hi justin I have a file tfe peptide water,cl .I minimized it and I want to preequilbrate it.when I do the grompp I get 1 warning: calling /lib/cpp... processing topology... Generated 165 of the 1596 non-bonded parameter combinations Excluding 3 bonded neighbours for Protein_A 1 turning all bonds into constraints... Excluding 3 bonded neighbours for TFE 200 turning all bonds into constraints... Excluding 2 bonded neighbours for SOL 913 turning all bonds into constraints... Excluding 1 bonded neighbours for CL- 1 turning all bonds into constraints... NOTE: System has non-zero total charge: -1.000003e+00
processing coordinates... double-checking input for internal consistency... Velocities were taken from a Maxwell distribution at 300 K Reading position restraint coords from emout.gro renumbering atomtypes... converting bonded parameters... # G96ANGLES: 1803 # PDIHS: 468 # IDIHS: 68 # LJ14: 1010 # POSRES: 105 # CONSTR: 1339 # SETTLE: 913 Walking down the molecule graph to make shake-blocks initialising group options... processing index file... Analysing residue names: Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat There are: 1114 OTHER residues There are: 14 PROTEIN residues There are: 0 DNA residues Analysing Protein... Analysing Other... WARNING 1 [file aminoacids.dat, line 1]: T-Coupling group Protein has fewer than 10% of the atoms (138 out of 4278) Maybe you want to try Protein and Non-Protein instead? Making dummy/rest group for Acceleration containing 4278 elements Making dummy/rest group for Freeze containing 4278 elements Making dummy/rest group for Energy Mon. containing 4278 elements Making dummy/rest group for VCM containing 4140 elements Number of degrees of freedom in T-Coupling group Protein is 272.00 Number of degrees of freedom in T-Coupling group Non-Protein is 8478.00 Making dummy/rest group for User1 containing 4278 elements Making dummy/rest group for User2 containing 4278 elements Making dummy/rest group for XTC containing 4278 elements Making dummy/rest group for Or. Res. Fit containing 4278 elements Making dummy/rest group for QMMM containing 4278 elements T-Coupling has 2 element(s): Protein Non-Protein Energy Mon. has 1 element(s): rest Acceleration has 1 element(s): rest Freeze has 1 element(s): rest User1 has 1 element(s): rest User2 has 1 element(s): rest VCM has 2 element(s): Protein rest XTC has 1 element(s): rest Or. Res. Fit has 1 element(s): rest QMMM has 1 element(s): rest Checking consistency between energy and charge groups... Calculating fourier grid dimensions for X Y Z Using a fourier grid of 50x50x50, spacing 0.120 0.120 0.120 writing run input file... Back Off! I just backed up prout.tpr to ./#prout.tpr.1# There was 1 warning In pr.mdp ,I creat two group protein and nonprotein but it is not correct. cpp = /lib/cpp define = -DPOSRES constraints = all-bonds comm_grps = protein integrator = md dt = 0.002 ; ps ! nsteps = 2000000 ; total . nstcomm = 1 nstxout = 100 nstvout = 1000 nstfout = 0 nstlog = 100 nstenergy = 100 nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb = 1 coulombtype = pme rvdw = 1 ewald_rtol = 1e-5 fourierspacing = 0.12 ; Berendsen temperature coupling is on Tcoupl = berendsen pcoupltype = isotropic tau_t = 0.1 0.1 tc-grps = Protein non-protein ref_t = 300 300 ; Pressure coupling is no pcoupl = no tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 please suggest me and advise. thanks -- sh-karbalaee _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
