<div>Thanks David for your quick reply</div>
<div> </div>
<div>you were write actually , there is no energy term corresponding to the postional restrain in the log file,</div>
<div> </div>
<div>but i am using the proper posre.itp file created by genpr command (restrain for whole protein) , </div>
<div> </div>
<div>genpr -f 4min_ion_water.pdb -o posre.itp -fc 50 </div>
<div> </div>
<div>then i have included define also in my .mdp file corresponding to this restrain file </div>
<div>i used grompp in the following way </div>
<div> <br>grompp -f 6eq_w.mdp -c 5min_w.gro -p aquapo_grom.top -r posre.itp -o 6eq_w.tpr<br> </div>
<div>then what else i should check to rectify this problem ?</div>
<div> </div>
<div> </div>
<div>{ Actually my protein is a dimer, earlier two .itp files were crested by pdb2gmx in the beginning but to reduce the restrain and to include all the hydrogens added this time in the restrain file i made another .itp file.}
</div>
<div> </div>
<div> </div>
<div>With regards</div>
<div>Gurpreet</div>
<div><span class="gmail_quote">On 7/21/07, <b class="gmail_sendername">David van der Spoel</b> <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>> wrote:</span>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">gurpreet singh wrote:<br>> Hello users<br>><br>> I am using the gromacs 3.3 with 43a1 force field.
<br>> I am using a restraint force of 50 intially during the beginning of<br>> protein simulation in water, even after such a high value of restraint<br>> force i can see some major deviations in my structure during the
<br>> simulation.<br>><br>> My doubt is that since i am applying enough restrain force on the<br>> protein it should not deviate at all from its native conformation.<br>> I want to know is this the usual behavior in gromacs or i am making some
<br>> mistake in applying restrain.<br>><br>> I am using a posre.itp file using define = -dposre in the .mdp file for<br>> applying the restraining force.<br>><br><br>are you sure the restraints are applied? check whether you have an
<br>energy term corresponding to it. typical force constants people use are<br>1000 kJ/mol/nm^2<br><br>><br>> With regards<br>> Gurpreet<br>><br>><br>><br>> ------------------------------------------------------------------------
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</a><br><br><br>--<br>David van der Spoel, Ph.D.<br>Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.<br>Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.<br><a href="mailto:spoel@xray.bmc.uu.se">
spoel@xray.bmc.uu.se</a> <a href="mailto:spoel@gromacs.org">spoel@gromacs.org</a> <a href="http://folding.bmc.uu.se">http://folding.bmc.uu.se</a><br>_______________________________________________<br>gmx-users mailing list
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