[gmx-users] Timestep and force field

David van der Spoel spoel at xray.bmc.uu.se
Sun Mar 22 10:30:13 CET 2009

varsha gautham wrote:
> Dear gmx user,
> Am a beginner to gromacs,I have a few questions to be clarified before
> getting started with gromacs.

You probably want to start by reading a textbook (or the gromacs manual) 
and some review papers.

> 1.on giving pdb2gmx gromacs offers force fields fom 0 to 6 and also i
> read like opls-aa is the best forcefield for protein? why is that
> so?What kind of forcefield do i have to choose for a protein? how are
> various forceields differ?
> 2.Then regarding the water models I have read various materials ,but
> still the concept is not clear to me. what are  all
> these,SPC,TIP3P,TIP4P,TIP5P,?
> It will be very helpful if someone explain me what are all these and
> how they differ and which water model is best suited for a protein?
> 3. hen how to choose a timestep for a simulation like a picosecond or
> a nanosecond?What is a timestep?
> I have gone through many materials and stuffs related to Gromacs.But i
> dint get a clear idea, addressing this 2 questions.I will be really
> thankful if someone took time to read to this mail patiently and reply
> me with a solution which am looking for months together.Thanks in
> advance.
> -varsha
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David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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