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On 11/11/2010 7:46 PM, NG HUI WEN wrote:
<blockquote
cite="mid:EE6BA5FF4C277348A3A297EDC1D54DC5C330BE@wsexbe2.nottingham.edu.my"
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<p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Thanks
a lot Justin and Mark for
your useful input.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Indeed
Justin was right, the
quest to dissect the total energy of the system to get that
contributed by the
protein alone was not trivial at all! </span></p>
</div>
</blockquote>
<br>
Indeed. If I'd observed you were doing PME, I'd have made the same
point.<span style="color: rgb(31, 73, 125);"><o:p> <br>
</o:p></span><br>
<blockquote
cite="mid:EE6BA5FF4C277348A3A297EDC1D54DC5C330BE@wsexbe2.nottingham.edu.my"
type="cite">
<div class="WordSection1">
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);">I
missed out this thread
yesterday <a moz-do-not-send="true"
href="http://www.mail-archive.com/gmx-users@gromacs.org/msg34610.html">http://www.mail-archive.com/gmx-users@gromacs.org/msg34610.html</a>
as well as Mark’s trick to decompose bonded terms by hacking
the .top
file. (However, I read from <a moz-do-not-send="true"
href="http://www.gromacs.org/Documentation/Gromacs_Utilities/g_energy">http://www.gromacs.org/Documentation/Gromacs_Utilities/g_energy</a>
that the Coul-recip term is not decomposable regardless of
the tricks used…)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Mark,
following your advice, I
added –nsteps 0 (-1 didn’t work) to tpbconv. I managed to
get the interactive
prompt succesfully this time. </span></p>
</div>
</blockquote>
<br>
Yes, nsteps=-1 is a GROMACS 4.5-ism, sorry.<span style="font-family:
"Courier New";"><o:p> <br>
</o:p></span><br>
<blockquote
cite="mid:EE6BA5FF4C277348A3A297EDC1D54DC5C330BE@wsexbe2.nottingham.edu.my"
type="cite">
<div class="WordSection1">
<p class="MsoPlainText"><span style="font-family: "Courier
New";">Reading toplogy
and shit from rerun1.tpr<br>
Reading file rerun1.tpr, VERSION 4.0.7 (single precision)<br>
Setting nsteps to 0<br>
Group 0 ( System) has
100581 elements<br>
Group 1 ( Protein) has
4002 elements<br>
Group 2 ( Protein-H) has 3145
elements<br>
Group 3 ( C-alpha)
has 412 elements<br>
Group 4 ( Backbone) has 1236
elements<br>
Group 5 ( MainChain) has 1649
elements<br>
Group 6 (MainChain+Cb) has 2027 elements<br>
Group 7 ( MainChain+H) has 2039 elements<br>
Group 8 ( SideChain) has 1963
elements<br>
Group 9 ( SideChain-H) has 1496 elements<br>
Group 10 ( Prot-Masses) has 4002 elements<br>
Group 11 ( Non-Protein) has 96579 elements<br>
Group 12 ( POPE)
has 13052 elements<br>
Group 13 (
SOL) has 83523 elements<br>
Group 14 (
CL-) has 4 elements<br>
Group 15 ( Other) has
96579 elements<br>
Group 16 ( SOL_CL-) has 83527
elements<br>
Group 17 (Protein_POPE) has 17054 elements<br>
Select a group: </span><o:p></o:p></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);">As
suggested, I have also tried
to compare the (average) values of subset.tpr and
fullsystem.tpr, these are the
total energies of:<o:p></o:p></span></p>
<p class="MsoListParagraph" style="text-indent: -0.25in;"><!--[if !supportLists]--><span
style="color: rgb(31, 73, 125);"><span style="">1)<span
style="font: 7pt "Times New Roman";">
</span></span></span><!--[endif]--><span style="color:
rgb(31, 73, 125);">System= -1.28209 e+06<o:p></o:p></span></p>
<p class="MsoListParagraph" style="text-indent: -0.25in;"><!--[if !supportLists]--><span
style="color: rgb(31, 73, 125);"><span style="">2)<span
style="font: 7pt "Times New Roman";">
</span></span></span><!--[endif]--><span style="color:
rgb(31, 73, 125);">Protein= -9571.86<o:p></o:p></span></p>
<p class="MsoListParagraph" style="text-indent: -0.25in;"><!--[if !supportLists]--><span
style="color: rgb(31, 73, 125);"><span style="">3)<span
style="font: 7pt "Times New Roman";">
</span></span></span><!--[endif]--><span style="color:
rgb(31, 73, 125);">Lipid= -296121<o:p></o:p></span></p>
<p class="MsoListParagraph" style="text-indent: -0.25in;"><!--[if !supportLists]--><span
style="color: rgb(31, 73, 125);"><span style="">4)<span
style="font: 7pt "Times New Roman";">
</span></span></span><!--[endif]--><span style="color:
rgb(31, 73, 125);">SOL_CL= -821353<o:p></o:p></span></p>
<p class="MsoListParagraph" style="text-indent: -0.25in;"><!--[if !supportLists]--><span
style="color: rgb(31, 73, 125);"><span style="">5)<span
style="font: 7pt "Times New Roman";">
</span></span></span><!--[endif]--><span style="color:
rgb(31, 73, 125);">Other= -1.22684e+06<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);">It
was found that the: <o:p></o:p></span></p>
<p class="MsoListParagraph" style="text-indent: -0.25in;"><!--[if !supportLists]--><span
style="color: rgb(31, 73, 125);"><span style="">1)<span
style="font: 7pt "Times New Roman";">
</span></span></span><!--[endif]--><span style="color:
rgb(31, 73, 125);">Total energies (Protein
+ lipid + SOL_CL-) not equal to total energy of the system<o:p></o:p></span></p>
<p class="MsoListParagraph" style="text-indent: -0.25in;"><!--[if !supportLists]--><span
style="color: rgb(31, 73, 125);"><span style="">2)<span
style="font: 7pt "Times New Roman";">
</span></span></span><!--[endif]--><span style="color:
rgb(31, 73, 125);">Total energies of
(Lipid + SOL_CL-) not equal to total energy of other<o:p></o:p></span></p>
<p class="MsoListParagraph" style="text-indent: -0.25in;"><!--[if !supportLists]--><span
style="color: rgb(31, 73, 125);"><span style="">3)<span
style="font: 7pt "Times New Roman";">
</span></span></span><!--[endif]--><span style="color:
rgb(31, 73, 125);">Total energies of
(others + protein) not equal to total energy of the system<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);">I
have yet to work out the
reasons for the discrepancies, will spend some time
pondering and trying to make
sense of these (and other) values.</span></p>
</div>
</blockquote>
<br>
Aren't you omitting the inter-group non-bonded terms? Anyway, I was
suggesting this comparison for seeing whether the bonded components
can be decomposed group-wise. It is already known that the
non-bonded decomposition works.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:EE6BA5FF4C277348A3A297EDC1D54DC5C330BE@wsexbe2.nottingham.edu.my"
type="cite">
<div class="WordSection1">
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Thanks
a bunch again!<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);">HW<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<div>
<div style="border-right: medium none; border-width: 1pt
medium medium; border-style: solid none none; border-color:
rgb(181, 196, 223) -moz-use-text-color -moz-use-text-color;
padding: 3pt 0in 0in;">
<p class="MsoNormal"><b><span style="font-size: 10pt;
font-family:
"Tahoma","sans-serif"; color:
windowtext;">From:</span></b><span style="font-size:
10pt; font-family:
"Tahoma","sans-serif"; color:
windowtext;"> <a class="moz-txt-link-abbreviated" href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</a>
[<a class="moz-txt-link-freetext" href="mailto:gmx-users-bounces@gromacs.org">mailto:gmx-users-bounces@gromacs.org</a>] <b>On Behalf Of
</b>Mark Abraham<br>
<b>Sent:</b> Wednesday, November 10, 2010 9:08 PM<br>
<b>To:</b> Discussion list for GROMACS users<br>
<b>Subject:</b> Re: [gmx-users] mdrun -rerun: bonded
interactions of protein<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">On 10/11/2010 11:29 PM, NG HUI WEN wrote: <o:p></o:p></p>
<p class="MsoNormal">Hi Gmxusers,<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">I have been trying to run mdrun –rerun to
get the
energy of the protein in my protein-lipid system. I know
similar questions have
been raised on this topic before, I have tried to glean useful
information from
them to solve my problem but unfortunately to no avail. Thanks
for your
patience! <o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">As I did not have energygrps in the initial
.mdp file, I
included it this time <o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoPlainText"><span style="font-size: 10pt;
font-family: "Courier New";">integrator
= md <br>
nsteps = 0 <br>
dt =
0.002 <br>
nstxout =
50000 <br>
nstvout = 50000
<br>
nstenergy = 500 <br>
nstlog = 500 <br>
Continuation =
yes <br>
constraint_algorithm = lincs <br>
constraints = all-bonds <br>
lincs_iter = 1 <br>
lincs_order = 4 <br>
ns_type =
grid <br>
nstlist =
5 </span><o:p></o:p></p>
<p class="MsoPlainText"><span style="font-size: 10pt;
font-family: "Courier New";">rlist
= 1.2 <br>
rcoulomb = 1.2 <br>
rvdw =
1.2 <br>
coulombtype = PME <br>
pme_order = 4 <br>
fourierspacing =
0.16 <br>
tcoupl =
Nose-Hoover <br>
tc-grps = Protein
POPE SOL_CL- </span><o:p></o:p></p>
<p class="MsoPlainText"><span style="font-size: 10pt;
font-family: "Courier New";">tau_t
= 0.1 0.1 0.1 <br>
ref_t = 323
323 323 <br>
pcoupl =
Parrinello-Rahman <br>
pcoupltype =
semiisotropic </span><o:p></o:p></p>
<p class="MsoPlainText"><span style="font-size: 10pt;
font-family: "Courier New";">tau_p
= 5.0 <br>
ref_p = 1.0
1.0 <br>
compressibility = 4.5e-5
4.5e-5 <br>
pbc =
xyz <br>
DispCorr = EnerPres <br>
gen_vel =
no <br>
nstcomm = 1<br>
comm-mode = Linear<br>
comm-grps = Protein_POPE SOL_CL-<br>
<b>energygrps = Protein SOL POPE</b></span><o:p></o:p></p>
<p class="MsoPlainText"><span style="font-size: 10pt;
font-family: "Courier New";"> </span><o:p></o:p></p>
<p class="MsoPlainText"><span style="font-size: 10pt;
font-family: "Courier New";">I
then did </span><o:p></o:p></p>
<p class="MsoPlainText"><span style="font-size: 10pt;
font-family: "Courier New";">1)grompp
–f new.mdp –n index.ndx –c old.tpr –o rerun.tpr
–p topol.top</span><o:p></o:p></p>
<p class="MsoPlainText"><span style="font-size: 10pt;
font-family: "Courier New";">2)trjconv
–f old.trr –n index.ndx –s rerun.tpr –o rerun.trr (when
prompted, I selected “0” system)</span><o:p></o:p></p>
<p class="MsoPlainText"><span style="font-size: 10pt;
font-family: "Courier New";">3)mdrun
–s rerun.tpr –rerun rerun.trr</span><o:p></o:p></p>
<p class="MsoPlainText"><span style="font-size: 10pt;
font-family: "Courier New";"> </span><o:p></o:p></p>
<p class="MsoPlainText"><span style="font-size: 10pt;
font-family: "Courier New";">I
notice that the previous post <a moz-do-not-send="true"
href="http://oldwww.gromacs.org/pipermail/gmx-users/2009-January/038968.html">http://oldwww.gromacs.org/pipermail/gmx-users/2009-January/038968.html</a>
suggested to use tpbconv (on rerun.tpr) and trjconv (on
rerun.trr) to extract
the protein only. While it was possible to do so with
trjconv, it wasn’t
feasible with tpbconv (I’m using gromacs 4.0.7) – I might
have
missed out something as I did not get any prompt/output (see
below)</span><o:p></o:p></p>
<p class="MsoPlainText"><span style="font-size: 10pt;
font-family: "Courier New";"> </span><o:p></o:p></p>
<p class="MsoPlainText"><span style="font-size: 9pt;
font-family: "Courier New";">tpbconv
-s topol.tpr -n index_P.ndx -o rerun2.tpr</span><o:p></o:p></p>
<p class="MsoPlainText"><span style="font-size: 10pt;
font-family: "Courier New";"> </span><o:p></o:p></p>
<p class="MsoPlainText"><span style="font-size: 9pt;
font-family: "Courier New";">Reading
toplogy and shit from topol.tpr<br>
Reading file topol.tpr, VERSION 4.0.7 (single precision)<br>
0 steps (0 ps) remaining from first run.<br>
You've simulated long enough. Not writing tpr file</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 12pt; font-family:
"Times New Roman","serif";"><br>
Looking at the code, tpbconv checks for whether there are
any more steps to
simulate before even considering letting you use it in the
"create subset"
mode. You could argue that this is buggy, because the way it
computes whether
there are any more steps will always indicate no more steps
in such cases.
However, the workaround is to use tpbconv -nsteps -1 (as
well as the other
stuff). Let me know how this goes and I'll update the
documentation.<br>
<br>
<br>
<o:p></o:p></span></p>
<p class="MsoPlainText"><span style="font-size: 10pt;
font-family: "Courier New";"> </span><o:p></o:p></p>
<p class="MsoNormal">Using the g_energy command on the output
energy.edr file, I
got among others, these options to choose<o:p></o:p></p>
<p class="MsoPlainText"><span style="font-size: 9pt;
font-family: "Courier New";">49
Coul-SR:Protein-Protein
50
LJ-SR:Protein-Protein
</span><o:p></o:p></p>
<p class="MsoPlainText"><span style="font-size: 9pt;
font-family: "Courier New";">51
Coul-14:Protein-Protein
52
LJ-14:Protein-Protein
</span><o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">In order to get the energy of the protein,
I reckon I have
to add 49,50,51,52 (to account for the nonbonded components)
and<o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 12pt; font-family:
"Times New Roman","serif";"><br>
I think that you can make a case either way for 1-4
interactions - they're
algorithmically similar to the other non-bonded
interactions, but their
parameter values should be tightly coupled to some other of
the bonded
parameters, but then in several forcefields those values are
just scaled
versions of the normal ones... I'd guess most people call
them non-bonded.<br>
<br>
<br>
<o:p></o:p></span></p>
<p class="MsoPlainText"><span style="font-size: 9pt;
font-family: "Courier New";">1
Angle 2
G96Angle 3
Proper-Dih. 4 Ryckaert-Bell. 5
Improper-Dih </span><o:p></o:p></p>
<p class="MsoPlainText"><span style="font-size: 9pt;
font-family: "Courier New";">f</span>or
the bonded components. However, I think 1-5 is the bonded
terms for the system
and not the protein alone. Can anyone help me with this?<o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 12pt; font-family:
"Times New Roman","serif";"><br>
Compare values from reruns on the subset-tpr and the
full-tpr. I don't know
whether/how well that works. In extremis, you should be able
to reduce the .tpr
to a single interaction.<br>
<br>
<br>
<o:p></o:p></span></p>
<p class="MsoPlainText"> <o:p></o:p></p>
<p class="MsoPlainText"> <o:p></o:p></p>
<p class="MsoPlainText">Also, on a slightly different note, this
post <span style="font-size: 10pt; font-family: "Courier
New ;","serif";"><a moz-do-not-send="true"
href="http://oldwww.gromacs.org/pipermail/gmx-users/2005-July/016307.html">http://oldwww.gromacs.org/pipermail/gmx-users/2005-July/016307.html</a></span>
suggested that the force constant of the solvent (DMSO) to be
adjusted to zero.<span style="font-size: 10pt; font-family:
"Courier New";"> Am I right to think that it
does not apply to my case as my protein-lipid system </span>is
solvated with
SPC? (I read that SPC is rigid water. I did not add –DFLEXIBLE
in .mdp)<o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 12pt; font-family:
"Times New Roman","serif";"><br>
That was in the context of a full-tpr rerun. The point is
that atoms that have
been constrained don't contribute to relevant sums. Because
you are using
constraints, there's no "Bonds" energy sum for any atom
pair. Because
the DMSO was a flexible model, its bonded-interactions
contributions need to be
subtracted (i.e. parameters set to zero) to get a group-wise
bonded-interaction
value.<br>
<br>
Mark<br>
<br>
<br>
<o:p></o:p></span></p>
<p class="MsoPlainText"> <o:p></o:p></p>
<p class="MsoPlainText">Any help would be highly
appreciated.Thanks!<o:p></o:p></p>
<p class="MsoPlainText"> <o:p></o:p></p>
<p class="MsoPlainText">HW<o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 12pt; font-family:
"Times New Roman","serif";"><<
<o:p></o:p></span></p>
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<p><font face="Arial" size="2">
This message and any attachment are intended solely for the
addressee and may contain confidential information. If you
have received this message in error, please send it back to
me, and immediately delete it. Please do not use, copy or
disclose the information contained in this message or in any
attachment. Any views or opinions expressed by the author of
this email do not necessarily reflect the views of the
University of Nottingham. <br>
<br>
This message has been checked for viruses but the contents of
an attachment may still contain software viruses which could
damage your computer system: you are advised to perform your
own checks. Email communications with the University of
Nottingham may be monitored as permitted by UK & Malaysia
legislation.</font></p>
>>
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