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David wrote:<br>
<blockquote type="cite"
cite="mid1080923023.5082.2.camel@h98n2fls34o1123.telia.com">
<pre wrap="">On Fri, 2004-04-02 at 18:18, Ilya Chorny wrote:
</pre>
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<pre wrap="">How many lambda values are you using?
Ilya
-----Original Message-----
From: <a class="moz-txt-link-abbreviated" href="mailto:gmx-users-admin@gromacs.org">gmx-users-admin@gromacs.org</a>
[<a class="moz-txt-link-freetext" href="mailto:gmx-users-admin@gromacs.org">mailto:gmx-users-admin@gromacs.org</a>]On Behalf Of Alexandre
Suman de Araujo
Sent: Friday, April 02, 2004 3:26 AM
To: gmx-users
Subject: [gmx-users] Bad calculated Free Energy values
Hi GMX-ers!!!
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, Metal Ions in
Solution):
DGh (kJ/mol)
Ion Calculated Experimental
Difference
Ca+2 -1391 -1591
200
Sr+2 -1248 -1442
194
Ba+2 -1107 -1317
210
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.
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<pre wrap=""><!---->You should first check numbers from other computations. Then you should
check which corrections should be made for Cut-off. These are
substantial. Check old papers by Straatsma and by Aqvist.
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Thank´s David. I´ve read Aqvist paper but not Straatsma... I´ll search
for it. But isn´t there any paper that report free energy calculations
made by GROMACS?? I didn´t find anyone.<br>
Thank´s.<br>
<br>
<pre class="moz-signature" cols="72">--
Alexandre Suman de Araujo
<a class="moz-txt-link-abbreviated" href="mailto:asaraujo@if.sc.usp.br">asaraujo@if.sc.usp.br</a>
UIN: 6194055
IFSC - USP - São Carlos - Brasil</pre>
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