Hi<br>Well the tutorial in the following website has mentioned about the importance of sc_alpha and sc-power. Also the manual gives you more information.<br><a href="http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial">http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial</a>.<br>
<br>Regards<br>Sai<br><br><div class="gmail_quote">On Sun, Jun 13, 2010 at 6:56 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div class="im"><br>
<br>
fancy2012 wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Dear GMX users,<br>
when I generate the input file of MD simulation using grompp, I get this error: ERROR: The soft-core power is 0 and can only be 1 or 2. I don't know how to figure it out? Could somebody give me a hand? Thanks very much in advance!<br>
</blockquote>
<br></div>
You haven't specified a value for sc-power, so the default of zero is taken. Manual section 7.3.23.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div><div></div><div class="h5">
Here is the mdp file:<br>
cpp = /lib/cpp<br>
constraints = all-bonds<br>
integrator = md<br>
tinit = 0.0<br>
dt = 0.002 nsteps = 25000 nstcomm = 1<br>
nstxout = 10000<br>
nstvout = 0<br>
nstfout = 0<br>
nstlog = 500<br>
nstenergy = 250<br>
nstxtcout = 1000<br>
xtc_precision = 1000<br>
xtc_grps = Protein<br>
nstlist = 5<br>
energygrps = Protein SOL<br>
ns_type = grid<br>
rlist = 0.9<br>
coulombtype = Reaction-Field<br>
epsilon_r = 78.0<br>
rcoulomb = 1.4<br>
rvdw = 1.4<br>
Tcoupl = Berendsen<br>
tc-grps = Protein SOL<br>
ref_t = 300 300<br>
tau_t = 0.1 0.1<br>
Pcoupl = Berendsen<br>
tau_p = 1.0<br>
compressibility = 4.6e-5<br></div></div>
ref_p ; = 1.0<div class="im"><br>
free_energy = yes<br>
init_lambda = 0.00<br>
sc-alpha = 1.51<br>
All the best,<br>
fancy<br>
<br>
</div></blockquote>
<br><div class="im">
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
-- <br></div><div><div></div><div class="h5">
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