<br clear="all"><div class="gmail_quote">Dear Gromacs users,<br><br>I have a MD simulated protein and i take frame from this and remove water and add water implicit in the interface and want to do energy minimization but while doing the minimization i get errors. The steps followed are-<br>
<br>pdb2gmx -ignh -f 1OC0.pdb -o 1oco.pdb -p 1oco.top -nocmap<br>grompp -f minim.mdp -c 1oco.pdb -p 1oco.top -o 1oco.tpr<br><br>The minim.mdp file =<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>; 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 = steep ; Algorithm (steep = steepest descent minimization)<br>emtol = 1000.0 ; Stop minimization when the maximum force < 1.0 kJ/mol<br>
nsteps = 5000 ; Maximum number of (minimization) steps to perform<br>nstenergy = 1 ; Write energies to disk every nstenergy steps<br>energygrps = System ; 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>ns_type = simple ; Method to determine neighbor list (simple, grid)<br>coulombtype = cut-off ; Treatment of long range electrostatic interactions<br>
rcoulomb = 1.0 ; long range electrostatic cut-off<br>rvdw = 1.0 ; 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>I get a note as =<br>System has non-zero total charge: -4.999996e+00<br><br>then i tried using genion step as=<br><br>genion -s 1oco.tpr -o 1oco.pdb -pname NA -np 5 -p 1oco.top -g ion.log<br><br>then again the grompp step and mdrun .<br>
but while doing mdrun i get an error as=<br><br>Stepsize too small, or no change in energy.<br>Converged to machine precision,<br>but not to the requested precision Fmax < 1000<br><br><br>but here i have given nsteps as 5000 so why does it stop.<span class="HOEnZb"><font color="#888888"><br>
-- <br>Aiswarya B Pawar<br><br><div>Project Assistant,<br>Bioinformatics Dept, <br>Indian Institute of Science<br>Bangalore<br><br></div><br>
</font></span></div><br><br clear="all"><br>-- <br>Aiswarya B Pawar<br><br><div>Project Assistant,<br>Bioinformatics Dept, <br>Indian Institute of Science<br>Bangalore<br><br></div><br>