<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:'times new roman', 'new york', times, serif;font-size:12pt;color:#000000;"><div style="color: rgb(0, 0, 0); font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; ">Dear All,</div><div style="color: rgb(0, 0, 0); font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; "><br></div><div style="color: rgb(0, 0, 0); font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; ">I minimized the energy of my CNT-DNA system with l-bfgs integrator, and then ran the mdrun with integrator = md. I am using a small ssDNA consisting of two residues only (66 atoms), and a small CNT of about 80 atoms. </div><div style="color: rgb(0, 0, 0); font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; "><br></div><div style="color: rgb(0, 0, 0); font-family: 'times new roman', 'new york', times,
serif; font-size: 12pt; ">My commands are:</div><div style="color: rgb(0, 0, 0); font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; ">For energy minimization,</div><div style="color: rgb(0, 0, 0); font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; "><br></div><div style="color: rgb(0, 0, 0); font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; ">grompp -f lbfgs.mdp -po mdoutlb.mdp -c gc.gro -p gc.top -o gclb.tpr -maxwarn 20</div><div style="color: rgb(0, 0, 0); font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; ">mdrun -s gclb.tpr -o gclb.trr -c gcoutlb.gro -e gclb.edr -g mdlb.log -pd</div><div style="color: rgb(0, 0, 0); font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; "><div style="color: rgb(0, 0, 0); font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; "><br></div><div style="color: rgb(0, 0, 0); font-family:
'times new roman', 'new york', times, serif; font-size: 12pt; ">and then I ran molecular dyamics,</div><div style="color: rgb(0, 0, 0); font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; "><br></div><div style="color: rgb(0, 0, 0); font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; ">grompp -f md.mdp -po mdoutmd.mdp -c gc.gro -p gc.top -o gcmd.tpr -maxwarn 20</div><div style="color: rgb(0, 0, 0); font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; ">mdrun -s gcmd.tpr -o gcmd.trr -c gcoutmd.gro -e gcmd.edr -g mdmd.log -pd</div></div><div style="color: rgb(0, 0, 0); font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; "><br></div><div><font class="Apple-style-span" face="'times new roman', 'new york', times, serif" size="3">For individual DNA, and CNT alone, b</font><span class="Apple-style-span" style="font-family: 'times new roman', 'new york', times, serif;
">oth produce reasonable results, where molecule stays together and jiggles around. However on combining the two molecules, b</span><font class="Apple-style-span" face="'times new roman', 'new york', times, serif" size="3">oth energy minimization and mdrun lead to distorted </font><font class="Apple-style-span" face="'times new roman', 'new york', times, serif">structures: bond lengths don't remain fixed neither for CNT nor for DNA, and atoms of both molecules get intertwined and produce a mess. I tried two .mdp files. </font></div><div><font class="Apple-style-span" face="'times new roman', 'new york', times, serif"><br></font></div><div><font class="Apple-style-span" face="'times new roman', 'new york', times, serif">I got the first .mdp from a colleague who used it for a simple </font><span class="Apple-style-span" style="font-family: 'times new roman', 'new york', times, serif; ">simulation of</span><span
class="Apple-style-span" style="font-family: 'times new roman', 'new york', times, serif; "> CNT only (without solvent, and any other molecule) . I made few changes in this file after going through manual e.g enabled free energy calculations, added "nsttcouple = -1" value, changed valued of "comm_mode" from Angular to Linear, changed "ns_type" value from grid to simple, changed "rcoulomb" and "rvdw" values from 0.9 to 1,</span></div><div><span class="Apple-style-span" style="font-family: 'times new roman', 'new york', times, serif; "> </span></div><div><font class="Apple-style-span" face="'times new roman', 'new york', times, serif"></font><span class="Apple-style-span" style="font-family: 'times new roman', 'new york', times, serif; "> Both .mdp files are placed at following addresses:</span></div><div><font class="Apple-style-span" face="'times new roman', 'new york', times, serif"><a
href="http://phas.ubc.ca/~majid/md.mdp">http://phas.ubc.ca/~majid/md.mdp</a> (first .mdp file)</font></div><div><a href="http://phas.ubc.ca/~majid/lbfgs.mdp">http://phas.ubc.ca/~majid/lbfgs.mdp</a> (modified .mdp file)</div><div><br></div><div>It seems to me that problem might be related to non-bonded interaction because this is the significant difference between one and two molecule system. Any help would be much appreciated. </div><div><br></div><div>Thanks,</div><div>Majid</div><div style="position: fixed; color: rgb(0, 0, 0); font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; "></div>
</div></body></html>