<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">Hi,<DIV><BR><DIV><DIV>On Oct 18, 2005, at 6:21 PM, Leonardo Sepulveda Durán wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite">Thanks Erik for your fast response. My reference of Encad FF is<SPAN style="font-style: italic;"> "<SPAN style="font-weight: bold;">Computer Physics Communications 91 (1995) 215-231"; </SPAN></SPAN>i have some questions about that. First, levitt used a Brook's modification of Beeman's algorithm to mantain energy. I have read from daggett's works this method is very conservative, better than normal CHARMM shift function, and very similar to FSHIFT, using only cutoff without PME for electrostatics (<SPAN style="font-weight: bold; font-style: italic;">Biochemistry 2005, 44, 609-616</SPAN>). Using Beeman and other considerations, levitt showed a 2fs can be used without SHAKE. My questions about that are: <BR> <BR> 1. Beeman can be used for integration with encadff, to avoid using SHAKE inside GROMACS?<BR></BLOCKQUOTE><DIV><BR class="khtml-block-placeholder"></DIV>No. Your best bet for long timesteps in general is to use LINCS, possibly in combination with dummy hydrogens.</DIV><DIV><BR><BLOCKQUOTE type="cite"> 2. Which is better for energy conservation? Leap frog (Which is the default GROMACS integrator, isn't?) Velocity verlet, verlet or Beeman? I found a reference about VER and SHAKED VER (<SPAN style="font-weight: bold;">J. Mol. Biol (1983) 168:595-620</SPAN>) but not comparisons with LEAP. Do you have some proper reference?<BR></BLOCKQUOTE><DIV><BR class="khtml-block-placeholder"></DIV>All verlet class integrators yield the same trajectory, but the velocity accuracy depends on how you do the averaging.<BR><BR><BLOCKQUOTE type="cite"> 3. In pdb2gmx two encadff are available. Which is the one described in Levitt1995??<BR> <BR></BLOCKQUOTE><DIV>"s" is the solvent one, "v" the vacuum version (scaled down charges).</DIV><BR><BLOCKQUOTE type="cite"> 4. In levitt1995, a <SPAN style="font-weight: bold;">Asc</SPAN> scaling factor is applied to repulsive LJ potential in order to compensate loss of dispersive interactions due to cutoff. Does <SPAN style="font-weight: bold; font-style: italic;"> encadshift </SPAN>uses that scaling?? If that is the case, Is required to define it explicitly, or the program decides based on encadshift value???<BR><BR class="khtml-block-placeholder"></BLOCKQUOTE><BR></DIV><DIV>You can use true integrated dispersion corrections in Gromacs.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>I would not recommend Encad for accurate solvent simulations at this point - the primary use is the vacuum version for rapid discrimination. Some trials we've done indicate that OPLS-AA/L combined with TIP4p produce cRMS values for some small test proteins around 1.1-1.2A, while Encad & F3C gives >=2A.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Cheers,</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Erik</DIV><DIV>---------------------------------</DIV><DIV><SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><DIV>Erik Lindahl <<A href="mailto:lindahl@sbc.su.se">lindahl@sbc.su.se</A>></DIV><DIV>Assistant Professor, Stockholm Bioinformatics Center</DIV><DIV>Stockholm University, SE 106 91 Stockholm</DIV><DIV>Phone: +46 8 5537 8564 Fax: +46 8 5537 8214</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><BR class="Apple-interchange-newline"></SPAN> </DIV><BR></DIV></BODY></HTML>