<br><br><div class="gmail_quote">On Sun, Mar 22, 2009 at 2:52 PM, varsha gautham <span dir="ltr"><<a href="mailto:varsha.gautham88@gmail.com">varsha.gautham88@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div><div class="h5">Dear gmx user,<br>
<br>
<br>
Am a beginner to gromacs,I have a few questions to be clarified before<br>
getting started with gromacs.<br>
<br>
1.on giving pdb2gmx gromacs offers force fields fom 0 to 6 and also i<br>
read like opls-aa is the best forcefield for protein? why is that<br>
so?What kind of forcefield do i have to choose for a protein? how are<br>
various forceields differ?<br>
</div></div></blockquote><div><div class="h5"><br><a href="http://en.wikipedia.org/wiki/Force_field_(chemistry)">http://en.wikipedia.org/wiki/Force_field_(chemistry)</a><br><br></div></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div><div class="h5">
2.Then regarding the water models I have read various materials ,but<br>
still the concept is not clear to me. what are all<br>
these,SPC,TIP3P,TIP4P,TIP5P,?<br>
It will be very helpful if someone explain me what are all these and<br>
how they differ and which water model is best suited for a protein?<br>
<br>
</div></div></blockquote><div><div class="h5"><a href="http://en.wikipedia.org/wiki/Water_model">http://en.wikipedia.org/wiki/Water_model</a><br><br></div></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div><div class="h5">
3. hen how to choose a timestep for a simulation like a picosecond or<br>
a nanosecond?What is a timestep?<br>
<br>
I have gone through many materials and stuffs related to Gromacs.But i</div></div></blockquote><div><br>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.<br>
<br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div class="h5"><br>
dint get a clear idea, addressing this 2 questions.I will be really<br>
thankful if someone took time to read to this mail patiently and reply<br>
me with a solution which am looking for months together.Thanks in<br>
advance.<br>
<br>
-varsha<br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Manik Mayur<br>Graduate student<br>Microfluidics Lab<br>Dept. of Mechanical Engg.<br>IIT Kharagpur<br>INDIA<br>