Dear Justin, I read a paper, in which the author equilibrated the collagen like this: Firstly, a 100 ps NVT MD simulation at a temperature 310 K was performed, in which velocity rescaling algorithm with 1ps coupling constant was used. Rigid bonds were used to constraint covalent bond length, allowing a time step of 2fs. Secondly, a 200ps NPT ensemble with 1bar pressure was used to equilibrate the system while keeping the temperature at 310 K, where Berendsen barostat with 1ps coupling constant was adopted. In this step, the whole protein was held fixed. Lastly, we further equilibrated the system in a NPT ensemble for 400ps, with a more accurate pressure coupling algorithm based on Parrinello-Rahman barostat (Parrinello and Rahman 1981). Only the first and the last C − α atoms of each chain were constrained.
I wonder whether they used genrestr to restrain atoms, like utilising -fc to add a quite large force in all directions to them, and considered those atoms are kept fixed during NPT equilibration? Thanks in advance. -----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 Ming Tang Sent: Monday, 15 June 2015 6:05 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] confusion on NPT MD simulation Dear Justin, I got a problem making me confused for weeks. I found 2 journals, in which the author kept parts of their protein to equilibrate their system in NPT. Is there any other methods to keep atoms fixed during NPT equilibrium besides freezing them? As you mentioned, freezing and pressure coupling are incompatible. My first understanding was that I cannot fix atoms during NPT. Therefore, I have been steering my collagen in NVT recently. After minimization, I equilibrated my collagen in NVT with the heavy atoms restrained (define = -DPOSRES) for 20ns, and then stretched it using pull code. Do you think this simple process can give a good starting point for SMD? Thanks very much. -----Original Message----- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se<mailto: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: Monday, 1 June 2015 9:46 PM To: gmx-us...@gromacs.org<mailto:gmx-us...@gromacs.org> Subject: Re: [gmx-users] confusion on NPT MD simulation On 6/1/15 4:40 AM, Ming Tang wrote: > Dear gromacs experts, > > I tried to equilibrate a triple helix using NPT, and the .mdp file is like > this: > > DEFINE = -DPOSRES > integrator = md > dt = 0.0009 > nsteps = 1000000 > nstxout = 0 > nstvout = 0 > nstlog = 10000 > nstxtcout = 10000 > xtc-precision = 10 > cutoff-scheme = verlet > coulombtype = reaction-field-zero > coulomb-modifier = potential-shift-verlet rcoulomb-switch = 0.8 > rcoulomb = 1.4 > epsilon_r = 15 > vdw-modifier = force-switch > rvdw-switch = 0.8 > rvdw = 1.4 > tcoupl = v-rescale > tc-grps = Protein non-protein > tau-t = 1.0 1.0 > ref-t = 310 310 > Pcoupl = parrinello-Rahman > Pcoupltype = isotropic > tau-p = 5 > compressibility = 3e-4 > ref-p = 1.0 > refcoord_scaling = all > pbc = xyz > freezegrps = C > freezedim = Y Y Y > > C is a group containing atoms of both the first and the last residues in all > the three chains. > But after 18ns' simulation, I found the one end of the triple helix moved. > Could you help to tell me whether this is normal or there is something wrong > with my simulation? > Then, I tried to use berendsen for both tcoupl and pcoupl. It turned out that > both ends were fixed. I need to keep the original geometry shape of the > triple helix, but berendsen algorithm is believed to be inaccurate. > Freezing and pressure coupling are incompatible; see notes in the manual. -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<mailto: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<mailto: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<mailto: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.
