By setting the emtol to 1.0, didnt work. Anyother way i could figure out.<br><br><div class="gmail_quote">On Thu, Feb 9, 2012 at 6:32 PM, Justin A. Lemkul <span dir="ltr">&lt;<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>&gt;</span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div class="im"><br>
<br>
lina wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
On Thu, Feb 9, 2012 at 6:17 PM, aiswarya pawar &lt;<a href="mailto:aiswarya.pawar@gmail.com" target="_blank">aiswarya.pawar@gmail.com</a>&gt; wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
Dear Gromacs users,<br>
<br>
I have a MD simulated protein and i take frame from this and remove water<br>
and add water implicit in the interface and want to do energy minimization<br>
but while doing the minimization i get errors. The steps followed are-<br>
<br>
pdb2gmx -ignh -f 1OC0.pdb -o 1oco.pdb -p 1oco.top -nocmap<br>
grompp -f minim.mdp -c 1oco.pdb -p 1oco.top -o 1oco.tpr<br>
<br>
The minim.mdp file =<br>
<br>
; Lines starting with &#39;;&#39; ARE COMMENTS<br>
; Everything following &#39;;&#39; is also comment<br>
<br>
title        = Energy Minimization    ; Title of run<br>
<br>
; The following line tell the program the standard locations where to find<br>
certain files<br>
cpp        = /lib/cpp    ; Preprocessor<br>
<br>
; Define can be used to control processes<br>
define          = -DFLEXIBLE<br>
<br>
; Parameters describing what to do, when to stop and what to save<br>
integrator    = steep        ; Algorithm (steep = steepest descent<br>
minimization)<br>
emtol        = 1000.0    ; Stop minimization when the maximum force &lt; 1.0<br>
</blockquote>
emtol = 1.0<br>
</blockquote>
<br></div>
If mdrun could not converge to 1000, setting a target of 1 will not solve anything.  The OP should refer to:<br>
<br>
<a href="http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision" target="_blank">http://www.gromacs.org/<u></u>Documentation/Errors#Stepsize_<u></u>too_small.2c_or_no_change_in_<u></u>energy._Converged_to_machine_<u></u>precision.2c_but_not_to_the_<u></u>requested_precision</a><br>

<br>
-Justin<br>
<br>
-- <br>
==============================<u></u>==========<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>
==============================<u></u>==========<div class="HOEnZb"><div class="h5"><br>
-- <br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Aiswarya  B Pawar<br><br><div>Project Assistant,<br>Bioinformatics Dept, <br>Indian Institute of Science<br>Bangalore<br><br></div><br>