<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div dir="ltr">Dear gmx users<br>I am simulation a system including carbon nanotube+water.I have done these things:<br>1. I copied oplsaa.ff folder in my working directory<br>2. I added following lines to atomname2type.n2t<br>C opls_995 0 12.011 2 C 0.142 C 0.142<br>C opls_996 0 12.011 3 C 0.142 C 0.142 C 0.142<br>C opls_997 0 12.011 1 C 0.142 <br>3.I added these to ffbonded.itp<br>[ bondtypes ]<br> C C 1 0.1418 478900<br><br> [ angletypes ]<br> C
C C 1 120.000 562.2<br><br>[ dihedraltypes ]<br> C C 1 0.000 167.360 1<br>4.I added these to ffnonbonded.itp<br> opls_995 C 6 12.01100 0.000 A 3.85100e-01 4.39600e-01<br> opls_996 C 6 12.01100 0.000 A 3.85100e-01 4.39600e-01<br> opls_997 C 6 12.01100 0.000 A 3.85100e-01 4.39600e-01<br> 5.then I run g_x2top with this command:<br>g_x2top -f cnt.pdb -o cnt.top -name CNT -nexcl 3 -kb 478900 -kt 562.2<br>6.then I used editconf and
genbox:<br>editconf -f cnt.pdb -o cnt.gro -d 1 -bt cubic<br>genbox -cp cnt.gro -cs spc216.gro -o sol.gro -p cnt.top<br>7.I run grompp for EM with this command:<br>grompp -f em.mdp -c sol.gro -p cnt.top -o em.tpr -maxwarn 1<br>mdrun -deffnm em<br>8.again I run grompp for equilibration phase:<br>grompp -f nvt.mdp -c em.gro -p cnt.top -o nvt.tpr -n index.ndx -maxwarn 1<br>mdrun -deffnm nvt<br>However as I looked into the nvt.gro I realized that the cylindrical shape of carbon nanotube<br> has been changed.I am not sure what I have done is correct or not?and how to keep nanotube cylindrical ? any help would be really appreciated.<br> Best regards<br></div></div></body></html>