output.grompp_em and output.mdrun_em. Output.pdb2gmx and output.grompp_em haven't any error message but output.mdrun_em has an error .I attached it to this mail. Thank you very much in advance for your kindness and your reply. Sincerely yours Karim Mahnam Institute of Biochemistry and Biophysics (IBB) Tehran University P.O.box 13145-1384 Tehran Iran http://www.ibb.ut.ac.ir/ output.mdrun_em>___ 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] Mdrun Error
Hi gmx-users, I am setting up a membrane inserted protein simulation. The protein is mutated at a specific place and attached to a label and this is inserted into the POPC membrane (434 lipids). The label is a small molecule whose force field params were generated on PRODRG server. Everything was setup fine but when I try running the energy minimisation I get the following error Program mdrun, VERSION 3.3.1 Source code file: nsgrid.c, line: 226 Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value -2147483648. It should have been within [ 0 .. 3179 ] Please report this to the mailing list (gmx-users@gromacs.org) --- What does it mean and how to go about correcting it? Thanks in advance. Venks -- Venky Krishnamani Graduate Student, Dr. Janos K. Lanyi Lab Univerisity of California, Irvine Irvine, CA (949) 202-9466 ___ 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
