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<DIV><SPAN class=578484916-21012010><FONT face=Arial color=#0000ff size=2>Hola
Deisy,</FONT></SPAN></DIV>
<DIV><SPAN class=578484916-21012010><FONT face=Arial color=#0000ff
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=578484916-21012010><FONT face=Arial color=#0000ff size=2>I have
used the implicit solvent which is built into mdrun-openmm. It works well: but
there are some setbacks:</FONT></SPAN></DIV>
<DIV><SPAN class=578484916-21012010><FONT face=Arial color=#0000ff size=2>1. As
far as I know it has only been tested with the amber 99 forcefield port for
mdrun-openmm. (see <A
href="http://chemistry.csulb.edu/ffamber/">http://chemistry.csulb.edu/ffamber/</A> )</FONT></SPAN></DIV>
<DIV><SPAN class=578484916-21012010><FONT face=Arial color=#0000ff size=2>and
there is no easy way to do a position restraint in mdrun-openmm. I have compared
the results of mdrun-openmm using the amber99 ff </FONT></SPAN></DIV>
<DIV><SPAN class=578484916-21012010><FONT face=Arial color=#0000ff size=2>to a
simulation suing sander and the results look well at a first
glance</FONT></SPAN></DIV>
<DIV><SPAN class=578484916-21012010><FONT face=Arial color=#0000ff
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=578484916-21012010><FONT face=Arial color=#0000ff
size=2>Hans</FONT></SPAN></DIV>
<DIV><SPAN class=578484916-21012010></SPAN> </DIV>
<BLOCKQUOTE>
<DIV class=OutlookMessageHeader dir=ltr align=left><FONT face=Tahoma
size=2>-----Ursprüngliche Nachricht-----<BR><B>Von:</B>
gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org]<B>Im
Auftrag von </B>deisy yurley rodriguez sarmiento<BR><B>Gesendet:</B>
Donnerstag, 21. Jänner 2010 17:12<BR><B>An:</B> Gromacs<BR><B>Betreff:</B>
[gmx-users] Implicit Solvent<BR><BR></FONT></DIV>
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<TD vAlign=top>Hi everyone!!!<BR>Can I use implicit solvent in a MD
simulations on gromacs?<BR>How can I do it?<BR>Thanks for your
help!!!<BR><BR>Deisy Y. Rodriguez S.<BR>Practicante de Computos
Avanzados<BR>Grupo de Investigacion en Fisicoquimica Teorica y
Experimental GIFTEX<BR>Tel. 6344000 ext. 2792<BR>Universidad
Industrial de
Santander<BR></TD></TR></TBODY></TABLE><BR></BLOCKQUOTE></BODY></HTML>