<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<title></title>
</head>
<body>
<a class="moz-txt-link-abbreviated" href="mailto:david.evans@ulsop.ac.uk">david.evans@ulsop.ac.uk</a> a écrit:<br>
<blockquote type="cite" cite="mid11581875001103@ams1.ulsop.ac.uk">
<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
_______________________________________________
gmx-users mailing list
<a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>
<a class="moz-txt-link-freetext" href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a>
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to <a class="moz-txt-link-abbreviated" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.
</pre>
</blockquote>
<pre wrap=""><!---->_______________________________________________
gmx-users mailing list
<a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>
<a class="moz-txt-link-freetext" href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a>
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to <a class="moz-txt-link-abbreviated" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.
</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>
</body>
</html>