Hi Tsjerk, This protein has a total charge of 35e, and I added 35 CL to balance the system. Is there any difference between adding CL and not adding CL? Thank you.
-----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 Tsjerk Wassenaar Sent: Monday, 18 May 2015 6:21 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] energy minimization problem 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. -- 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.