Dear Justin Thank you For your Previous reply I have used the EM.gro file of Cyclic Peptide For NPT Equlibrartion Without using Lincs Algorithim it run Suceesfully But with Lincs Algorithm It shows Errror As follows Though I have reduce the time step relative constraint deviation after LINCS: rms 3069855679.355833, max 11186146428.941977 (between atoms 164 and 165) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 166 167 143.7 0.1935 179340257.0542 0.1530 166 167 143.7 0.1935 179340257.0542 0.1530 168 169 158.7 1.4560 636653487.7409 0.1230 168 169 158.7 1.4560 636653487.7409 0.1230 164 168 171.7 2.0007 1704071509.3304 0.1530 164 165 169.7 1.8838 1711480403.7811 0.1530 164 168 171.7 2.0007 1704071509.3304 0.1530 164 165 169.7 1.8838 1711480403.7811 0.1530 165 166 165.2 0.6922 762944969.2944 0.1530 165 166 165.2 0.6922 762944969.2944 0.1530 1 2 139.5 0.1011 1465776.5396 0.1000 1 168 169.4 1.1190 546331954.5273 0.1330 145 147 38.1 0.1330 0.1781 0.1330 step 0: Water molecule starting at atom 7265 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Back Off! I just backed up step0b_n1.pdb to ./#step0b_n1.pdb.2# Back Off! I just backed up step0c_n1.pdb to ./#step0c_n1.pdb.2# Wrote pdb files with previous and current coordinates Segmentation fault
Normally The Gromacs Does Not Have terminal option for cyclic Peptide While constructing .top for Cyclic Peptide (By using pdb2gmx) As Advised By mark I Have Edited My initial pdb file final .top file compatible to cyclic Peptide (by Making Bond between first and Last residue And then Making proper angle,Dihedral and other factors) Now I am confident on that topology . Also Bond Between First and Last Residue Are Intact throughout Entire Dynamics ( Here I am Running Without Lincs Algorithm) My Question is Is it Reasonable and Meaningful To equilibrate And do Production MD Without Lincs otherwise Is My EM Not well Enough ? Because I am doing Three Cycles of EM Output is as follows Steepest Descents converged to Fmax < 6800 in 2 steps Potential Energy = -2.08749539864389e+05 Maximum force = 6.52976950643761e+03 on atom 17042 Norm of force = 4.52145850945473e+02 But When I Equilibrate With Lincs still It Shows Bad contacts As Mentioned Above My NPT.mdp file are as follows title = NPT Equilibration define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator nsteps = 100000 ; 2 * 50000 = 100 ps dt = 0.0002 ; 2 fs ; Output control nstxout = 1000 ; save coordinates every 2 ps nstvout = 1000 ; save velocities every 2 ps nstenergy = 1000 ; save energies every 2 ps nstlog = 1000 ; update log file every 2 ps ; Bond parameters continuation = no ; Initial simulation 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 = 1.4 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.4 ; short-range electrostatic cutoff (in nm) rvdw = 1.4 ; 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 = V-rescale ; Weak coupling for initial equilibration tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 310 310 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Berendsen ; Pressure coupling on in NPT, also weak coupling pcoupltype = isotropic ; uniform scaling of x-y-z box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure (in bar) compressibility = 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 = yes ; Velocity generation is on gen_temp = 310 ; temperature for velocity generation gen_seed = -1 ; random seed ; COM motion removal ; These options remove COM motion of the system nstcomm = 10 comm-mode = Linear comm-grps = System Thanks In Advance -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists