Hi Ming Tang, Can you run in NVT? Then afterwards you can try NPT without position restraints.
Cheers, Tsjerk On May 18, 2015 10:14, "Ming Tang" <m21.t...@qut.edu.au> wrote: > Thanks a lot, Justin > > It really makes me feel weird. The small triple helix with 30 amino acids > per chain(generated simply by deleting other atoms in .pdb file of the real > triple helix) can be equilibrated for 1ns using exactly the same control > files, and the real triple helix can be used for full atomic simulation > without any problem. The CG topology is generated using the same > mitinize.py downloaded from the website. I will try for another time, and > will tell you if I fix it. > > Thanks. > > -----Original Message----- > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin > Lemkul > Sent: Sunday, 17 May 2015 7:07 AM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] energy minimization problem > > > > On 5/16/15 8:30 AM, Ming Tang wrote: > > Dear Justin, > > > > I tried to use small time step. First, set dt=0.005ps, after running > 20ps, I found one chain of the triple helix just went to another water box > totally. I guess there is something wrong with the martini ff because of > the small time step. > > Then, I increased it to 0.01ps, after running 40ps, I checked the .gro, > and found all the three chains stay together, which is reasonable. However, > even use dt=0.01, the simulation can only run about 1ns. And, after > simulating 100 ps using dt=0.01ps, the simulation can just run thousands of > steps when dt is increased to 0.02ps. I tried many times and many different > time steps, but still could not see the possibility for it to run hundreds > of nanoseconds, which is quite normal when using martini force. If the > system can be further minimized, then it can run longer maybe. > > > > This seems entirely random and suggests instead that there is something > simply physically unstable with the system or problematic in the topology. > I don't use MARTINI (or CG models in general) so there's little else I can > suggest. Maybe someone more experienced with such systems will chime in. > > Also note that a chain "moving into another box" is probably just a PBC > effect and not a true dissociation. If it is a dissociation, it's not > simply because of the time step. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > 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.