Dear all, I am carrying out a simulation of membrane protein with a ligand. I am using DPPC [slipids (http://www.fos.su.se/~sasha/SLipids/Downloads.html)].
I had modified amber 03 ff by including the non-bonded and bonded parameters from slipids website as suggested in the tutorial by Justin ( http://www.mdtutorials.com/gmx/membrane_protein/). I had monitored NVT and NPT stages and as things were okay. I had proceeded with the production stage. However, at the end of 30ns simulation, I observe that the box gets compressed from a square to a highly compressed elongated rectangle (when viewed using both Chimera and VMD). Here is the md.mdp (for production run). ---- title = 4yl3-DPP-LIG Production MD ; Run parameters integrator = md ; leap-frog integrator nsteps = 15000000 ; 2 * 15000000 = 30000 ps (1 ns) dt = 0.002 ; 2 fs ; Output control nstxout = 1000 ; save coordinates every 2 ps nstvout = 1000 ; save velocities every 2 ps nstxtcout = 1000 ; xtc compressed trajectory output every 2 ps nstenergy = 1000 ; save energies every 2 ps nstlog = 1000 ; update log file every 2 ps ; Bond parameters continuation = yes ; Restarting after NPT constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained 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 rlist = 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) rvdw = 1.2 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = Nose-Hoover ; More accurate thermostat tc-grps = Protein_LIG_DPP Water_and_ions ; tau_t = 0.5 0.5 ; time constant, in ps ref_t = 323 323 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = semiisotropic ; uniform scaling of x-y box vectors, independent z tau_p = 2.0 ; time constant, in ps ref_p = 1.0 1.0 ; reference pressure, x-y, z (in bar) compressibility = 4.5e-5 4.5e-5 ; isothermal compressibility, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no ; Velocity generation is off ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 1 comm-mode = Linear comm-grps = Protein_LIG_DPP Water_and_ions --- *LIG is ligand and DPP is DPPC. I request you to help me understand why this is happening and how i can overcome this. Thank you in advance. -- Regards, Prasanth. -- 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.