<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:'bookman old style', 'new york', times, serif;font-size:12pt">
<div style="font-family:'bookman old style', 'new york', times, serif;font-size:12pt;color:#000000;"><div>Dear gmx-users...</div><div><br></div><div>I am new to gromacs, I am trying to obtain the intermolecular hydrogen bonds formed during 10ns simulation of 125 ionic liquid (tetraethylammonium L-Lysinate). I use OPLS-AA force field for this simulation. When I do this by using g_hbond and selecting the LYS group, I am getting hydrogen bonds at all. The angle that I get is 0.33 degree, number of hydrogen bonds = 160.13, and the distance for hydrogen bond =0.16 nm.</div><div><br></div><div><br></div><div>This is the command I am using:</div><div><br></div><div>g_hbond -f mixture_mdpr_compilefile.trr -s mixture_mdpr_ext1.tpr -n index.ndx -num hbnum.xvg -dist hbdist.xvg -ang hbang.xvg -hbn hbond.ndx -d 500 -e 10000 -a 30 -r 0.35 </div><div><br></div><div>This is the output that I obtain :</div><div><br></div><div>No option -sel</div><div>Reading file
mixture_mdpr_ext1.tpr, VERSION 3.3.3 (double precision)</div><div>Specify 2 groups to analyze :</div><div><span class="Apple-style-span" style="font-size: medium; "><pre><font class="Apple-style-span" face="'bookman old style', 'new york', times, serif">Group 0 ( System) has 6500 elements
Group 1 ( N2222) has 3625 elements
Group 2 ( LYS) has 2875 elements
Select a group: 2
Selected 2: 'LYS'
Select a group: 2
Selected 2: 'LYS'</font></pre><pre><font class="Apple-style-span" face="'bookman old style', 'new york', times, serif">Calculating hydrogen bonds in LYS (2875 atoms)</font></pre></span></div><div>Found 250 donors and 500 acceptors </div><div>trn version: GMX_trn_file (single precision)</div><div>Reading frame 2000 time 500.000</div><div>Will do grid-seach on 9x9x9 grid, rcut=0.35</div><div>Last frame 40000 time 10000.00</div><div>Found 2353 different hydrogen bonds in trajectory</div><div>Found 2271 different atom-pairs within hydrogen bonding distance</div><div>Merging hbonds with Acceptor and Donor swapped</div><div>250/250</div><div>-Reduced number of hbonds from 2353 to 1783</div><div>-Reduced number of distances from 2271 to 2271</div><div>Average number of hbonds per timeframe 160.130 out of 62500 possible</div><div><br></div><div>gcq#44: "May the Force Be With You" (Star Wars)</div><div><br></div><div>My question
is; </div><div>1) Is it correct the command that I used to get the number of hydrogen bonding, angle and distance for hydrogen bonding?</div><div>2) Is it reasonable the value for number of hydrogen bonding, angle and distance for hydrogen bonding that I calculate?</div><div><br></div><div>Thanks </div><div><br></div><div>IMA</div><div><br></div><div><br></div><div><br></div><div><br></div><div style=""></div>
</div><div style="position:fixed"></div>
</div><br>
</body></html>