Prof. Justin thank you for replay. The leaflets are not simply separating, the membrane is deformed and resembles a "chromosome". The image is in the following URL: https://spaces.hightail.com/space/8l6z0Tncyv/files/fi-f3882907-6f37-4230-8c12-40b1f7b1ef22/fv-41ef812d-a030-412f-890f-677af406ebe6/on%20DOPC.JPG
The protein is on the DOPC surface, that's why I'm not sure about the setting of the .mdp file. I used the same .mdp settings for the membrae-protein system, where the protein is embedded in a membrane. I would be very grateful if you can help me with that. Best regards, Olga בתאריך יום א׳, 27 באוק׳ 2019 ב-18:04 מאת Justin Lemkul <jalem...@vt.edu >: > > > On 10/27/19 11:10 AM, Olga Press wrote: > > Dear Gromacs users, > > I run 10ns NVT equilibration with position restains (on the protein) for > a > > system in which the protein is on the membrane surface. > > I used the following .mdp file > > > > title = NVT equilibration for p1-DOPC > > define = -DPOSRES ; position restrain the protein > > ; Run parameters > > integrator = md ; leap-frog integrator > > nsteps = 5000000 ; 0.002ps * 5000000 = 10000 > ps=10ns > > dt = 0.002 ; 2 fs > > > > ; OUTPUT CONTROL OPTIONS > > ; Output frequency for coords (x), velocities (v) and forces (f) > > nstxout = 0 > > nstvout = 0 > > nstfout = 0 > > ; Output frequency for energies to log file and energy file > > nstlog = 10000 > > nstcalcenergy = 100 > > nstenergy = 1000 > > ; Output frequency and precision for .xtc file > > nstxout-compressed = 10000 > > compressed-x-precision = 1000 > > ; This selects the subset of atoms for the compressed > > ; trajectory file. You can select multiple groups. By > > ; default, all atoms will be written. > > compressed-x-grps = > > ; Selection of energy groups > > energygrps = > > ; Bond parameters > > continuation = no ; first dynamics run > > constraint_algorithm = lincs ; holonomic constraints > > constraints = h-bonds ; H bonds constrained fit > > to charmm36 ff > > lincs_iter = 1 ; accuracy of LINCS > > lincs_order = 4 ; also related to accuracy > > ; Neighborsearching > > ns_type = grid ; search neighboring grid cels > > nstlist = 5 ; 10 fs > > cutoff-scheme = Verlet > > vdwtype = cutoff > > vdw-modifier = force-switch ; same as vfswitch > > rvdw-switch = 1.0 > > rlist = 1.2 ; short-range neighborlist cutoff (in nm) > > rcoulomb = 1.2 ; short-range electrostatic cutoff (in > nm) > > ; Electrostatics > > coulombtype = PME ; Particle Mesh Ewald for long-range > > electrostatics > > pme_order = 4 ; cubic interpolation > > fourierspacing = 0.12 ; grid spacing for FFT > > ; Temperature coupling is on > > tcoupl = V-rescale ; modified Berendsen > thermostat > > *tc-grps = Protein DOPC SOL_SOD_CLA* ; three coupling > groups - > > more accurate > > tau_t = 0.1 0.1 0.1 ; time constant, in ps > > ref_t = 310.15 310.15 310.15 ; reference temperature, > > one for each group, in K > > ; Pressure coupling is off > > pcoupl = no ; no pressure coupling in NVT > > ; Periodic boundary conditions > > pbc = xyz ; 3-D PBC > > ; Dispersion correction > > DispCorr = no ; Do not apply dispertion correction for bilayers > > by using charmm36 ff > > ; Velocity generation > > gen_vel = yes ; assign velocities from Maxwell > > distribution > > gen_temp = 310.15 ; temperature for Maxwell > > distribution > > gen_seed = -1 ; generate a random seed > > ; COM motion removal > > ; These options remove motion of the protein/bilayer relative to the > > solvent/ions > > nstcomm = 100 > > comm-mode = Linear > > *comm-grps = Protein_DOPC SOL_SOD_CLA* > > > > However, the membrane seems to be breaking apart, the image of the system > > is attached to the mail. > > The mailing list does not accept attachments. If you wish to share a > file or an image, upload it to a file-sharing service and provide a URL. > If the leaflets are simply separating, this is normal during NVT and > will resolve when running NPT. > > -Justin > > > I think that it is the issue of the center-of-mass motion removal, but > I'm > > not sure and would be very grateful for any suggestions. > > Best regards, > > Olga > > > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > 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. > -- *Olga Press-Sandler* Ph.D. student, Yifat Miller's lab Department of Chemistry Ben-Gurion University, Israel -- 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.