Hi Gromacs users ,<br>as per the link given on gromacs website...<br><a class="external text" href="http://nmr.chem.uu.nl/%7Etsjerk/course/molmod/" rel="nofollow" title="http://nmr.chem.uu.nl/~tsjerk/course/molmod/">Introduction to Molecular Dynamics Simulations and Analysis</a>
- Tutorial for performing and analyzing simulations of proteins.
Includes examples of many of the gromacs analysis tools and addresses a
number of issues that are commonly raised on the GROMACS user list. This
tutorial uses GROMACS version 3.3.1 (Tsjerk A. Wassenaar).<br><br><br>editconf -f protein-EM-vacuum.pdb -o protein-PBC.gro -bt dodecahedron -d 1.0
<br><br>mdp file parameter are as follow ,<br><pre>coulombtype = Reaction-Field
rcoulomb = 1.4
epsilon_rf = 78
epsilon_r = 1
vdw-type = Cut-off
rvdw = 1.4<br> <br> so my query is ..<br></pre>As mention in manual ...<br>(Page no 14 manual 4.5.4 I am using the Gromacs 4.5.4 )<br><b>This means that the length of each box vector must exceed the length of the macromolecule in the<br>
direction of that edge plus two times the cut-off radius Rc </b>. <br> <i>In the tutorial -d 1.0 is less than 1.4 .</i>..<br> I noticed that manual version and tutorial gromacs version are different ...<br>But it raise a lot of confusion for new users like me..<br>
<br>1. Is the -d .. should be equal or more than cutt off ???<br> or <br> Is the -d .. should be equal or more than cutt-off??<br><br><br><br>