Thanks Christopher for the answer. Will take the bigger system and see if it works. Thanks.
Yogesh > On 16-Jun-2017, at 12:24 AM, Christopher Neale <chris.ne...@alum.utoronto.ca> > wrote: > > Dear Yogesh: > > > you either need to make the system larger in the dimension(s) of your pulling > or you need to not pull out to such a far distance. Once you straighten that > out, and if the lincs problems remain, then we can tackle that separately. > > > What are your mdp options for pulling? Maybe you really only care about Z > dimension pulling but you are actually pulling in XYZ and that could have > some effect on largest distance vs box size? I presume that if you pull only > in Z and you have large Z but small X and Y that the simulation will not > complain, but I don't remember. > > ________________________________ > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of jay patil > <jpatil...@gmail.com> > Sent: 15 June 2017 09:18:39 > To: gmx-us...@gromacs.org > Subject: [gmx-users] Errors during pull constrained NPT simulation for > permeability calculations. > > Hi Experts, > I am doing simulation for permeability calculation. > In my simulation, water molecule is constrained (inside the Bilayer) at > fixed distance from centre of the Bilayer. And another constrained in bulk > water. I am doing equilibration with V-rescale(thermostat) and berendsen(for > barostat) for 5ns and then production run with Nose-Hoover and > parrinello-Rahman for 15ns. Simulation is crashing during production run > after few nanoseconds run. > Sometimes I get error "distance between pull group 1(Bilayer COM) and > 3(water) is large than 0.49 times the box size. You might want to consider > using 'pull-geometry =direction-periodic' instead " > But I cannot use direction-periodic in NPT. > Sometimes I get error, "water molecule starting at atom XXX can not be > settled." > I observed, these XXX water molecules are not constrained one's but they > are from bulk water surrounding Bilayer. > Question: > 1. What is alternative for "pull-geometry=distance" if my constrained > molecule going outside the box due to volume fluctuations, since we cannot > use direction-periodic in NPT. > Molecule is constrained around 1nm inside the initial box boundary. > 2. What might be the reason for instability in bulk water which is SPC. > 3. If there is distortions in Bilayer during pulling, leading to overlap, > simulation would have crashed in initial stages, why it is crashing in later > stages. > > Any helpful tips, suggestions will be much appreciated. > > Yogesh > -- > 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. -- 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.
