Hi users,<br><br>Iam running a minimization on protein complex in vacuum. i have set the parameters as following-<br><br>; Lines starting with ';' ARE COMMENTS<br>; Everything following ';' is also comment<br>
<br>title = Energy Minimization ; Title of run<br><br>; The following line tell the program the standard locations where to find certain files<br>cpp = /lib/cpp ; Preprocessor<br><br><br>; Define can be used to control processes<br>
define = -DFLEXIBLE<br><br>; Parameters describing what to do, when to stop and what to save<br>integrator = steepest ; Algorithm (steep = steepest descent minimization)<br>emtol = 1000.0 ; Stop minimization when the maximum force < 1.0 kJ/mol<br>
emstep = 0.01<br>nsteps = 50000 ; Maximum number of (minimization) steps to perform<br>nstenergy = 1 ; Write energies to disk every nstenergy steps<br>energygrps = Protein ; Which energy group(s) to write to disk<br>
<br>; Parameters describing how to find the neighbors of each atom and how to calculate the interactions<br>nstxout = 1<br>nstlist = 10 ; Frequency to update the neighbor list and long range forces<br>ns_type = grid ; Method to determine neighbor list (simple, grid)<br>
rlist = 1.0 ; Cut-off for making neighbor list (short range forces)<br>coulombtype = cutoff ; Treatment of long range electrostatic interactions<br>rcoulomb = 1.0 ; long range electrostatic cut-off<br>
rvdw = 1.4 ; long range Van der Waals cut-off<br>constraints = none ; Bond types to replace by constraints<br>pbc = no ; Periodic Boundary Conditions (yes/no)<br><br>But from this i could write only 2 frames i need to increase the time frames, what is to be changed in the parameters.<br>
<br>Thanks,<br>Aiswarya<br>