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

majid hasan pu_majidhasan at yahoo.com
Thu Apr 21 20:52:29 CEST 2011 

Okay, so here is the file that I used for both energy minimization (with 
integrator = l-bfgs), and MD (integrator = md). Everything other than the value 
of integrator was same for both energy minimization and MD.
 http://phas.ubc.ca/~majid/md.mdp

and here is what I see by running .trr files obtained from EM, and MD.

On running EM.trr file:
In the beginning of simulation, DNA is very stretched i.e atoms of DNA are 
widely separated from each other, and CNT crumples. Then, gradually DNA shrinks 
and converges onto CNT. 

On running MD.trr file:
CNT suddenly moves toward and DNA and one part is mixed with DNA and whole 
structure is crumpled (similar to the final state of EM.trr simulation). Then 
this crumpled structure wiggles around until the end of simulation.


Yes, I ran the whole process in vacuum. I am going to do this simulation by 
changing cutoff to shift, and see which one works better, and then I will do it 
with a solvent.

Thanks,
Majid


________________________________
From: Justin A. Lemkul <jalemkul at vt.edu>
To: Gromacs Users' List <gmx-users at gromacs.org>
Sent: Thu, April 21, 2011 10:25:35 AM
Subject: Re: [gmx-users] dna and cnt get distorted in md simulation



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.

-Justin

> 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
> MILES-IGERT Trainee
> 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
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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