[gmx-users] How can I reconstruct the system in CGMD simulation?

Justin A. Lemkul jalemkul at vt.edu
Fri Dec 18 22:04:29 CET 2009

rasoul nasiri wrote:
> Dear Cesar,
> Thank you for your reply,
> There are two different kind of water gro in this site (one of them is 
> water.gro in :
> http://md.chem.rug.nl/~marrink/MARTINI/Coordinates.html 
> and another is water-1bar-303k.gro in :
>  http://md.chem.rug.nl/~marrink/MARTINI/Tutorial.html . Is there 
> difference between them?

Maybe, but if you do sufficient equilibration, it probably won't matter.

> Can I build water.gro with coarse graining beads (P4) from spc216.gro 
> with using atom2cg.awk script?

No.  This has been stated before - the awk script is explicitly for protein. 
And besides, each "W" CG particle corresponds to about four water molecules, so 
there is no trivial way to decide how to build the CG water system from spc216.gro.

> Another question; How can I change secondary structure information 
> during CGMD simulation, If I want to perform CGMD simulation for finding 
> of the folding/unfolding mechanism in proteins completely? Because 
> Martini CGFF consider fix it.

You specify the secondary structure when building the initial topology.  As 
you've been advised already, this "fixed" representation of secondary structure 
is going to be a major limitation of using the MARTINI force field for your 
simulations.  How do you know that whatever alternate secondary structure you've 
applied is valid?  If you have some experimental evidence to suggest that 
certain peptide regions convert between one form and another, that's fine, but 
how do you know that the pathway taken is not an artifact of your choice to 
abruptly impose a change in the topology?



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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