Am 07.09.2017 um 21:10 schrieb Justin Lemkul: > > On 9/7/17 10:29 AM, Vedat Durmaz wrote: >> i really appreciate this pretty informative answer. and do you also know, >> what the infix "n254" or "n2" stands for? > Node ID. > >> what i found strange is that the error occurs after nearly 10M MD steps. in >> other copies of the same system, the error doesn't occur at all even after >> the entire predefines time span (40ns). >> >> it's a long fibril chain (>200 repeating units) of a 7mer polypeptide. the >> walls of the triclinic simulation box of size 10x8x70 nm have an initial >> distance of 1.5 nm to the fibril and i have chosen "comm-mode = linear" in >> order to keep the system centered. i'm actually wondering, whether that >> might have caused the error or whether the system will for sure crash if the >> long chain changes its shape to some spheric one that doesn't fit the slim >> box anymore. >> >> do you have any experience with that? > Nope, sorry. A crash after a long simulation time is very unusual and > hard to diagnose. Normally things fail rather quickly. Does your > GROMACS installation pass all regression tests? > > -Justin >
ok. since i haven't compiled this gromacs installation i haven't seen any results of its test runs. anyway, i carried out the simulations again and this time no error occurred. thanks again for your help! vedat
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