<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Dear Gromacs Users,<br><br>I am using ver 4.5.1.<br><br>I completed a 500 ps run of NPT (the mdp file is below). after when i try to do a prod run with both velocity and pressure read from the output of NPT, I get a error<br><br>newgrompp -f eq3npt.mdp -o eq3npttpr.tpr -p dimertop.top -c eq2nptpdb.pdb -t eq2npttrr.trr -e eq2nptedr.edr<br><br>**********<br> <br><br>READ 3 BOX VELOCITIES FROM eq2nptedr.edr<br><br><br>-------------------------------------------------------<br>Program newgrompp, VERSION 4.5.1<br>Source code file: enxio.c, line: 1022<br><br>Fatal error:<br>Could not find energy term named 'Xi-0-Protein'<br>For more information and tips for troubleshooting, please check the GROMACS<br>website at http://www.gromacs.org/Documentation/Errors<br>-------------------------------------------------------<br><br>I cannot judge where I
go wrong. Kindly help.<br><br>Best,<br>nahren<br><br>***********<br><br>**** mdp file *******<br><br>define = -DPOSRES ; position restrain the protein<br>; Run parameters<br>integrator = md ; leap-frog integrator<br>nsteps = 250000 ; 2 * 250000 = 500 ps<br>dt = 0.002 ; 2 fs<br>; Output control<br>nstxout = 500 ; save coordinates every 0.2 ps<br>nstvout = 500 ; save velocities every 0.2 ps<br>nstenergy = 250 ; save energies every 0.2 ps<br>nstlog =
500 ; update log file every 0.2 ps<br>; Bond parameters<br>continuation = yes ; first dynamics run<br>constraint_algorithm = lincs ; holonomic constraints <br>constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained<br>lincs_iter = 1 ; accuracy of LINCS<br>lincs_order = 4 ; also related to accuracy<br>; Neighborsearching<br>ns_type = grid ; search neighboring grid cels<br>nstlist = 5 ; 10 fs<br>rlist = 1.0 ; short-range neighborlist cutoff (in
nm)<br>rcoulomb = 1.5 ; short-range electrostatic cutoff (in nm)<br>rvdw = 1.0 ; short-range van der Waals cutoff (in nm)<br>; Electrostatics<br>coulombtype = cut-off ; Particle Mesh Ewald for long-range electrostatics<br>;<br>; Temperature coupling is on<br>tcoupl = Nose-Hoover ; More accurate thermostat<br>tc-grps = Protein SOL ; three coupling groups - more accurate<br>tau_t = 0.2 0.2 ; time constant, in ps<br>ref_t = 300 300 ; reference temperature, one for
each group, in K<br>; Pressure coupling is on<br>pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT<br>pcoupltype = semiisotropic ; uniform scaling of x-y box vectors, independent z<br>tau_p = 5.0 ; time constant, in ps<br>ref_p = 1.0 1.0 ; reference pressure, x-y, z (in bar)<br>compressibility = 4.5e-5 4.5e-5 ; isothermal compressibility, bar^-1<br>; Periodic boundary conditions<br>;pbc = xyz ; 3-D PBC<br>; Dispersion correction<br>;DispCorr = EnerPres ; account for cut-off vdW scheme<br>; Velocity
generation<br>gen_vel = no ; assign velocities from Maxwell distribution<br>; COM motion removal<br>; These options remove motion of the protein/bilayer relative to the solvent/ions<br>nstcomm = 1<br>comm-mode = Linear<br>comm-grps = system<br><br></td></tr></table><br>