<div><span style="background-color: rgb(255, 255, 255); -webkit-text-stroke-color: initial !important; font-family: sans-serif; background-image: none !important; "><div style="font-family: arial; font-size: small; "><span class="Apple-style-span" style="font-family: sans-serif; font-size: medium; ">There was no water. Version 4.5.5. Single precision. </span><span class="Apple-style-span" style="font-family: sans-serif; font-size: medium; ">This is what I ran:</span></div>
<div style="font-family: arial; font-size: small; "><div style="font-family: sans-serif; font-size: medium; "><div><br></div><div>pdb2gmx -f 1.pdb -p g1 -o g1</div><div>grompp -f 1.mdp -c g1.gro -o g1.tpr -p g1.top</div><div>
mdrun -v -s g1.tpr -c ag1.gro -g g1.log -e g1.ene</div><div>Potential energy: 1.19780e+02 kJ/mol</div><div><br></div><div>grompp -f 1.mdp -c 1.pdb -o g1.tpr -p g1.top</div><div>mdrun -v -s g1.tpr -c ag1.gro -g g1.log -e g1.ene</div>
<div>Potential energy: 1.15997e+02 kJ/mol</div></div><span class="Apple-style-span" style="font-family: sans-serif; font-size: medium; "><div style="font-family: arial; font-size: small; "><span class="Apple-style-span" style="font-family: sans-serif; font-size: medium; "><br>
</span></div>The mdp file:</span></div></span></div><div><span style="background-color: rgb(255, 255, 255); -webkit-text-stroke-color: initial !important; font-family: sans-serif; background-image: none !important; font-size: medium; "><div>
<br></div><div>integrator = md</div><div>nsteps = 0</div><div>nstcomm = 1</div><div>nstxout = 1</div><div>nstvout = 1</div><div>nstfout = 0</div>
<div>nstlog = 1</div><div>nstenergy = 1</div><div>nstxtcout = 0</div><div>nstlist = 0</div><div>ns_type = simple</div><div>pbc = no</div>
<div>rlist = 0</div><div>rcoulomb = 0</div><div>rvdw = 0</div><div>gen_vel = no</div><div>unconstrained-start = yes</div><div>lincs-warnangle = 30</div>
<div><br></div></span></div><div><span style="background-color: rgb(255, 255, 255); -webkit-text-stroke-color: initial !important; font-family: sans-serif; background-image: none !important; font-size: medium; ">The pdb file :</span></div>
<div><span style="background-color: rgb(255, 255, 255); -webkit-text-stroke-color: initial !important; font-family: sans-serif; background-image: none !important; font-size: medium; "><br></span></div><div><span style="background-color: rgb(255, 255, 255); -webkit-text-stroke-color: initial !important; font-family: sans-serif; background-image: none !important; font-size: medium; "><div>
HETATM 1 1HH3 ACE 1 -1.449 0.109 -0.581 H</div><div>HETATM 2 CH3 ACE 1 -2.101 -0.268 0.202 C</div><div>HETATM 3 2HH3 ACE 1 -1.708 0.090 1.151 H</div>
<div>HETATM 4 3HH3 ACE 1 -2.109 -1.350 0.189 H</div><div>HETATM 5 C ACE 1 -3.491 0.269 0.000 C</div><div>HETATM 6 O ACE 1 -4.453 -0.401 -0.152 O</div>
<div>ATOM 7 N GLY 2 -3.601 1.734 0.000 N</div><div>ATOM 8 H GLY 2 -3.039 2.278 -0.623 H</div><div>ATOM 9 CA GLY 2 -4.525 2.391 0.903 C</div>
<div>ATOM 10 HA1 GLY 2 -5.539 2.051 0.696 H</div><div>ATOM 11 HA2 GLY 2 -4.263 2.147 1.932 H</div><div>ATOM 12 C GLY 2 -4.461 3.901 0.720 C</div>
<div>ATOM 13 O GLY 2 -3.677 4.400 -0.128 O</div><div>HETATM 14 N NME 3 -5.316 4.776 1.535 N</div><div>HETATM 15 H NME 3 -6.182 4.876 1.044 H</div>
<div>HETATM 16 CH3 NME 3 -4.685 6.072 1.731 C</div><div>HETATM 17 1HH3 NME 3 -3.754 5.941 2.272 H</div><div>HETATM 18 2HH3 NME 3 -5.328 6.697 2.341 H</div>
<div>HETATM 19 3HH3 NME 3 -4.465 6.615 0.809 H</div><div>END</div><div><br></div><div><br></div></span></div><b style="background-color: rgb(255, 255, 255); -webkit-text-stroke-color: initial !important; font-family: sans-serif; background-image: none !important; font-size: medium; ">In reply to chris.neale at <a href="http://utoronto.ca">utoronto.ca</a>:</b><div>
<span class="Apple-style-span" style="font-family: monospace; white-space: pre; background-color: rgb(255, 255, 255); "><br></span></div><div><span class="Apple-style-span" style="font-family: monospace; white-space: pre; background-color: rgb(255, 255, 255); "><font class="Apple-style-span" size="4">It's more useful if you provide more information. What was the .pdb </font></span></div>
<div><span class="Apple-style-span" style="font-family: monospace; white-space: pre; background-color: rgb(255, 255, 255); font-size: large; "><br></span></div><div><span class="Apple-style-span" style="font-family: monospace; white-space: pre; background-color: rgb(255, 255, 255); font-size: large; ">file (can I download it from the pdb databank?) was there water? what </span></div>
<pre style="background-color: rgb(255, 255, 255); -webkit-text-stroke-color: initial !important; background-image: none !important; "><span class="Apple-style-span" style="font-size: large; ">version of gromacs? was it compiled in double or single precision? </span></pre>
<pre style="background-color: rgb(255, 255, 255); -webkit-text-stroke-color: initial !important; background-image: none !important; "><span class="Apple-style-span" style="font-size: large; ">what were your mdp parameters?</span></pre>