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<DIV><FONT face=Arial size=2>Dear All,</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>After my system equilibrated, I have performed 2ns
production phase md simulation. I am expecting my calulation is in the NPT
ensemble. From the g_energy analysis, temperature is well
consistent around 300K, but the pressure is fluctuating significantly from
-340 bar 300 bar.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>The parameter setup in the .mdp file
is as following:</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>*******</FONT></DIV>
<DIV><FONT face=Arial
size=2>Pcoupl
=
berendsen<BR>pcoupltype
=
isotropic<BR>tau_p
= 1<BR>compressibility =
4.5e-5<BR>ref_p
= 1</FONT></DIV>
<DIV><FONT face=Arial size=2>********</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Could anyone please let me kwow what's wrong in the
file setup???</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Thanks,</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>nancy</FONT></DIV>
<DIV><FONT face=Arial size=2> </DIV>
<DIV><BR></DIV></FONT>
<BLOCKQUOTE
style="PADDING-RIGHT: 0px; PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #000000 2px solid; MARGIN-RIGHT: 0px">
<DIV style="FONT: 10pt arial">----- Original Message ----- </DIV>
<DIV
style="BACKGROUND: #e4e4e4; FONT: 10pt arial; font-color: black"><B>From:</B>
<A title=m.kreissler@lpcm.u-bordeaux1.fr
href="mailto:m.kreissler@lpcm.u-bordeaux1.fr">Marc Kreissler</A> </DIV>
<DIV style="FONT: 10pt arial"><B>To:</B> <A title=gmx-users@gromacs.org
href="mailto:gmx-users@gromacs.org">Discussion list for GROMACS users</A>
</DIV>
<DIV style="FONT: 10pt arial"><B>Sent:</B> Friday, March 04, 2005 10:11
AM</DIV>
<DIV style="FONT: 10pt arial"><B>Subject:</B> Re: [gmx-users] DNA/RNA records
for OPLS force fieldin GROMACS format.</DIV>
<DIV><BR></DIV><A class=moz-txt-link-abbreviated
href="mailto:david.evans@ulsop.ac.uk">david.evans@ulsop.ac.uk</A> a écrit:<BR>
<BLOCKQUOTE cite=mid11581875001103@ams1.ulsop.ac.uk type="cite"><PRE wrap="">Hi,
I think that 60 water molecules is far too few. One would typically
add a few thousand in a box extending about 10 angstroms from
the solute.
If it's not too heretical for this list, might I suggest looking
at the DNA tutorial on the Amber web site? This, and the
cited references, give a good idea of what people do in the
successful DNA simulations to date.
good luck,
Dave
-
</PRE>
<BLOCKQUOTE type="cite"><PRE wrap="">after some work and many "try and error" i have succeeded to
build the various files which are necessary for running Gromacs
calculations on a DNA_decamer with about 60 water molecules,
2 Ca++ ions and 15 Na+ ions to neutralise the excess negative
charges due to phosphate groups.
i get a surprising result after 1ns of simulation ( about 3hours
</PRE></BLOCKQUOTE><PRE wrap=""><!----> on a Linux_PC) :
</PRE>
<BLOCKQUOTE type="cite"><PRE wrap="">the double-helix ends up in a dissociated state.
for this calculation i use - a triclinic box
- pme for electrostatics
- T_coupling at 300K
- no P_coupling
- oplsaar force field
my experience in MD_simulations is not tremendous, especially
concerning the simulation parameters.
- i am wondering if i have choosen the right box form ?
- what about the box dimensions ?
- may be the number of water molecules is too small for this system
</PRE></BLOCKQUOTE><PRE wrap=""><!---->?
</PRE>
<BLOCKQUOTE type="cite"><PRE wrap="">- and last but not least i don't know if the periodic boundary
</PRE></BLOCKQUOTE><PRE wrap=""><!---->conditions
</PRE>
<BLOCKQUOTE type="cite"><PRE wrap="">are on or off ?
a lot of questions.
i would appreciate your helpfull advices.
merci , cordialement
marc kreissler
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</PRE></BLOCKQUOTE>bonsoir david evans,<BR><BR>thank's for the usefull hint
to have a look at the "DNA tutorial"<BR>located on the Amber website. "keep on
learning, learning,..." ( a quote from vladimir<BR>illitch
lenin).<BR><BR>cordialement,<BR>marc kreissler<BR><BR><BR>
<P>
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