[gmx-users] dna and cnt get distorted in md simulation
pu_majidhasan at yahoo.com
Thu Apr 21 04:48:43 CEST 2011
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.
My commands are:
For energy minimization,
grompp -f lbfgs.mdp -po mdoutlb.mdp -c gc.gro -p gc.top -o gclb.tpr -maxwarn 20
mdrun -s gclb.tpr -o gclb.trr -c gcoutlb.gro -e gclb.edr -g mdlb.log -pd
and then I ran molecular dyamics,
grompp -f md.mdp -po mdoutmd.mdp -c gc.gro -p gc.top -o gcmd.tpr -maxwarn 20
mdrun -s gcmd.tpr -o gcmd.trr -c gcoutmd.gro -e gcmd.edr -g mdmd.log -pd
For individual DNA, and CNT alone, both produce reasonable results, where
molecule stays together and jiggles around. However on combining the two
molecules, both energy minimization and mdrun lead to distorted 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.
I got the first .mdp from a colleague who used it for a simple simulation
of 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,
Both .mdp files are placed at following addresses:
http://phas.ubc.ca/~majid/md.mdp (first .mdp file)
http://phas.ubc.ca/~majid/lbfgs.mdp (modified .mdp file)
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.
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