<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div id="yiv10573665"><div><div style="color: rgb(0, 0, 0); background-color: rgb(255, 255, 255); font-size: 12pt; font-family: 'times new roman', 'new york', times, serif; "><div id="yiv10573665yui_3_2_0_15_132795064070840">Dear Sir,</div><div id="yiv10573665yui_3_2_0_15_132795064070840">I'm a novice user.</div><div id="yiv10573665yui_3_2_0_15_132795064070840">I compiled Gromacs in single precision.</div><div id="yiv10573665yui_3_2_0_15_132795064070840">I tried to set up a simulation between Hypericin and the DNA molecule and to see how they interact.</div><div id="yiv10573665yui_3_2_0_15_132795064070840">I created the Hypericin molecule with MarvinSketch and exported to a pdb file,then with Avogadro I set up both molecules ,so that they are on a distance of 2-3 A and saved to a pdb file.</div><div
id="yiv10573665yui_3_2_0_15_132795064070840">With pdb2gmx generated DNA's topology file(amber99sb,amber94 forcefield) and in the log file says that the total charge of the System is -32.431e,later when I tried to create a neutral system it's not a total 0,but -0.430.</div><div id="yiv10573665yui_3_2_0_15_132795064070840">I would like to ask ,how reliable are the results,if the charge is not an integer and i'm running in single precision mode?</div><div id="yiv10573665yui_3_2_0_15_132795064070840">Later I added the hydrogen atoms and added a charge to the Hypericin molecule with Chimera USCF and then generated topology files with acpype script.</div><div id="yiv10573665yui_3_2_0_15_132795064070840">Before running md ,i created an index file linking the DNA and Hypercin into on tc-grps and ran the simulation for 1 ns. Is it enough or it should run longer?</div><div id="yiv10573665yui_3_2_0_15_132795064070840">My PC is
quadcore Q6600 with 2 gigs of ram.</div><div id="yiv10573665yui_3_2_0_15_132795064070840">Thanks in advance</div><div id="yiv10573665yui_3_2_0_15_132795064070840"><br></div><div id="yiv10573665yui_3_2_0_15_132795064070840">Hovakim Grabski</div><div id="yiv10573665yui_3_2_0_15_132795064070840">Russian Armenian (Slavonic) University</div><div id="yiv10573665yui_3_2_0_15_132795064070840">Bionformatics Department</div><div id="yiv10573665yui_3_2_0_15_132795064070840"><br></div><div id="yiv10573665yui_3_2_0_15_132795064070840"><br></div><div id="yiv10573665yui_3_2_0_15_132795064070840"><br></div><div id="yiv10573665yui_3_2_0_15_132795064070840"><br></div><div id="yiv10573665yui_3_2_0_15_132795064070840"><br></div><div id="yiv10573665yui_3_2_0_15_132795064070840"><br></div><div id="yiv10573665yui_3_2_0_15_132795064070840"><br></div></div></div></div></div></body></html>