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<DIV><FONT face=Arial size=2>Your potential energy seems good, so my guess is
that minimization went just fine.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>That error you are receiving iis just an warnig. No
problem at all.</FONT></DIV>
<DIV><FONT face=Arial size=2>Regards,</FONT></DIV>
<DIV><FONT face=Arial size=2>Nuno</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV>######################################<BR>Nuno Ricardo Santos Loureiro da
Silva Ferreira<BR>Departamento de Química<BR>Faculdade de Ciências e
Tecnologia<BR>Universidade de Coimbra<BR>3004-535 Coimbra - Portugal<BR>Fax:
+351 239 827703 - <A
href="http://www.biolchem.qui.uc.pt">www.biolchem.qui.uc.pt</A><BR>########################################</DIV>
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<DIV style="FONT: 10pt arial">----- Original Message ----- </DIV>
<DIV
style="BACKGROUND: #e4e4e4; FONT: 10pt arial; font-color: black"><B>From:</B>
<A title=gold_smith@rediffmail.com
href="mailto:gold_smith@rediffmail.com">gold gunaseelan</A> </DIV>
<DIV style="FONT: 10pt arial"><B>To:</B> <A title=spoel@xray.bmc.uu.se
href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</A> ; <A
title=spoel@gromacs.org href="mailto:spoel@gromacs.org">spoel@gromacs.org</A>
</DIV>
<DIV style="FONT: 10pt arial"><B>Cc:</B> <A title=gmx-users@gromacs.org
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A> </DIV>
<DIV style="FONT: 10pt arial"><B>Sent:</B> Monday, April 05, 2004 12:11
PM</DIV>
<DIV style="FONT: 10pt arial"><B>Subject:</B> [gmx-users] minimization</DIV>
<DIV><BR></DIV>
<P>dear sir ,<BR>Iam using gromacs 3.2.1<BR>I changed the following in
em.mdp file as<BR><BR>define = -DFLEXIBLE and ran energy minimisation
but it converged as <BR><BR>Stepsize too small, or no change in
energy.<BR>Converged to machine precision,<BR>but not to the requested
precision Fmax < 2000<BR><BR>Double precision normally gives you higher
accuracy.<BR><BR>writing lowest energy coordinates.<BR><BR>Steepest Descents
converged to machine precision in 202 steps,<BR>but did not reach the
requested Fmax < 2000.<BR>Potential Energy =
-4.0429609e+05<BR>Maximum force = 4.6900386e+03 on atom
1650<BR>Norm of force = 1.4885711e+04<BR><BR>Previously i
had given define =-DFLEX_SPC it gave the same error but it converged in 57
steps.I looked in one of ur old reply,in which u have asked to see toplogy
file <BR><BR>> ; Include water topology<BR>> #ifdef FLEX_SPC<BR>>
#include "flexspc.itp"<BR>> #else<BR>> #include "spc.itp"<BR>>
#endif<BR>> <BR>> then you can try with this file:<BR>> <BR>>
<BR>> title
= xxxx<BR>> cpp
= /lib/cpp<BR>> include
= -I../top<BR>> define
= -DFLEX_SPC<BR><BR>I
would like to point out that tis has been changed a bit in 3.2<BR>If you use
spc water this still will work, but for other models the more<BR>generic way
of writing is:<BR><BR>#include "water.itp" (either tip3p, tip4p, spc,
spce)<BR><BR>define = -DFLEXIBLE<BR><BR>But i didnot find this in top
file<BR><BR>; Include water topology<BR>#include "spc.itp"<BR><BR>#ifdef
POSRES_WATER<BR>I found these terms missing as specified by u above.<BR>sir
please suggest whats wrong .is protein minimized properly.thanks in advance
-gsmith </P><BR><BR><A
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