Hi friends,<br> <br> I have a DNA sequence (5'-GAG TCT GTG GAG GAG GTA GTC-3') and a CNT(6,5) of 90 Angstroms in length. I kept the DNA & CNT at a distance of 1 angstrom. Solvents molecules(water) inside CNT are removed at a radius of CNT at 4.2 . Equilibration at 1000 steps, results in diminished quality of CNT (like bonds between carbons are no more visible!), i repeat equilibration with larger steps( 5000), the same problem result. Also,the DNA is suppose to wraped around the CNT, but it didnot seems to happen. I am using GROMACS. Any help will be highly appreciated.<br>
My equil.mdp file is<br><br>; LINES STARTING WITH ';' ARE COMMENTS<br>title = Minimization of "-----" ; Title of run<br>; The following lines tell the program the standard locations where to find certain files<br>
Define =-Dflexible<br>cpp = cpp ; Preprocessor<br><br>; Parameters describing what to do, when to stop and what to save<br>integrator = steep ; Algorithm (steep = steepest descent minimization)<br>
emtol = 1.0 ; Stop minimization when the maximum force < 1.0 kJ/mol<br>nsteps = 1000 ; Maximum number of (minimization) steps to perform<br>nstenergy = 5 ; Write energies to disk every nstenergy steps<br>
nstxtcout = 10 ; Write coordinates to disk every nstxtcout steps<br>xtc_grps = Protein SOL ; Which coordinate group(s) to write to disk<br>energygrps = Protein SOL ; 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>nstlist = 5 ; Frequency to update the neighbor list and long range forces<br>ns_type = simple ; Method to determine neighbor list (simple, grid)<br>
coulombtype = PME-switch ; Treatment of long range electrostatic interactions<br>rcoulomb = 0.9 ; long range electrostatic cut-off<br>rlist = 1.0 ; Cut-off for making neighbor list (short range forces)<br>
vdwtype = Shift <br>rvdw = 0.9 ; long range Van der Waals cut-off<br>constraints = all-bonds ; Bond types to replace by constraints<br>pbc = xyz ; Periodic Boundary Conditions (yes/no)<br>
constraint_algorithm=LINCS<br>lincs_order =4<br>lincs_iter =2<br>periodic_molecules = yes<br>nstcomm = 1<br>comm_mode = Linear<br>comm_grps = Protein SOL <br clear="all"><br>-- <br>Best Regards,<br>
<br>Siam<br>Theoretical Sciences Unit,<br>JNCASR,<br>(Lab) +91-080-2208-2581, (M) +91-8971001405<br>e-mail: <a href="mailto:sktn06@gmail.com">sktn06@gmail.com</a>, <a href="mailto:siam@jncasr.ac.in">siam@jncasr.ac.in</a><br>
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