<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman">Dear Gmx users,</font></font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3" face="Times New Roman"> </font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman">I am working on a transmembrane protein and my system contains protein, DPPC</font></font></p>
<p style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none" class="MsoNormal"><font size="3"><font face="Times New Roman">bilayer, water (spc) and ions. After adding ions I energy minimized the system and used trjconv to remove periodicity. <span style="mso-spacerun: yes"> </span>In the equilibration phase the lipid molecules were entering the voids in the solvent leaving the protein naked. So, I used position restraint on the Z-plane and restrained t<span style="mso-fareast-font-family: CMR12">he phosphate head (atom 8) and one carbon atom on each tail (atoms 31, 50 with a force constant of 1,000 kJ mol<i>−</i>1 nm<i>−</i>2. </span></font></font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman">-----------------------------------------------------------</font></font></p>
<p style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Courier New'; FONT-SIZE: 10pt">; position restraint file for DPPC </span></p>
<p style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Courier New'; FONT-SIZE: 10pt"> </span></p>
<p style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Courier New'; FONT-SIZE: 10pt">[ position_restraints ]</span></p>
<p style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Courier New'; FONT-SIZE: 10pt">;<span style="mso-spacerun: yes"> </span>i funct<span style="mso-spacerun: yes"> </span>fcx<span style="mso-spacerun: yes"> </span>fcy<span style="mso-spacerun: yes"> </span>fcz</span></p>
<p style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Courier New'; FONT-SIZE: 10pt"><span style="mso-spacerun: yes"> </span>8<span style="mso-spacerun: yes"> </span>1<span style="mso-spacerun: yes"> </span>0<span style="mso-spacerun: yes"> </span>0<span style="mso-spacerun: yes"> </span>1000</span></p>
<p style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Courier New'; FONT-SIZE: 10pt"><span style="mso-spacerun: yes"> </span>31<span style="mso-spacerun: yes"> </span>1<span style="mso-spacerun: yes"> </span>0<span style="mso-spacerun: yes"> </span>0<span style="mso-spacerun: yes"> </span>1000</span></p>
<p style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Courier New'; FONT-SIZE: 10pt"><span style="mso-spacerun: yes"> </span>50<span style="mso-spacerun: yes"> </span>1<span style="mso-spacerun: yes"> </span>0<span style="mso-spacerun: yes"> </span>0<span style="mso-spacerun: yes"> </span>1000</span></p>
<p style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Courier New'; FONT-SIZE: 10pt"> </span></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman">-----------------------------------------------------------</font></font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3" face="Times New Roman">But after running a simulated annealing for 500ps I get a distorted lipid membrane where the lipids tend to pack at one end but open at the other end of the box.</font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3" face="Times New Roman">After this I had put position restraint on all the atoms of the lipid on the z-plane and again tried the simulated annealing but it gave the same result. </font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3" face="Times New Roman">I am not able to understand where I am going wrong. </font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman">Thanks,</font></font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3" face="Times New Roman">Parul Tewatia</font></p>