<br><br><div class="gmail_quote">On 29 February 2012 14:04, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"><div class="im">
On 29/02/2012 8:33 PM, Thomas Evangelidis wrote:
<blockquote type="cite">Dear GROMACS community,<br>
<br>
I use the following parameters to run MD of ethane in vacuo. Then
I calculate the H-C-C-H dihedral angle distribution and from that
the rotational energy barrier using the formula DeltG=-k*T*ln(x),
where x is the dihedral value. The rotational energy barrier is
correct (~ 12 kJ) with all-bond constraints, but not with h-bond
or no bond constraints. Could anyone tell me which other
parameters to tweak in order to get the correct dihedral angle
distribution without any bond constraints.<br>
<br>
Thanks in advance.<br>
Thomas<br>
<br>
<br>
<br>
integrator = md<br>
tinit = 0.0<br>
dt = 0.002<br>
</blockquote>
<br></div>
This is too long if you are not using all-atom constraints. See
manual 6.5 for discussion.<br><font color="#888888">
<br></font></div></blockquote><div>Yes, I am sorry, I forgot to mention that in that case I use dt=0.001 and nsteps=5000000.<br> </div><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"><font color="#888888">
Mark</font><div><div></div><div class="h5"><br>
<br>
<blockquote type="cite">nsteps = 2500000<br>
init_step = 0<br>
simulation_part = 1<br>
comm-mode = Angular<br>
nstcomm = 20<br>
comm-grps = <br>
emtol = 0.01<br>
emstep = 0.01<br>
niter = 0<br>
fcstep = 0<br>
nstcgsteep = 1000<br>
nbfgscorr = 10<br>
nstxout = 0<br>
nstvout = 0<br>
nstfout = 0<br>
nstlog = 500<br>
nstcalcenergy = -1<br>
nstenergy = 500<br>
nstxtcout = 100<br>
xtc-precision = 1000<br>
xtc-grps = <br>
energygrps = System<br>
nstlist = 0<br>
ns_type = simple<br>
pbc = no<br>
periodic_molecules = no<br>
rlist = 0<br>
rlistlong = -1<br>
coulombtype = Cut-off<br>
rcoulomb-switch = 0<br>
rcoulomb = 0.0<br>
epsilon_r = 1.0<br>
epsilon_rf = 1<br>
vdw-type = Cut-off<br>
rvdw-switch = 0<br>
rvdw = 0<br>
DispCorr = no<br>
table-extension = 1<br>
energygrp_table = <br>
implicit_solvent = No<br>
tcoupl = v-rescale<br>
nsttcouple = 5<br>
nh-chain-length = 10<br>
tc-grps = System<br>
tau_t = 0.1<br>
ref_t = 300<br>
Pcoupl = no<br>
Pcoupltype = Isotropic<br>
nstpcouple = -1<br>
tau_p = 1<br>
compressibility = <br>
ref_p = 1.0 1.0 1.0<br>
refcoord_scaling = No<br>
andersen_seed = 815131<br>
gen_vel = yes<br>
gen_temp = 300.0<br>
gen_seed = 173529<br>
constraints = all-bonds<br>
constraint-algorithm = Lincs<br>
continuation = no<br>
Shake-SOR = no<br>
shake-tol = 1e-04<br>
lincs-order = 4<br>
lincs-iter = 1<br>
lincs-warnangle = 30<br>
morse = no<br>
<br clear="all">
<br>
<br>
<br>
<br>
-- <br>
<p style="margin-bottom:0cm" align="LEFT">======================================================================</p>
<p style="margin-bottom:0cm" align="LEFT">Thomas Evangelidis</p>
<p style="margin-bottom:0cm" align="LEFT">PhD student</p>
<p style="margin-bottom:0cm" align="LEFT">Biomedical Research
Foundation, Academy of Athens</p>
<p style="margin-bottom:0cm" align="LEFT">4 Soranou Ephessiou ,
115 27
Athens, Greece<br>
<br>
email: <a href="mailto:tevang@bioacademy.gr" target="_blank">tevang@bioacademy.gr</a></p>
<p style="margin-bottom:0cm" align="LEFT"> <a href="mailto:tevang3@gmail.com" target="_blank">tevang3@gmail.com</a></p>
<p style="margin-bottom:0cm" align="LEFT"><br>
website:
<a href="https://sites.google.com/site/thomasevangelidishomepage/" target="_blank">https://sites.google.com/site/thomasevangelidishomepage/</a></p>
<p style="margin-bottom:0cm" align="LEFT"><br>
</p>
<br>
<br>
<fieldset></fieldset>
<br>
</blockquote>
<br>
</div></div></div>
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<p style="margin-bottom:0cm" align="LEFT">======================================================================</p>
<p style="margin-bottom:0cm" align="LEFT">Thomas Evangelidis</p>
<p style="margin-bottom:0cm" align="LEFT">PhD student</p>
<p style="margin-bottom:0cm" align="LEFT">Biomedical Research
Foundation, Academy of Athens</p>
<p style="margin-bottom:0cm" align="LEFT">4 Soranou Ephessiou , 115 27
Athens, Greece<br><br>email: <a href="mailto:tevang@bioacademy.gr" target="_blank">tevang@bioacademy.gr</a></p>
<p style="margin-bottom:0cm" align="LEFT"> <a href="mailto:tevang3@gmail.com" target="_blank">tevang3@gmail.com</a></p>
<p style="margin-bottom:0cm" align="LEFT"><br>website:
<a href="https://sites.google.com/site/thomasevangelidishomepage/" target="_blank">https://sites.google.com/site/thomasevangelidishomepage/</a></p>
<p style="margin-bottom:0cm" align="LEFT"><br>
</p>
<br>