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<DIV>Hi<BR> Thanks for ur precious advise !<BR>but now i
am facing problem in mdrun .<BR>upto grompp all thing are going fine but when i
start mdrun i am facing some problem ..<BR> I was trying to genrate .gro
(output which only contain coordinates i.e. dppc128out.gro) and
.xtc(dppc128.xtc) file but these file<BR>are not genrating . or there is any
other way to genrate a file which contain only coordinates not other
outputs(like velocity,energy etc..).<BR>can u give me some advise again
.......<BR>my input for mdrun is as follows (dppc128 is my file name)<BR>mdrun
-v -s dppc128 -e dppc128 -o dppc128 -c dppc128out -x dppc128 -g<BR>dppc128
>& dppc128.job &<BR><BR>Thanks
!<BR><BR>
Alok Jain</DIV>
<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=asg2000@bol.com.br href="mailto:asg2000@bol.com.br">Arlan
Gonçalves</A> </DIV>
<DIV style="FONT: 10pt arial"><B>To:</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> Sunday, September 12, 2004 2:50
AM</DIV>
<DIV style="FONT: 10pt arial"><B>Subject:</B> [gmx-users] Re: Problem in
grompp</DIV>
<DIV><BR></DIV>
<DIV><FONT face=Arial size=2>Hello Alok,</FONT></DIV>
<DIV><FONT face=Arial size=2> Try to
follow this order, before the energy minimization, where ache is the name of
your pdb file:</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT size=2>
<P>pdb2gmx -f ache.pdb -o ache.gro -p ache.top</P><FONT size=2>
<P>editconf -bt cubic -f ache.gro -o ache.gro -c -d 0.65</P><FONT size=2>
<P>genbox -cp ache.gro -cs spc216.gro -o ache_st.gro -p ache.top</P><FONT
size=2>
<P>make_ndx -f ache</P></FONT>
<P><FONT face=Arial></FONT> </P>
<P><FONT face=Arial></FONT> </P>
<P><FONT
face=Arial>
Arlan da Silva Gonçalves</FONT></P>
<P> </P></FONT>
<P><FONT face=Arial></FONT> </P></FONT>
<P><FONT face=Arial></FONT> </P></FONT></DIV>
<P>
<HR>
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