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

Justin A. Lemkul jalemkul at vt.edu
Thu Apr 21 19:25:35 CEST 2011

majid hasan wrote:
> 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.

The reason I asked is that the two are very different - one is for MD and the 
other is for EM, and in some cases, many of the options are irrelevant for 
either process so it is somewhat hard to deduce what you're actually trying to 
accomplish with each, especially given the differences.  It is best to only post 
the actual .mdp files you're using and a description of the output corresponding 
to each.

> 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. 

So, the "first" .mdp file is the one that actually specifies an MD run, not EM? 
  Or does "first" correspond to the order of the workflow?  It might be best to 
focus on one process at a time, rather than trying to troubleshoot both EM and 
MD with some arbitrary designators.

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

Bonds don't break or form during classical MD.  Any bonds "forming" or 
"breaking" are simply a visualization artifact since you're not reading a 
topology into the visualization software.

 From your description, it sounds like these simulations are being conducted in 
vacuo?  I tend to suspect that is the source of the problems.  Plain cutoffs for 
electrostatics lead to nasty artifacts and the presence of a highly charged 
molecule (DNA) that has no shielding between these charges is quite likely to 
become very distorted due to its own intrinsic repulsion.


> Thank You,
> Majid
> ------------------------------------------------------------------------
> *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 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)
> 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 instability.
> Turn off the free energy options and see if you get stable trajectories.
> -Justin
>  > Thanks,
>  > Majid
>  >
> -- ========================================
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> ========================================
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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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