Re: [gmx-users] Re: forward and reverse free energy not consistant (Li Qiang) (Diana Lousa)
Thanks for advice. I will test it. Qiang ggroenh wrote: To rule out a sampling problem you can perform the simulations with everything else frozen or position restraints. Both backwards and forwards, and you can do it very fast, as there is nothing to equilibrate. If there is still a discrepancy between the two paths, you should suspect a problem with your topology, with the bonded interactions for instance. Gerrit ___ 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 ___ 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] forward and reverse free energy not consistant
Dear all Gmxers, I am calculating a mutation free energy from L<->A for a five AA peptides using G96 53a6 force field. however, my dG_for and dG_rev is quite different. dG_for(lambda=0.00) = - 9.9 kJ/mol dG_rev(lambda=1.00) = 1.33 kJ/mol Is there anything wrong with setting up topologies? Here is the [atoms] part for morphed atoms. and I attached the full .top in the attachment. For L->A: [ atoms ] 17CH2 2LEU CB 6 0 14.027 CH3 0 15.035; qtot 1 18CH1 2LEU CG 7 0 13.019 DUM 0 13.019; qtot 1 19CH3 2LEUCD1 7 0 15.035 DUM 0 15.035; qtot 1 20CH3 2LEUCD2 7 0 15.035 DUM 0 15.035; qtot 1 For A->L : [ atoms ] 17CH3 2ALA CB 6 0 15.035 CH2014.027; qtot 1 60DUM 6DUMDUM 24 013.019 CH1013.019 61DUM 6DUMDUM 24 015.035 CH3015.035 62DUM 6DUMDUM 24 015.035 CH3015.035 thanks for help LQ topol_A2L.top Description: application/extension-top topol_L2A.top Description: application/extension-top ___ 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] free energy calculation
Dear all, Can anybody tell me how to calculate the free energy difference after running simulation with lamda(0, 0.1,...1)? I am following the tutorial on wiki, but i have no idea about the details to do the "data analysis". any software can do it? and any reference for the instruction? I am new here. thanks a lot Qiang ___ 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] center of mass removal
hi Christian,
Thanks for the reply. I have plotted the the rate of center of mass
motion and found there are peaks with certain time interval. I think
that is not only a visual problem but like fly ice cube problem(not
sure). As a comparison, when a large protein is simulated, the
rate(velocity) of COM is "constant".
Yes. the default way GROMACS do is system COM removal at each step.
how does the program remove this center of mass motion?
Merry Xmas
Qiang
On Wed, 2007-12-26 at 14:52 +0800, Christian Burisch wrote:
> Li Qiang schrieb:
> > Dear all,
>
> Hi Qiang,
>
> > I am simulating short peptide in GROMACS. Center of mass need to be
> > removed to keep the peptide from jumping out.
>
> I guess this is only a visual problem, but read page 18 in the manual.
>
> > I have two questions about this:
> > 1, when I remove COM of the peptide using comm_grps, do I need to put
> > the solvent(including the counter ion) at the same time for COM removal?
>
> In a solvent simulation I would do linear COM removal of the whole
> system only (as is done automatically). I guess there will be
> artifacts if you just remove the translation of the solute (slight
> collisions with the solvent on one side and underpressure on the other
> side). But anyone please correct me if there is a clever algorithm to
> prevent that! ;-)
>
> > or the program will take care of the whole system automatically?
>
> Gromacs does COM removal automatically ("linear" on a group called
> "rest", which means the whole system if no comm_grps is given, as
> written in the log file) if you don't explicitly turn it off ("none"
> or nstcomm=0).
>
> Merry Xmas
>
> Christian
>
>
> > 2, Can anybody tell how the COM removal is achieved (in gromacs or other
> > methods available)?
> >
> > thank you
> >
> > Qiang
> >
> > ___
> > gmx-users mailing listgmx-users@gromacs.org
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> >
>
___
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[gmx-users] center of mass removal
Dear all, I am simulating short peptide in GROMACS. Center of mass need to be removed to keep the peptide from jumping out. I have two questions about this: 1, when I remove COM of the peptide using comm_grps, do I need to put the solvent(including the counter ion) at the same time for COM removal? or the program will take care of the whole system automatically? 2, Can anybody tell how the COM removal is achieved (in gromacs or other methods available)? thank you Qiang ___ 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] plot velocity of center of mass
Dear all users, I want to plot the velocities of center of mass for my peptide. Reading from 3.3 manual, there seems to be two ways--g_com and g_traj. However, 1, g_com can not be found in /usr/local/gromacs/bin. Is there anything missed for my installation? 2, $> g_traj -f md.trr -s md.tpr -ov veloc.xvg -com but there is only one line in the output file, i.e. the last frame of my trajectory. The same thing happens for "-of force.xvg". but for "-ox -coord.xvg" all the times are written out! Is there any physical meaning for this? or something is wrong? GROMACS 3.3.1 is used. thank you Qiang ___ 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] make gives error in futil.c with mpi and ccc-6.5.6.002-1
Dear Gromacs Users, I wonder if it is normal for a protein to move out of the box during MD runs. periodic boundary conditions are applied. system is neutralized. 0.9nm for the distance between box side and protein. thanks the md.mdp for your reference: title = trp-Cage cpp = /usr/bin/cpp constraints = none integrator = md dt = 0.002 ; ps ! nsteps = 250 ; total 5000 ps. nstcomm = 1 nstxout = 500 ; collect data every 1 ps nstvout = 0 nstfout = 0 nstlist = 5 ns_type = grid rlist = 1.0 coulombtype= PME rcoulomb= 1.0 rvdw= 1.0 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in two groups Tcoupl= berendsen tau_t = 0.1 tc_grps = system ref_t = 498 ; Pressure coupling is on Pcoupl = berendsen tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 ___ 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] gmx 3.3.2 explodes with libc.so.6
Yes. Mine is 32-bit. Intel P4 3.0G. On Fri, 2007-11-09 at 10:47 +, Bruce Milne wrote: > Dear Li Qiang, > > >> it seems another guy get the same error(cannot pass gmxtest with > >> rb1/acetonitrilRF) as me. and it sounds like the compatible problem > >> between GROMACS 3.3.2 and and UBUNTU 7.10. Both are rather new. > >> > >> Herein I just suggest and hope others may help to install 3.3.2 on new > >> ubuntu 7.10 to confirm the problem. > > > I have just installed 3.3.2 on my (64-bit) Ubuntu 7.10 machine > (dual-core Athlon64 4000+, 2GB RAM) and run the serial tests. All the > single and double precision tests passed with and without assembly loop > optimizations so I guess it's not simply Ubuntu 7.10 that is to blame > (unless what you are seeing is a 32-bit distribution-specific problem?). > > Cheers, > > Bruce > ___ 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] gmx 3.3.2 explodes with libc.so.6
I see. thanks for the information. but one of my friends nearby failed on this combination just few hours ago. Maybe we need more test for the conclusion. Li Qiang On Fri, 2007-11-09 at 10:47 +, Bruce Milne wrote: > Dear Li Qiang, > > >> it seems another guy get the same error(cannot pass gmxtest with > >> rb1/acetonitrilRF) as me. and it sounds like the compatible problem > >> between GROMACS 3.3.2 and and UBUNTU 7.10. Both are rather new. > >> > >> Herein I just suggest and hope others may help to install 3.3.2 on new > >> ubuntu 7.10 to confirm the problem. > > > I have just installed 3.3.2 on my (64-bit) Ubuntu 7.10 machine > (dual-core Athlon64 4000+, 2GB RAM) and run the serial tests. All the > single and double precision tests passed with and without assembly loop > optimizations so I guess it's not simply Ubuntu 7.10 that is to blame > (unless what you are seeing is a 32-bit distribution-specific problem?). > > Cheers, > > Bruce > ___ 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] gmx 3.3.2 explodes with libc.so.6
hi all, it seems another guy get the same error(cannot pass gmxtest with rb1/acetonitrilRF) as me. and it sounds like the compatible problem between GROMACS 3.3.2 and and UBUNTU 7.10. Both are rather new. Herein I just suggest and hope others may help to install 3.3.2 on new ubuntu 7.10 to confirm the problem. thanks to all the information Li Qiang On Fri, 2007-11-09 at 00:11 +0800, Yang Ye wrote: > got solved? > > I am using Ubuntu 6.10 after updating its packages, gromacs still fail > on the simple/rb1 test, in a symptom similar to Li Qiang's. > 3.3.1 is able to pass all the tests. > > Another thing is that acetonitrilRF also failed in 3.3.2 (both on > Opteron and P4) but not with 3.3.1 > --- > Program mdrun, VERSION 3.3.2 > Source code file: network.c, line: 437 > > Routine should not have been called: > gmx_sumi > --- > > Perhaps gmx-developer is a better place for this thread. > > Regards, > Yang Ye > > On 11/8/2007 5:03 AM, Dmytro Kovalskyy wrote: > > The problem was solved by updating system libraries. > > > > [EMAIL PROTECTED] exchange]# rpm -qf /lib/libc.so.6 > > glibc-core-2.5-alt5 > > > > Sorry, for wrong hypothesis. > > > > Dima > > > > ___ > > gmx-users mailing listgmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] can not pass gmxtest
hi, I just try to remove and rebuild and install GROMACS. This time the self-built one also can not pass the test. The same errors are reported: + [EMAIL PROTECTED]:~/gromacs-3.3.2$ sudo make tests (if test -d "gmxtest"; then cd "gmxtest"; ./gmxtest.pl all; cd ..; \ else echo "No gmxtest directory found. Please download and unpack it here.";\ fi) *** glibc detected *** mdrun: realloc(): invalid next size: 0x08296ec8 *** === Backtrace: = /lib/tls/i686/cmov/libc.so.6[0x401b1b0c] /lib/tls/i686/cmov/libc.so.6(realloc+0x106)[0x401b3a66] mdrun[0x8137065] === Memory map: 08048000-08278000 r-xp 08:04 2567562/usr/local/gromacs/bin/mdrun 08278000-0827f000 rwxp 0023 08:04 2567562/usr/local/gromacs/bin/mdrun 0827f000-082a5000 rwxp 0827f000 00:00 0 [heap] 4000-4001a000 r-xp 08:04 2747274/lib/ld-2.6.1.so 4001a000-4001c000 rwxp 00019000 08:04 2747274/lib/ld-2.6.1.so 4001c000-4001f000 rwxp 4001c000 00:00 0 4001f000-40029000 r-xp 08:04 2747267/lib/libgcc_s.so.1 40029000-4002a000 rwxp a000 08:04 2747267/lib/libgcc_s.so.1 4002c000-4004 r-xp 08:04 2747206/lib/tls/i686/cmov/libnsl-2.6.1.so 4004-40042000 rwxp 00013000 08:04 2747206/lib/tls/i686/cmov/libnsl-2.6.1.so 40042000-40044000 rwxp 40042000 00:00 0 40044000-4011b000 r-xp 08:04 2488482/usr/lib/libfftw3f.so.3.1.2 4011b000-40121000 rwxp 000d7000 08:04 2488482/usr/lib/libfftw3f.so.3.1.2 40121000-40144000 r-xp 08:04 2747187/lib/tls/i686/cmov/libm-2.6.1.so 40144000-40146000 rwxp 00023000 08:04 2747187/lib/tls/i686/cmov/libm-2.6.1.so 40146000-4028a000 r-xp 08:04 2747161/lib/tls/i686/cmov/libc-2.6.1.so 4028a000-4028b000 r-xp 00143000 08:04 2747161/lib/tls/i686/cmov/libc-2.6.1.so 4028b000-4028d000 rwxp 00144000 08:04 2747161/lib/tls/i686/cmov/libc-2.6.1.so 4028d000-40291000 rwxp 4028d000 00:00 0 40291000-402a5000 r-xp 08:04 2747231/lib/tls/i686/cmov/libpthread-2.6.1.so 402a5000-402a7000 rwxp 00013000 08:04 2747231/lib/tls/i686/cmov/libpthread-2.6.1.so 402a7000-402aa000 rwxp 402a7000 00:00 0 4030-40321000 rwxp 4030 00:00 0 40321000-4040 ---p 40321000 00:00 0 bf808000-bf82 rwxp bf808000 00:00 0 [stack] e000-f000 r-xp 00:00 0 [vdso] FAILED. Check files in rb1 1 out of 16 simple tests FAILED FAILED. Check files in acetonitrilRF FAILED. Check files in dec+water 2 out of 14 complex tests FAILED All 63 kernel tests PASSED All 45 pdb2gmx tests PASSED + On Wed, 2007-11-07 at 16:45 +0800, Yang Ye wrote: > To "uninstall" GROMACS, you can type "which mdrun" to get its path and > try to figure out where it has been installed. For GROMACS, it may > reside under > /usr/local/gromacs > > remove the whole directory with rm -fr. > > To ensure that you are using the self-built GROMACS, look for a file > > GMXRC.bash in the locations which you can find in "make install". > > Run it with > source /path/to/GMXRC.bash > > Then you can make sure that you are using your own version. > > Put that line "source ..." into ~/.bashrc shall make it default for > every login session. > > Regards, > Yang Ye > > On 11/7/2007 4:35 PM, Li Qiang wrote: > > hi yang, > > > > thanks for the reply. Do you mean that the installation from SMP is not > > right? > > > > The error with self-compiled gromacs is in position restrain step with > > unusual distances and the mdrun stops at step0 with "Segmentation fault > > (core dumped)". but the mdrun with constraint can run, though I do not > > know if it is right. > > > > The possible reason is that I install from SMP of ubuntu but forget to > > remove the self-compiled one. Several days ago the gromacs version from > > SMP is 3.3.1. I though it was simpler to install GROMACS automatically > > from that. > > > > Could tell me how to remove GROMACS entirely so that I can reinstall > > from fresh? Hope we can do it. > > > > thank you very much. > > > > Li Qiang > > > > On Wed, 2007-11-07 at 16:16 +0800, Yang Ye wrote: > > > >> Hi, > >> > >> You shall always try to build gromacs yourself. What's the error with > >> tutorial? > >> > >> Regards, > >> Yang Ye > >> > >> On 11/7/2007 10:14 AM, Li Qiang wrote: > >> > >>> hi all, > >>> > >>> I newly installed GROMACS on UBUNTU 7.10 from Synaptic Package > >
Re: [gmx-users] can not pass gmxtest
hi yang, thanks for the reply. Do you mean that the installation from SMP is not right? The error with self-compiled gromacs is in position restrain step with unusual distances and the mdrun stops at step0 with "Segmentation fault (core dumped)". but the mdrun with constraint can run, though I do not know if it is right. The possible reason is that I install from SMP of ubuntu but forget to remove the self-compiled one. Several days ago the gromacs version from SMP is 3.3.1. I though it was simpler to install GROMACS automatically from that. Could tell me how to remove GROMACS entirely so that I can reinstall from fresh? Hope we can do it. thank you very much. Li Qiang On Wed, 2007-11-07 at 16:16 +0800, Yang Ye wrote: > Hi, > > You shall always try to build gromacs yourself. What's the error with > tutorial? > > Regards, > Yang Ye > > On 11/7/2007 10:14 AM, Li Qiang wrote: > > hi all, > > > > I newly installed GROMACS on UBUNTU 7.10 from Synaptic Package > > Manager(SPM). However, it can not pass the gamxtest with log as below, > > but Tutorials seems OK. > > Actually I try to compile myself at the beginning. It is weird that the > > self-compiled one can pass the test but failed to run Tutorials with > > Segmental fault at PR MD step. > > > > Does anyboby know how to solve it? and how to uninstall GROMACS clear? > > thanks a lot. > > > > output from gmxtest: > > ++ > > *** glibc detected *** mdrun: realloc(): invalid next size: 0x08076ec8 > > *** > > === Backtrace: = > > /lib/tls/i686/cmov/libc.so.6[0xb7a45b0c] > > /lib/tls/i686/cmov/libc.so.6(realloc+0x106)[0xb7a47a66] > > /usr/lib/libgmx.so.4(save_realloc+0x39)[0xb7cbe439] > > /usr/lib/libgmx.so.4(mk_graph+0x494)[0xb7cadde4] > > mdrun[0x8059f50] > > mdrun[0x805a72a] > > /lib/tls/i686/cmov/libc.so.6(__libc_start_main+0xe0)[0xb79f0050] > > mdrun[0x804a491] > > === Memory map: > > 08048000-08062000 r-xp 08:04 2490502/usr/bin/mdrun > > 08062000-08063000 rw-p 00019000 08:04 2490502/usr/bin/mdrun > > 08063000-08085000 rw-p 08063000 00:00 0 [heap] > > b780-b7821000 rw-p b780 00:00 0 > > b7821000-b790 ---p b7821000 00:00 0 > > b79cc000-b79cd000 rw-p b79cc000 00:00 0 > > b79cd000-b79cf000 r-xp 08:04 > > 2747181/lib/tls/i686/cmov/libdl-2.6.1.so > > b79cf000-b79d1000 rw-p 1000 08:04 > > 2747181/lib/tls/i686/cmov/libdl-2.6.1.so > > b79d1000-b79d5000 r-xp 08:04 > > 2486327/usr/lib/libXdmcp.so.6.0.0 > > b79d5000-b79d6000 rw-p 3000 08:04 > > 2486327/usr/lib/libXdmcp.so.6.0.0 > > b79d6000-b79d8000 r-xp 08:04 > > 2485527/usr/lib/libXau.so.6.0.0 > > b79d8000-b79d9000 rw-p 1000 08:04 > > 2485527/usr/lib/libXau.so.6.0.0 > > b79d9000-b79da000 rw-p b79d9000 00:00 0 > > b79da000-b7b1e000 r-xp 08:04 > > 2747161/lib/tls/i686/cmov/libc-2.6.1.so > > b7b1e000-b7b1f000 r--p 00143000 08:04 > > 2747161/lib/tls/i686/cmov/libc-2.6.1.so > > b7b1f000-b7b21000 rw-p 00144000 08:04 > > 2747161/lib/tls/i686/cmov/libc-2.6.1.so > > b7b21000-b7b24000 rw-p b7b21000 00:00 0 > > b7b24000-b7c11000 r-xp 08:04 > > 2486347/usr/lib/libX11.so.6.2.0 > > b7c11000-b7c15000 rw-p 000ed000 08:04 > > 2486347/usr/lib/libX11.so.6.2.0 > > b7c15000-b7c2a000 r-xp 08:04 > > 2488182/usr/lib/libICE.so.6.3.0 > > b7c2a000-b7c2c000 rw-p 00014000 08:04 > > 2488182/usr/lib/libICE.so.6.3.0 > > b7c2c000-b7c2d000 rw-p b7c2c000 00:00 0 > > b7c2d000-b7c34000 r-xp 08:04 2487000/usr/lib/libSM.so.6.0.0 > > b7c34000-b7c35000 rw-p 6000 08:04 2487000/usr/lib/libSM.so.6.0.0 > > b7c35000-b7c58000 r-xp 08:04 > > 2747187/lib/tls/i686/cmov/libm-2.6.1.so > > b7c58000-b7c5a000 rw-p 00023000 08:04 > > 2747187/lib/tls/i686/cmov/libm-2.6.1.so > > b7c5a000-b7c6e000 r-xp 08:04 > > 2747206/lib/tls/i686/cmov/libnsl-2.6.1.so > > b7c6e000-b7c7 rw-p 00013000 08:04 > > 2747206/lib/tls/i686/cmov/libnsl-2.6.1.so > > b7c7-b7c73000 rw-p b7c7 00:00 0 > > b7c73000-b7e27000 r-xp 08:04 > > 2491023/usr/lib/libgmx.so.4.0.0 > > b7e27000-b7e3 rw-p 001b3000 08:04 > > 2491023/usr/lib/libgmx.so.4.0.0 > > b7e3-b7e35000 rw-p b7e3 00:00 0 > > b7e35000-b7f4a000 r-xp 08:04 2491025/usr/lib/libmd.so.4.0.0 > > b7f4a000-b7f4b000 rw-p 00114000 08:04 2491025/usr/lib/libmd.so.4.0.0 > &g
[gmx-users] can not pass gmxtest
hi all, I newly installed GROMACS on UBUNTU 7.10 from Synaptic Package Manager(SPM). However, it can not pass the gamxtest with log as below, but Tutorials seems OK. Actually I try to compile myself at the beginning. It is weird that the self-compiled one can pass the test but failed to run Tutorials with Segmental fault at PR MD step. Does anyboby know how to solve it? and how to uninstall GROMACS clear? thanks a lot. output from gmxtest: ++ *** glibc detected *** mdrun: realloc(): invalid next size: 0x08076ec8 *** === Backtrace: = /lib/tls/i686/cmov/libc.so.6[0xb7a45b0c] /lib/tls/i686/cmov/libc.so.6(realloc+0x106)[0xb7a47a66] /usr/lib/libgmx.so.4(save_realloc+0x39)[0xb7cbe439] /usr/lib/libgmx.so.4(mk_graph+0x494)[0xb7cadde4] mdrun[0x8059f50] mdrun[0x805a72a] /lib/tls/i686/cmov/libc.so.6(__libc_start_main+0xe0)[0xb79f0050] mdrun[0x804a491] === Memory map: 08048000-08062000 r-xp 08:04 2490502/usr/bin/mdrun 08062000-08063000 rw-p 00019000 08:04 2490502/usr/bin/mdrun 08063000-08085000 rw-p 08063000 00:00 0 [heap] b780-b7821000 rw-p b780 00:00 0 b7821000-b790 ---p b7821000 00:00 0 b79cc000-b79cd000 rw-p b79cc000 00:00 0 b79cd000-b79cf000 r-xp 08:04 2747181/lib/tls/i686/cmov/libdl-2.6.1.so b79cf000-b79d1000 rw-p 1000 08:04 2747181/lib/tls/i686/cmov/libdl-2.6.1.so b79d1000-b79d5000 r-xp 08:04 2486327/usr/lib/libXdmcp.so.6.0.0 b79d5000-b79d6000 rw-p 3000 08:04 2486327/usr/lib/libXdmcp.so.6.0.0 b79d6000-b79d8000 r-xp 08:04 2485527/usr/lib/libXau.so.6.0.0 b79d8000-b79d9000 rw-p 1000 08:04 2485527/usr/lib/libXau.so.6.0.0 b79d9000-b79da000 rw-p b79d9000 00:00 0 b79da000-b7b1e000 r-xp 08:04 2747161/lib/tls/i686/cmov/libc-2.6.1.so b7b1e000-b7b1f000 r--p 00143000 08:04 2747161/lib/tls/i686/cmov/libc-2.6.1.so b7b1f000-b7b21000 rw-p 00144000 08:04 2747161/lib/tls/i686/cmov/libc-2.6.1.so b7b21000-b7b24000 rw-p b7b21000 00:00 0 b7b24000-b7c11000 r-xp 08:04 2486347/usr/lib/libX11.so.6.2.0 b7c11000-b7c15000 rw-p 000ed000 08:04 2486347/usr/lib/libX11.so.6.2.0 b7c15000-b7c2a000 r-xp 08:04 2488182/usr/lib/libICE.so.6.3.0 b7c2a000-b7c2c000 rw-p 00014000 08:04 2488182/usr/lib/libICE.so.6.3.0 b7c2c000-b7c2d000 rw-p b7c2c000 00:00 0 b7c2d000-b7c34000 r-xp 08:04 2487000/usr/lib/libSM.so.6.0.0 b7c34000-b7c35000 rw-p 6000 08:04 2487000/usr/lib/libSM.so.6.0.0 b7c35000-b7c58000 r-xp 08:04 2747187/lib/tls/i686/cmov/libm-2.6.1.so b7c58000-b7c5a000 rw-p 00023000 08:04 2747187/lib/tls/i686/cmov/libm-2.6.1.so b7c5a000-b7c6e000 r-xp 08:04 2747206/lib/tls/i686/cmov/libnsl-2.6.1.so b7c6e000-b7c7 rw-p 00013000 08:04 2747206/lib/tls/i686/cmov/libnsl-2.6.1.so b7c7-b7c73000 rw-p b7c7 00:00 0 b7c73000-b7e27000 r-xp 08:04 2491023/usr/lib/libgmx.so.4.0.0 b7e27000-b7e3 rw-p 001b3000 08:04 2491023/usr/lib/libgmx.so.4.0.0 b7e3-b7e35000 rw-p b7e3 00:00 0 b7e35000-b7f4a000 r-xp 08:04 2491025/usr/lib/libmd.so.4.0.0 b7f4a000-b7f4b000 rw-p 00114000 08:04 2491025/usr/lib/libmd.so.4.0.0 b7f4b000-b7f4c000 rw-p b7f4b000 00:00 0 b7f4e000-b7f58000 r-xp 08:04 2747267/lib/libgcc_s.so.1 b7f58000-b7f59000 rw-p a000 08:04 2747267/lib/libgcc_s.so.1 b7f59000-b7f5c000 rw-p b7f59000 00:00 0 b7f5c000-b7f76000 r-xp 08:04 2747274/lib/ld-2.6.1.so b7f76000-b7f78000 rw-p 00019000 08:04 2747274/lib/ld-2.6.1.so bfa98000-bfaad000 rwxp bfa98000 00:00 0 [stack] bfaad000-bfaae000 rw-p bfaad000 00:00 0 e000-f000 r-xp 00:00 0 [vdso] FAILED. Check files in rb1 1 out of 16 simple tests FAILED FAILED. Check files in acetonitrilRF FAILED. Check files in dec+water 2 out of 14 complex tests FAILED All 63 kernel tests PASSED All 45 pdb2gmx tests PASSED ___ 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
