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On 8/01/2011 1:38 PM, Vlad Isaev wrote:
<blockquote
cite="mid:AANLkTinnCxSNCLvBoGe0s88n8YHwfGuvGcPe5mDpZ2fL@mail.gmail.com"
type="cite">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>
</blockquote>
<br>
OK, well this must be a consequence of the algorithms, despite being
zero-step.<br>
<br>
<blockquote
cite="mid:AANLkTinnCxSNCLvBoGe0s88n8YHwfGuvGcPe5mDpZ2fL@mail.gmail.com"
type="cite"><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>
</blockquote>
<br>
There's zero-step MD, so long as you make sure the start is
unconstrained. The mdrun -rerun functionality does single point
energies over a trajectory, which can be one configuration. By
definition, the latter doesn't change configurations.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:AANLkTinnCxSNCLvBoGe0s88n8YHwfGuvGcPe5mDpZ2fL@mail.gmail.com"
type="cite"><br>
-Vlad<br>
<br>
On 8/01/2011 12:10 AM, Vlad Isaev wrote:<br>
<div class="gmail_quote">
<pre>><i> Hi,
</i>><i>
</i>><i> I want to calculate the energy of a peptide. No minimization, or md,
</i>><i> just the energy at 0 K. I use this input:
</i>><i>
</i>><i> integrator = steep
</i>><i> nsteps = 0
</i>><i> nstenergy = 1
</i>><i> nstlist = 0
</i>><i> ns_type = simple
</i>><i> pbc = no
</i>><i> rlist = 0
</i>><i> rcoulomb = 0
</i>><i> rvdw = 0
</i>><i>
</i>><i>
</i>><i> I get:
</i>><i>
</i>><i> Potential Energy = -1.1744482e+02
</i>><i>
</i>><i> Changing steep to cg changes the potential energy even though nsteps=0:
</i>><i>
</i>><i> Potential Energy = -1.2410449e+02
</i>><i>
</i>><i> The corresponding energy from AMBER10 is : -1.20172848e+02 (conversion
</i>><i> factor 4.184).
</i>><i>
</i>><i> Any ideas why these are so different?
</i>
< That's pretty weird. Please double check that you were really using the
< same input coordinates to grompp (and that mdrun wasn't picking up a
< checkpoint file).
< Mark</pre>
</div>
<br>
</blockquote>
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