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] <javascript:>> 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.
> 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 .... 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] <javascript:>. > > To post to this group, send email to [email protected] > <javascript:>. > > 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.
