<DIV><BR>Dear GROMACS users,</DIV> <DIV> </DIV> <DIV>Thanks for all the replies. They're very helpful. Actually, i have no expertise in this field around me. Moreover i'm from chemistry, so statistical and quantum mechanics are no familiar to me. Thats made my progress become slower (but not impossible right?). </DIV> <DIV> </DIV> <DIV>I have done several simualtions using the .mdp file that i modify from the example included in the online manual. I'm using the OPLS-AA force field with the reason i'm doing liquid simulations. I have succeeded in doing some simulations (as a practice), got some problems and i solved it most based on these helpful mailing-lists. Its just that i wan to make sure what i'm doing is right until now. </DIV> <DIV> </DIV> <DIV>I am doing MD simulation on the mixture of Oleyl oleate (palm oil ester) / Sorbitan Monolaurate (Surfactant) in water. The composition is
based on experimental results. I packed these molecules using Packmol (excluding water).I added water molecules using genbox in calculated box size. After conjugated-gradients and steepest descents energy minimizations, i run MD simulation.</DIV> <DIV> </DIV> <DIV>Here's my .mdp file.. any comments and suggestions are very welcomed and helpful.</DIV> <DIV> </DIV> <DIV><FONT size=2> <div>title = MICELLE #7</div> <div>cpp = cpp</div> <div>include =
-I/usr/local/gromacs/share/gromacs/top</div> <div>define = </div> <div>integrator = md</div> <div>dt = 0.001</div> <div>nsteps = 5000000</div> <div>emtol = 50.0</div>
<div>emstep = 0.01</div> <div>niter = 20</div> <div>nstcgsteep = 1000</div> <div>nbfgscorr = 10</div> <div>nstxout = 50000</div>
<div>nstvout = 50000</div> <div>nstlog = 5000</div> <div>nstenergy = 250</div> <div>nstxtcout = 250</div> <div>xtc-precision = 1000</div> <div>xtc_grps = System</div>
<div>energygrps = System</div> <div>nstlist = 10</div> <div>ns_type = grid</div> <div>pbc = xyz </div> <div>rlist = 0.8</div>
<div>coulombtype = cut-off</div> <div>rcoulomb = 1.2</div> <div>vdw-type = Cut-off </div> <div>rvdw = 0.8</div> <div>table-extension = 10.0</div> <div>pme_order = 4</div>
<div>ewald_rtol = 1e-05</div> <div>tcoupl = Berendsen</div> <div>tc-grps = System</div> <div>tau_t = 0.1</div> <div>ref_t = 298 </div>
<div>Pcoupl = Berendsen</div> <div>pcoupltype = isotropic</div> <div>tau_p = 1.0</div> <div>compressibility = 4.5e-5</div> <div>ref_p = 1.01325</div>
<div>gen_vel = yes</div> <div>gen_temp = 298</div> <div>gen_seed = 173529</div> <div>constraints = none</div></FONT> <BR>Thank You for reading.<BR><BR>-------------------------------------------------------------------------------------------------------------------------------------<BR><BR>M. Alif M. Latif<BR>Chemistry Department, Faculty of Science,<BR>Universiti Putra Malaysia,<BR>43400 UPM Serdang, Selangor,<BR><SPAN id=lw_1188499832_14 style="CURSOR:
hand; BORDER-BOTTOM: #0066cc 1px dashed; HEIGHT: 1em">Malaysia</SPAN><BR></DIV><p> 
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