Hello<div><br></div><div>I think what you have been told is wrong. You need to include both "ffcharmm27.itp" and "tip3p.itp" as the atomtypes in your tip3p.itp will otherwise not be defined. There is an easy way to check though - take out the include ffcharmm27.itp and try to run grompp on your new topology. My bet would be that it won't work and, if you are using rigid molecules, it will tell you that it finds a settles section in the wrong place.</div>
<div><br></div><div>ciao</div><div>Gareth<br><br><div class="gmail_quote">On Mon, Apr 5, 2010 at 7:26 PM, Lum Nforbi <span dir="ltr"><<a href="mailto:lumngwegia@gmail.com">lumngwegia@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Hello all,<br><br> Below are the contents of a water1.top file that I used to simulate 2000 molecules of TIP3P water (NPT). I made this topology file according to the pattern on page 114 of the manual (topology for Urea in water). My diffusion coefficient, viscosity and radial distribution functions matched those for tip3p water in literature.<br>
Recently I was told that I did not need to use another force field in the topology like ffcharmm27.itp since tip3p.itp is already a forcefield on its own. Could this be true? I just wanted to verify the authenticity of my simulation. If the structure of the topology below is not correct, please let me know.<br>
<br>; The force field files to be included<br>#include "ffcharmm27.itp"<br><br>; Include TIP3P water topology<br>#include "tip3p.itp"<br><br>[ system ]<br>Pure Water <br><br>[ molecules ]<br>;molecule name number<br>
SOL 1936<br>SOL 64<br><br>I appreciate your answers.<br><font color="#888888"><br>Lum<br>
</font><br>--<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br></blockquote></div><br></div>