[gmx-users] dna and cnt get distorted in md simulation

majid hasan pu_majidhasan at yahoo.com
Thu Apr 21 04:48:43 CEST 2011

Dear All,

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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