<P>
yes , I had gone through the manual, but is that all? I mean to say that even if the protein <BR>
suffers from high solvent forces (though the energy minimisation can be done over the <BR>
whole system ie protein in solvated state) that may not pose much of a problem , in case we <BR>
simulate for sufficiently long time.<BR>
I am sorry if I understood wrong.<BR>
Sarbani<BR>
<BR>
<BR>
<BR>
On Tue, 23 Oct 2007 Mark Abraham wrote :<BR>
>sarbani chattopadhyay wrote:<BR>
>> Hi,<BR>
>> I am new to the field of MD.I want to know what is the effectivity of position restricted <BR>
MD<BR>
>>ie. where is the advantage of doing Position restricted MD.I have a small peptide of 3<BR>
>>reidues.Is it necessary to do a Position restricted MD. What difference will it make?<BR>
>> I may sound very unintelligent but any suggestions are welcome.<BR>
><BR>
>Have you checked out the section on position restraints in the GROMACS manual?<BR>
><BR>
>Mark<BR>
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