Thank a lot to all for your inputs.. Ramya.
> Hi, > > In principle Gromacs should never just crash with a segmentation > fault, but at least give you a (perhaps cryptic) error message and > exit somewhat gracefully. > > As far as I know there is only one exception to this: If you are > using tabulated interactions the table can only be of finite size, > and thus there will be a cutoff beyond which there is no data. > Unfortunately it is not possible to determine this automatically, so > you have to set the table extension beyond your normal cutoffs in the > mdp file (table-ext). The obvious question is of course why we > don't do a check for the distance before the table lookup, but that > would be a conditional statement in the very innermost nonbonded > loop, and drastically reduce performance. > > I don't think your system will explode completely with 3fs steps > though, so the best options might be to compile with debug flag (./ > configure CFLAGS="-O3 -g") and run the simulation in a debugger to > see where it crashes. > > Cheers, > > Erik > > > On Aug 7, 2007, at 8:30 PM, Xavier Periole wrote > >> >> It is not possible to answer your question from the information you >> give. >> A lot of things can cause a segmentation fault. From compilation to >> your particular system. Put a search on the user-list, you'll get >> an idea >> of possible problems. >> >> It depends what you will be looking at but I would suggest to stick >> to a 2 fs time step. >> >> XAvier >> >>> Thanks to Xavier for his prompt reply.. >>> Actually my objective is a bit longer[50-60ns] but the problem is >>> that >>> even if i cant change the time-step to 0.003 it is exiting saying >>> segmentation fault then how is it possible with 1fs [or 4 fs as >>> suggested] which i want to do to reduce time. >>> I wanted to know where the problem is... why cant i increase the >>> time >>> step and the only error shown is 'segmentation fault'..so is the >>> reason >>> in compilation or coding or machine precision or is it with molecular >>> system wise thats what i was trying to understand.. >>> Thanks again.. >>> Ramya. >>>> >>>> 10 ns of a solvated protein of regular size should not require much >>>> computing time. >>>> >>>> Increasing the time-step above 2 fs is a solution to increase the >>>> speed of the run but then you face the problem of not integrating >>>> the fast movement correctly and this can end up in large forces >>>> and then you run crashes. >>>> You could use dummy hydrogens (see manual) and heavy water and >>>> use a 4 fs time step. This is ok for a simple protein in a box >>>> of water. >>>> >>>> But again 10ns of a protein solvated is not a long simulation. >>>> >>>> XAvier >>>>> >>>>> I am trying to perform a simulation run of 10ns for my system >>>>> [protein+waterbox].The system works fine if i use timestep[dt=0.002 >>>>> fs]. To balance the run time and time-consumption, when we try a >>>>> .mdp file with slight increase of timestep i.e., to 0.003 fs; >>>>> grompp >>>>> works fine and generates input tpr, but when going further with >>>>> mdrun, >>>>> the program crashes, giving error: >>>>> "Segmentation Fault" >>>>> >>>>> So i have to increase the number of steps[nsteps] to achieve >>>>> required >>>>> run >>>>> time.But this'll be time consuming.I am unable to figure out any >>>>> alternative. >>>>> I am using Gromacs 3.3 on IBM Power5 machine with SLES9. >>>>> Please suggest me the required to be done.Thanks in advance. >>>>> >>>>> The .mdp file i've used: >>>>> >>>>> integrator = md >>>>> ;Total simulation time: 5000 ps >>>>> :time step in femtoseconds >>>>> dt = 0.002 >>>>> ;number of steps >>>>> nsteps = 2500000 >>>>> nstxout = 100 >>>>> nstvout = 100 >>>>> nstlog = 10 >>>>> nstenergy = 10 >>>>> nstxtcout = 10 >>>>> ;xtc_grps = prot >>>>> ;group(s) to write to energy file >>>>> energygrps = protein non-protein >>>>> Frequency to update the neighbor list (and the long-range forces, >>>>> ;when using twin-range cut-off's). >>>>> nstlist = 10 >>>>> cut-off distance for the short-range neighbor list >>>>> rlist = 0.8 >>>>> ;treatment of electrostatic interactions >>>>> coulombtype = PME >>>>> rcoulomb = 0.9 >>>>> >>>>> >>>>> >>>>> *********$$$********* >>>>> >>>>> Ramya Cherukupalli, >>>>> Final year, >>>>> M.S Bioinformatics, >>>>> IIIT - H. >>>>> >>>>> >>>>> -- >>>>> This message has been scanned for viruses and >>>>> dangerous content by MailScanner, and is >>>>> believed to be clean. >>>>> >>>>> _______________________________________________ >>>>> gmx-users mailing list gmx-users@gromacs.org >>>>> http://www.gromacs.org/mailman/listinfo/gmx-users >>>>> Please search the archive at http://www.gromacs.org/search before >>>>> posting! >>>>> Please don't post (un)subscribe requests to the list. Use the >>>>> www interface or send it to [EMAIL PROTECTED] >>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>>> >>>> ----------------------------------------------------- >>>> XAvier Periole - PhD >>>> >>>> 1- Institute of Molecular Assemblies >>>> City University of New York - USA >>>> 2- Molecular Dynamics-Group >>>> University of Groningen - The Netherlands >>>> http://md.chem.rug.nl/~periole >>>> ----------------------------------------------------- >>>> _______________________________________________ >>>> gmx-users mailing list gmx-users@gromacs.org >>>> http://www.gromacs.org/mailman/listinfo/gmx-users >>>> Please search the archive at http://www.gromacs.org/search before >>>> posting! >>>> Please don't post (un)subscribe requests to the list. Use the >>>> www interface or send it to [EMAIL PROTECTED] >>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>>> >>>> -- >>>> This message has been scanned for viruses and >>>> dangerous content by MailScanner, and is >>>> believed to be clean. >>>> >>>> >>> *********$$$********* >>> Ramya Cherukupalli, >>> Final year, >>> M.S Bioinformatics, >>> IIIT - H. >>> -- >>> This message has been scanned for viruses and >>> dangerous content by MailScanner, and is >>> believed to be clean. >>> _______________________________________________ >>> 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 >> >> ----------------------------------------------------- >> XAvier Periole - PhD >> >> 1- Institute of Molecular Assemblies >> City University of New York - USA >> 2- Molecular Dynamics-Group >> University of Groningen - The Netherlands >> http://md.chem.rug.nl/~periole >> ----------------------------------------------------- >> _______________________________________________ >> 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 > > _______________________________________________ > 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 > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > *********$$$********* Ramya Cherukupalli, Final year, M.S Bioinformatics, IIIT - H. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. _______________________________________________ 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