[gmx-users] Timestep and force field

[Manik Mayur]

On Sun, Mar 22, 2009 at 2:52 PM, varsha gautham
<varsha.gautham88 at gmail.com>wrote:

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

http://en.wikipedia.org/wiki/Force_field_(chemistry)

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?
>
> http://en.wikipedia.org/wiki/Water_model

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
>

These things are not related to Gromacs but to molecular modelling in
general. Going through some literatures specific to your field of
application will help a lot regarding deciding various parameters like
timestep etc.


>
> 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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-- 
Manik Mayur
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
INDIA
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