On Thu, Apr 26, 2018 at 9:12 AM, Alexander Alexander <[email protected]> wrote: > Thank Christoph. > > On Thursday, April 26, 2018 at 10:49:25 AM UTC-4, Christoph Junghans wrote: >> >> On Thu, Apr 26, 2018 at 1:37 AM, Alexander Alexander >> <[email protected]> wrote: >> > >> > Dear all, >> > Using IBI over nonbonded parameters I intend to parameterize the CG >> > parameter for a molecule which has 3 beads in 2 types. The initial >> > CG-configuration.gro was extracted from the trajectory of an atomistic >> > simulation over the system which I am pretty sure that it has been >> > enough >> > equilibrated with different ensemble and for enough computational time >> > as >> > all of its properties are being stable by time. Even in each CG step I >> > do >> > the minimization (pre.simulation). However, the CG nonbonded >> > parametrization >> > crashes due to the issue of "1 of the 692 bonded interactions could not >> > be >> > calculated because some atoms involved moved further apart than the >> > multi-body ...". >> Usually that error means your system is exploding. >> Have a look at the simulation movie with vmd. > > Yes, I see how the system somehow collapses. BUT: Actually it works fine (it > is now in step_003) with "mpirun -np 1 gmx_mpi mdrun" and no explosion > happens in the system, which means the system itself is enough stable, but I > really need more than 1 slot and more than 1 slot even with -np 2 the > crashing shows up again. So, I think it is more the matter of computation > rather than the physics of the system, am I right? I want -np 16. On a single node the domains are just bigger and hence it takes longer to trigger the " bonded interactions could not be calculated" >> >> Try to replace the related bonded interaction with a potential with a >> stronger spring constant. > > I have already changed the following lines one by one or together I hope > correct!?; > [ bonds ] > 1 2 8 1 1 ; 1:bond-LA-C:1 ------ changed -----> 1 2 X Y Z with > different combinations of X =1 or2, Y=1,4 and Z = 1000 ---6000 > [ angles ] > 1 2 3 8 1 1 ; 1:angle-LA-C-RA:1 ------ changed -----> 1 2 3 X Y' Z I think that is correct, but I would consult the gromacs manual to be sure.
Christoph > .... > But still the problem is here. > > Regards, > Alex >> >> >> Christoph >> > I have been trying most of the suggested solutions for such an error, >> > but no >> > success. I even reduced the number of beads from my initial mapping (5 >> > beads) to the current one (3 beads), but it crashes even earlier. >> > The materials for this system have been shared in the below link, I >> > would be >> > so appreciated if you could kindly help me solve the problem. >> > https://drive.google.com/open?id=12VIJ3W9BgE0IlEls8ZlJ1uIAG3jqbNG0 >> > >> > Thank you very much. >> > >> > Best regards, >> > Alex >> > >> > -- >> > You received this message because you are subscribed to the Google >> > Groups >> > "votca" group. >> > To unsubscribe from this group and stop receiving emails from it, send >> > an >> > email to [email protected]. >> > To post to this group, send email to [email protected]. >> > Visit this group at https://groups.google.com/group/votca. >> > For more options, visit https://groups.google.com/d/optout. >> >> >> >> -- >> Christoph Junghans >> Web: http://www.compphys.de > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
