Hi, Those are all good things, but have you actually got out a molecular viewer and looked at the input and output of your resolution conversion?
Mark On Wed, Jul 12, 2017 at 4:25 PM edesantis <edesan...@roma2.infn.it> wrote: > Hi, > thanks for the prompt answer, > > > I've found the same problem even if I try to convert the coarse grained > pdb obtained from martinize.py, so in that case it should be not a > problem to have the conversion, for this reason I though it is a > methodological problem... > > I've seen the blowing-up issues , but I think: > - the timestep is enough small (0.0002) > -the system should be enough minimized via the previous steps (in fact > the sd converged to the machine precision in both cases, actually the > potential energy is ~10^5, but I don't know how to reduce it, I tried a > cg after the sd, but the proble is still there) > -there in not any pressure coupling > -I've tried a different temperature coupling (berensden, nose-hoover) > and it doesn't work > - the md stops at the first step, so there is not any .edr file produced > to be looked at > > > > I don't know what else to do... > > maybe, do you know another conversion protocol to use?? > > > thank you again > Emiliano > > On 2017-07-12 15:11, Mark Abraham wrote: > > Hi, > > > > Sounds like you might be > > http://www.gromacs.org/Documentation/Terminology/Blowing_Up because the > > conversion doesn't work for your configuration. You should start by > > doing a > > visual check of the configuration for sanity, then follow the advice in > > that link. > > > > Mark > > > > On Wed, Jul 12, 2017 at 3:04 PM edesantis <edesan...@roma2.infn.it> > > wrote: > > > >> dear all, > >> > >> I am facing a problem with the conversion from Martini CG > >> representation > >> to All-atomistic one. > >> > >> I am using the initram.sh wrapper around the backward.py. > >> > >> There is a LINCS warning problem when the energy relaxation is > >> performed > >> using position restrained md > >> (I've also tried to run grompp and mdrun commands directly from the > >> terminal and the error persists, so it is not a wrapper problem). > >> > >> this is the .mdp file generated by the script: > >> > >> "define = -DPOSRES > >> integrator = md > >> nsteps = 500 > >> dt = 0.0002 > >> pbc = xyz > >> > >> rcoulomb = 0.9 > >> rlist = 0.9 > >> rvdw = 0.9 > >> > >> tcoupl = v-rescale > >> ref_t = 200 > >> tau_t = 0.1 > >> tc_grps = System > >> > >> gen_vel = yes > >> gen_temp = 300 > >> > >> constraints = all-bonds " > >> > >> > >> this is the error I found in the .log file: > >> > >> "Fatal error: > >> Too many LINCS warnings (1034) > >> If you know what you are doing you can adjust the lincs warning > >> threshold in your mdp file > >> or set the environment variable GMX_MAXCONSTRWARN to -1, > >> but normally it is better to fix the problem " > >> > >> I tired to comment the constrains part and all is working, but since > >> the > >> structure should not be altered too much, I think the constraints are > >> required (if I constrain only the h-bonds, it is also working). > >> > >> I've also added to the .mdp file the lines: > >> " lincs-order = 4 (or 2 or 8) > >> lincs-iter = 1 (or 2 or 10) > >> " > >> but it is still not working... > >> > >> > >> any of you have suggestions to solve the problem?? > >> how is it possible to change the environment variable? > >> > >> > >> thanks in advance for your help > >> Emiliano > >> > >> -- > >> Emiliano De Santis > >> > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-requ...@gromacs.org. > >> > > -- > Emiliano De Santis > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
