Hi, On Thursday, April 26, 2018 at 12:23:36 PM UTC-4, Christoph Junghans wrote: > > On Thu, Apr 26, 2018 at 9:12 AM, Alexander Alexander > <[email protected] <javascript:>> 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" > Each step now run for 1.5ns and it works. You mean even if I get converge result using 1 slot and 1.5ns in each step, the potential might be wrong?
> >> > >> 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. > With the different combination I used the job still crashes. > Regards, Alex > 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] <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.
