Re: [gmx-users] Segmentation fault with gromacs 3.3.3
It seems to be a problem related to the debian package. I have compiled gromacs 3.3.3 from source with gcc-4.3 and apparently the problem has dissapeared. Perhaps, the binaries on the debian package were compiled with gcc-4.1. Cesar Avila escribió: > Dear all, > I am new to the gromacs simulation package. Thus far I have been using > Charmm and NAMD, but now I am interested on testing Marrink's > Coarse-Grained Martini FF. I managed to setup an initial configuration for > a protein in a water box. After a few minimization steps, I ran the > simulation for about 10 ns until it crashed with a Segmentation fault > message. > Using tpbconv, I resumed the simulation from 10200 ps step. Nevertheless I > systematically found a segmentation fault error on step 6530. Using mdrun > -nocompact gives no additional information about the crash. When I use > mdrun -debug the simulation is able to run without any problem (until I > run out of disk space). > I found the same error to occur on both a Pentium IV (debian etch) and an > Intel Core 2 Duo (Debian lenny). Both systems > are running gromacs 3.3.3 from Debian testing packages. If anyone is > interested on reproducing the error on their own computer, I can send them > the tpr file (476K compressed). > Best regards > Cesar Avila > Universidad Nacional de Tucuman. > > > ___ > 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 with gromacs 3.3.3
Dear all, I am new to the gromacs simulation package. Thus far I have been using Charmm and NAMD, but now I am interested on testing Marrink's Coarse-Grained Martini FF. I managed to setup an initial configuration for a protein in a water box. After a few minimization steps, I ran the simulation for about 10 ns until it crashed with a Segmentation fault message. Using tpbconv, I resumed the simulation from 10200 ps step. Nevertheless I systematically found a segmentation fault error on step 6530. Using mdrun -nocompact gives no additional information about the crash. When I use mdrun -debug the simulation is able to run without any problem (until I run out of disk space). I found the same error to occur on both a Pentium IV (debian etch) and an Intel Core 2 Duo (Debian lenny). Both systems are running gromacs 3.3.3 from Debian testing packages. If anyone is interested on reproducing the error on their own computer, I can send them the tpr file (476K compressed). Best regards Cesar Avila Universidad Nacional de Tucuman. ___ 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] Uncharged Lysine Charges on Hydrogens from NH2 group 0.36??
I was wondering why the Hydrogens from the non N-terminus NH2 group in the uncharged Lysine molecule had charges of 0.36 as specified by gromacs(H1 and H2) when the Jorgensen published value for H's in RCH2NH2 was 0.35. All of the other charges in this molecule I have found in publications except for those. The overall charge of the molecule is 0.02 and if the H's were changed to 0.35 it would make the overall molecule uncharged. Would this alteration be valid? This is part of the topol.top file. [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 opls_900 1 LYSH N 1 -0.9 14.0067 ; qtot -0.9 2 opls_909 1 LYSH H1 1 0.36 1.008 ; qtot -0.54 3 opls_909 1 LYSH H2 1 0.36 1.008 ; qtot -0.18 4 opls_283 1 LYSH CA 1 0.04 12.011 ; qtot -0.14 5 opls_140 1 LYSH HA 1 0.06 1.008 ; qtot -0.08 6 opls_136 1 LYSH CB 2 -0.12 12.011 ; qtot -0.2 7 opls_140 1 LYSH HB1 2 0.06 1.008 ; qtot -0.14 8 opls_140 1 LYSH HB2 2 0.06 1.008 ; qtot -0.08 9 opls_136 1 LYSH CG 3 -0.12 12.011 ; qtot -0.2 10 opls_140 1 LYSH HG1 3 0.06 1.008 ; qtot -0.14 11 opls_140 1 LYSH HG2 3 0.06 1.008 ; qtot -0.08 12 opls_136 1 LYSH CD 4 -0.12 12.011 ; qtot -0.2 13 opls_140 1 LYSH HD1 4 0.06 1.008 ; qtot -0.14 14 opls_140 1 LYSH HD2 4 0.06 1.008 ; qtot -0.08 15 opls_292 1 LYSH CE 5 0.19 12.011 ; qtot 0.11 16 opls_140 1 LYSH HE1 5 0.06 1.008 ; qtot 0.17 17 opls_140 1 LYSH HE2 5 0.06 1.008 ; qtot 0.23 18 opls_287 1 LYSH NZ 6 -0.3 14.0067 ; qtot -0.07 19 opls_290 1 LYSH HZ1 6 0.33 1.008 ; qtot 0.26 20 opls_290 1 LYSH HZ2 6 0.33 1.008 ; qtot 0.59 21 opls_290 1 LYSH HZ3 6 0.33 1.008 ; qtot 0.92 22 opls_271 1 LYSH C 7 0.7 12.011 ; qtot 1.62 23 opls_272 1 LYSH O1 7 -0.8 15.9994 ; qtot 0.82 24 opls_272 1 LYSH O2 7 -0.8 15.9994 ; qtot 0.02 ___ 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[2]: [gmx-users] RE: can gmx be used to simulation NaCl
Tsjerk, Well, the best way would be AIMD, no doubt. William, Look here http://www.mpibpc.mpg.de/groups/grubmueller/start/teaching/vorlesung_computerbiophysik_2004/p4/index.html for an example how freezing/melting of argon is processed by means of GROMACS. TW> Hi William, TW> I'm not very sure you can simulate crystallization of salt with TW> classical MD. In any case, the force field is not parameterized to TW> reproduce crystallization or melting c.q. the melted state of NaCl. TW> It's therefore unlikely that it will produce meaningful results. The TW> best approach :) would be to determine parameters for Na/Cl for this TW> purpose. TW> Cheers, TW> Tsjerk TW> On Sat, Jun 28, 2008 at 8:47 AM, Vitaly Chaban <[EMAIL PROTECTED]> wrote: >> I see no problems to use gromacs for it. You make find the parameters >> in /top/ions.itp (include ions.itp to your topology) in your gromacs >> directory. >> Then you can use 'genconf' to create a system of the desired size. >> >>> hi gmx users, >>> Can Gromacs be used to simulate NaCl crystallization and melting? >>> If it could, where can I find pdb/top/itp etc. input files? Thanks in >>> advance. -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svobody sq.,4, Kharkiv 61077, Ukraine email: [EMAIL PROTECTED] skype: vvchaban ___ 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] High number of steps are adding
Hi Sudheer, I would say you just try to add a nanosecond to a run which still has ten to go (10+1=11). That also tells me you're not trying to extend a run already performed (properly), as it has a starting step of 0 (starting time 0.000). Then on another note, it seems that you didn't copy-paste your command line, as it is not very common to call the files .trr .tpr and .edr. Assuming you did properly feed a trajectory file, it must have been empty except for the starting frame. But we would only be able to tell for sure if you would have given the output of the command, rather than the few lines you think are most significant. Anyway, you can probably read the output again for yourself to see if this reply already describes your situation. Cheers, Tsjerk On Fri, Jun 27, 2008 at 4:04 PM, sudheer babu <[EMAIL PROTECTED]> wrote: > Hi , > When I run tpbconv command for extending run its adding high number of > steps rather than I need, > The command line is > *tpbconv -f .trr -s .tpr -e .edr -o out.tpr -extend 1000 > it has run without error at final lines it showed that > > Extending remaining runtime of by 1000 ps (now 550 steps) > Writing statusfile with starting step 0 and length550 steps... > time 0.000 and length 11000.001 ps > > Actually it suppose to be showed 1000ps(50 steps = 5lakh) > > Any comments will be appreciated > > Thanks in advance. > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- 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] Magic number error
Hi Minnale, You could try another version as was suggested... Never hurts to try. The magic number error occurs if the file is screwed. trjconv will correctly process the trajectory up to the point where the magic number error occurs, so you can restart from the last good entry in the file. Out of luck when the whole trajectory is bad. However, you didn't say what you did with the .tpr files for the separate runs, and with the individual trajectory (.xtc) files. If you still have these you can restart from there. Cheers, Tsjerk On Fri, Jun 27, 2008 at 3:54 PM, minnale <[EMAIL PROTECTED]> wrote: > > Hi Users, > I have run the protein simulation for 9ns, with 1ns each time by using > tpbconv *command, after converting all9ns .trr files to .xtc i have deleted > all .trr files. Later I have catenated all the 9ns simulation files by using > trjcat command. Now I want restart my simulation, so > when I used trjconv command for getting 9th ns .trr file its showing > following error > > The command i have given > trjconv -f 9ns_all.xtc -s 9ns_prot.tpr -o 9ns_tpbout.trr -b 8000 -e 9000 > > Program trjconv, VERSION 3.3.1 > Source code file: xtcio.c, line: 83 > > Fatal error: > Magic Number Error in XTC file (read -1727167416, should be 1995) > --- > I have searched in list archives one person > suggested(http://www.mail-archive.com/gmx-users@gromacs.org/msg08375.html) > change version to 3.2, iam using 3.3.1 > The way iam doing is doing wrong? > Could you give me any suggestion > Thanks alot in advance > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- 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] Protein is moving out of box.
Hi, Well, I think it should also be incorporated into (Gromacs) MD tutorial material. It's on my to do list. I don't think there's much use in adding a message in the mdrun output (might as well always add it, not even checking for jumps). It's basic PBC, which, with a bit of thinking, can be understood/deduced from what's in the manual and on the wiki. If people don't read that (anybody who does read that will be excluded from the set of people hereafter referred to by "they"), I assume they don't read the log file either. They'll simply run the simulation and if they have a trajectory, will do analysis (visual inspection) and run into this "problem". If they don't have a trajectory, we'll probably get a question about step files, ci-values or something along those lines. That may be a bit pessimistic, but on the other hand, let's not forget that there are many students/researchers getting involved in Gromacs every week and many of them do know how to search archives/wiki and read a manual. Also, there's a lot of (new) people asking sensible questions on this list, making it worthwhile to keep answering posts. And, to be honest, it does sometimes feel good to shout 'RTFM!' (RTFML, RTFW) when somebody's not doing his homework :p Tsjerk On Fri, Jun 27, 2008 at 6:32 PM, <[EMAIL PROTECTED]> wrote: > While the frequency with which this question is asked does of course say > something about how diligently some users are searching the list archives > and using the wiki before posting a question, it remains true that this is > causing headaches for a significant number of new users. I therefore wonder > if there is something that can be done to alleviate this. One possibility is > to automatically detect the occurrence of this during mdrun and have it > write out a notice to the user along the lines of what is refereed to in the > wiki at the end of the log file. I am saying, basically, that although this > is not a bona-fide problem, I still think that it deserves to be 'solved'. > > Chris. > > Browse the archives, check the wiki. > http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions > > Tsjerk > > On Fri, Jun 27, 2008 at 8:06 AM, Bhanu <[EMAIL PROTECTED]> wrote: > > [Hide Quoted Text] > Hi all, > am new to Gromacs. I tried a 10 ps simulation with a protein and after the > run, the protein came out of the box.. is it good or bad? How can I keep the > protein in the box? > Waiting for ur reply. > > Bhanu. > > > ___ > 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 thewww 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] RE: can gmx be used to simulation NaCl
Hi William, I'm not very sure you can simulate crystallization of salt with classical MD. In any case, the force field is not parameterized to reproduce crystallization or melting c.q. the melted state of NaCl. It's therefore unlikely that it will produce meaningful results. The best approach :) would be to determine parameters for Na/Cl for this purpose. Cheers, Tsjerk On Sat, Jun 28, 2008 at 8:47 AM, Vitaly Chaban <[EMAIL PROTECTED]> wrote: > I see no problems to use gromacs for it. You make find the parameters > in /top/ions.itp (include ions.itp to your topology) in your gromacs > directory. > Then you can use 'genconf' to create a system of the desired size. > >> hi gmx users, >> Can Gromacs be used to simulate NaCl crystallization and melting? >> If it could, where can I find pdb/top/itp etc. input files? Thanks in >> advance. >> >> Best regards, >> William > > > -- > Vitaly V. Chaban > School of Chemistry > National University of Kharkiv > Svobody sq.,4, Kharkiv 61077, Ukraine > email: [EMAIL PROTECTED] > skype: vvchaban > > ___ > 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] instalation in FC7i386
On Fri, 2008-06-27 at 18:24 -0400, Justin A. Lemkul wrote: > > Why do you want to use GCC 3.4 instead of the default compiler of the > > distribution which is GCC 4.1.2 invoked with gcc? > > > From the Downloads section of the home page: > > "WARNING: do not use the gcc 4.1.x set of compilers. They are broken. > These compilers come with recent Linux distrubutions like Fedora 5/6 etc." Hmm. The newest gcc for Fedora 7 is gcc 4.1.2-27. RHEL 5.0 had gcc 4.1.1-52 and 5.1 had 4.1.2-14. I've been using Gromacs in CentOS 5 (an RHEL 5 clone) without any problems using the default compiler and system libraries openmpi, fftw3 and so on. Try just with ./configure . If it doesn't work, then you might consider updating your OS to a supported version. -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto [EMAIL PROTECTED], p. 191 50673 -- Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of Physics, University of Helsinki, Finland [EMAIL PROTECTED] -- ___ 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
