[gmx-users] Questions about protein simulations.

Justin A. Lemkul jalemkul at vt.edu
Wed Jul 15 19:52:35 CEST 2009

quantrum75 wrote:
> Dear Gromacs users,
> Hi I wanted to ask a begnniner's question regarding protein MD. I have 
> prior experience with MD simulations through simulating lipid systems. 
> However I beginning to do some protein MD simulations and wanted the 
> anyone's advice regarding the forcefields to be used for proteins.
> 1) Is OPLS-AA the standard for protein simulations using GROMACS? I 
> havent seen that many papers using OPLS-AA Gromacs for protein 
> simulations as I have seen say AMBER or CHARMM. In fact I have also seen 
> a CHARMM port for GROMACS making me wonder if there is somthing wrong 
> with using OPLS-AA for proteins. Any advice or pointers in this 
> direction would be very helpful. Any pitfalls regarding the same? My 
> protein is pretty much a standard protein without any funny amino acids 
> or additional molecules.

There is no "standard" force field for use with Gromacs.  Just about all of the 
major force fields are available under the newest version of Gromacs, and the 
Amber ports can be obtained from their developers.

The ultimate choice of force field should be based on your reading and 
understanding of their derivation and known applications/limitations, all of 
which comes from the literature.  Choose the one that you think is most sound :)

> 2) Water model - which is the best model to use....TIP or SPC? why would 
> one choose one versus another for protein simulations?

The literature contains recommendations on which water models to use with which 
force field.

> 3) Scientific resources for decent protein simulations in GROMACS? I 
> have read some of Van Der Spoel s publications, but they are more in the 
> nature of optimizing protein simulations rather than running basic 
> applied ones. Put in another way, i am more interested in the applied 
> aspect of the protein simulations rather than the optimization of the same.

Application is dependent upon the question you want to ask.  If you need more 
detail, then you'll have to explain what kind of techniques or analysis you need 
to perform.  Otherwise, literature and textbook reading are your best friend 
once again.


> I understand these are basic questions. But I'd grateful for sage and 
> cogent replies.
> Thanks to the group for the wonderful service rendered.
> Regards
> Rama
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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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