Thanks, Mark. <br><br>No, it is not picking any chk files. But the coordinates in the gro file after mdrun change slightly for some of the atoms on using cg and l-bfgs, whereas with steep they remain the same.<br><br>e.g., in b4min.gro submitted to cg or l-bfgs or steep:<br>
<br>2GLY O 13 0.736 0.922 -0.350<br><br>in min.gro after cg and l-bfgs:<br><br> 2GLY O 13 0.735 0.920 -0.349<br><br>in min.gro after steep:<br><br>2GLY O 13 0.736 0.922 -0.350<br><br>So, I guess I have to trust steep on this if I just need the energy of the molecule as the coordinates of atoms do not change.<br>
<br>By the look of it, AMBER10 also changes coordinates slightly on using:<br><br> imin=0, maxcyc = 0, ncyc = 0, ntb = 0, cut = 99999<br><br>Is there any other way of calculating a single point energy by GROMACS?<br><br>-Vlad<br>
<br>On 8/01/2011 12:10 AM, Vlad Isaev wrote:<br><div class="gmail_quote"><pre>><i> Hi,<br></i>><i><br></i>><i> I want to calculate the energy of a peptide. No minimization, or md, <br></i>><i> just the energy at 0 K. I use this input:<br>
</i>><i><br></i>><i> integrator = steep<br></i>><i> nsteps = 0<br></i>><i> nstenergy = 1<br></i>><i> nstlist = 0<br></i>><i> ns_type = simple<br>
</i>><i> pbc = no<br></i>><i> rlist = 0<br></i>><i> rcoulomb = 0<br></i>><i> rvdw = 0<br></i>><i><br></i>><i><br></i>><i> I get:<br>
</i>><i><br></i>><i> Potential Energy = -1.1744482e+02<br></i>><i><br></i>><i> Changing steep to cg changes the potential energy even though nsteps=0:<br></i>><i><br></i>><i> Potential Energy = -1.2410449e+02<br>
</i>><i><br></i>><i> The corresponding energy from AMBER10 is : -1.20172848e+02 (conversion <br></i>><i> factor 4.184).<br></i>><i><br></i>><i> Any ideas why these are so different?<br></i><br>< That's pretty weird. Please double check that you were really using the <br>
< same input coordinates to grompp (and that mdrun wasn't picking up a <br>< checkpoint file).<br><br>< Mark</pre></div><br>