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

majid hasan pu_majidhasan at yahoo.com
Thu Apr 21 19:12:55 CEST 2011

first .mdp file is the original one, and modified .mdp is the one where I made 
modifications, and I have tried both, and both lead to stable structures for 
individual molecules, and distorted structures for combined system.

In the first .mdp file, free energy calculations are turned off, but even with 
this file, I get huge distortions in the shape of molecules. 

CNT, DNA atoms do form bonds in the simulation, but they lose their shapes. 

Thank You,

From: Justin A. Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Thu, April 21, 2011 4:02:57 AM
Subject: Re: [gmx-users] dna and cnt get distorted in md simulation

majid hasan wrote:
> 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 
> 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)

Is this the file that has had the above modifications made to it for MD?  If so, 
please post the actual file, not the unmodified one.

> 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. 

Why are you employing the free energy code?  It seems to me this could be the 
source of your problems.  Each molecule alone is fine, but then by decoupling 
van der Waals and Coulombic interactions between them, you could be getting 

Turn off the free energy options and see if you get stable trajectories.


> Thanks,
> Majid

-- ========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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