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<p class=MsoNormal><b><font size=2 color=black face=Tahoma><span
style='font-size:10.0pt;font-family:Tahoma;color:windowtext;font-weight:bold'>From:</span></font></b><font
size=2 color=black face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma;
color:windowtext'> gmx-users-admin@gromacs.org
[mailto:gmx-users-admin@gromacs.org] <b><span style='font-weight:bold'>On
Behalf Of </span></b>Alexandre Suman de Araujo<br>
<b><span style='font-weight:bold'>Sent:</span></b> Friday, April 02, 2004 7:26
PM<br>
<b><span style='font-weight:bold'>To:</span></b> gmx-users<br>
<b><span style='font-weight:bold'>Subject:</span></b> [gmx-users] Bad
calculated Free Energy values</span></font><font color=black><span
style='color:windowtext'><o:p></o:p></span></font></p>
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<p class=MsoNormal><font size=3 color=black face="Times New Roman"><span
style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 color=black face="Times New Roman"><span
style='font-size:12.0pt'>Hi GMX-ers!!!<br>
<br>
I´m performing some simulations to obtain free energy of hydration of some ions
(Ca+2, Sr+2 and Ba+2) using oplsaa(tip3p for water) force field and the results
aren´t so good in my opinion. Look at the results below and the experimental
values (taken from book Burgess, <i><span style='font-style:italic'>Metal Ions
in Solution</span></i>):<br>
<br>
DGh (kJ/mol)<br>
<br>
Ion
Calculated
Experimental Difference<br>
<br>
Ca+2 -1391
-1591
200<br>
Sr+2 -1248
-1442
194<br>
Ba+2 -1107
-1317
210<br>
<br>
<br>
Look that the difference between calc. and exp. values are something about 200
kJ/mol, then I think this can be something I´m not including in the
calculations that results in error with almost same values in three cases.<br>
<br>
The .mdp file that I´m using is this one:<br>
<br>
;<br>
; Input file<br>
;<br>
title
= Calculo da energia livre de solvatacao do ion de Na em
H2O ; a string<br>
cpp
=
/lib/cpp
; c-preprocessor<br>
dt
=
0.001
; time step (ps)<br>
integrator =
md
; Tipo de simulacao a fazer<br>
nsteps
=
800000
; number of steps<br>
;Faca energia livre<br>
free_energy =
yes
; calcule a energia livre<br>
init_lambda =
0
; valor inicial de lambda<br>
delta_lambda =
1.25e-6
; 1/n_passos<br>
nstcomm
=
1
; reset c.o.m. motion<br>
nstxout
=
100
; write coords<br>
nstvout
=
100
; write velocities<br>
nstlog
=
100
; print to logfile<br>
nstenergy =
100
; print energies<br>
nstlist
=
10
; update pairlist<br>
ns_type
=
grid
; pairlist method<br>
pbc
=
xyz
; Usar PBC em todas as direcoes<br>
rlist
=
1.3
; cut-off for ns<br>
coulombtype =
Cut-off
; <st1:country-region w:st="on"><st1:place w:st="on">Usa</st1:place></st1:country-region>
cut-off por causa do calculo de e livre.<br>
rcoulomb
=
1.3
; cut-off for coulomb<br>
fourierspacing =
0.12
; Parametro pra PME<br>
pme_order =
4
; Parametro pra PME<br>
ewald_rtol =
1e-5
; Parametro PME<br>
optimize_fft =
yes
; Optimiza a FFT, claro.. hahah<br>
vdwtype
=
cut-off
; Tipo de VdW<br>
rvdw
=
1.3
; raio de calculo de Vdw<br>
tcoupl
=
berendsen
; Temperature coupling<br>
ref_t
=
300
; Temperatura referencia<br>
tc-grps
=
System
; Quais grupos sera afetados pelo tcoupl<br>
tau_t
=
0.01
; Tempo que sera verificada a temperatura<br>
pcoupl
=
berendsen
; pressure bath<br>
pcoupltype =
isotropic
; pressure geometry<br>
tau_p
=
1
; p-coupoling time<br>
compressibility =
4.4e-5
; compressibilidade da acetonitrila<br>
ref_p
= 1.0<br>
<br>
<br>
Somebody could help me telling me if I´m forgetting anything or making
something wrong?<br>
Or this difference is normal in free energy calculations????<br>
<br>
Thank´s very much and waiting answers.<br>
<br>
<br>
<o:p></o:p></span></font></p>
<pre><font size=2 color=black face="Courier New"><span style='font-size:10.0pt'>-- <o:p></o:p></span></font></pre><pre><font
size=2 color=black face="Courier New"><span style='font-size:10.0pt'>Alexandre Suman de Araujo<o:p></o:p></span></font></pre><pre><font
size=2 color=black face="Courier New"><span style='font-size:10.0pt'><a
href="mailto:asaraujo@if.sc.usp.br">asaraujo@if.sc.usp.br</a><o:p></o:p></span></font></pre><pre><font
size=2 color=black face="Courier New"><span style='font-size:10.0pt'>UIN: 6194055<o:p></o:p></span></font></pre><pre><font
size=2 color=black face="Courier New"><span style='font-size:10.0pt'>IFSC - USP - São Carlos - Brasil<o:p></o:p></span></font></pre></div>
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