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<p class=MsoPlainText dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span style='font-size:12.0pt'>I think you
should try using:<o:p></o:p></span></font></p>
<p class=MsoPlainText dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><b><font size=2 face=Tahoma><span style='font-size:10.0pt;font-family:
Tahoma;font-weight:bold'>trjconv –f file.trr –o file_with_groups_of_interest.trr
–n index.ndx <o:p></o:p></span></font></b></p>
<p class=MsoPlainText dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Tahoma><span style='font-size:12.0pt;font-family:Tahoma'><o:p> </o:p></span></font></p>
<p class=MsoPlainText dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span style='font-size:12.0pt'>You should create
the relevant index group (that includes all atoms of interest) before invoking
the above command. You'll be prompted to choose a group so choose the group you
created and trjconv will write an output trr that includes the group you picked
alone.<o:p></o:p></span></font></p>
<p class=MsoPlainText dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span style='font-size:12.0pt'>Hope that helps.<o:p></o:p></span></font></p>
<p class=MsoPlainText dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span style='font-size:12.0pt'>-Shay<o:p></o:p></span></font></p>
<p class=MsoPlainText dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span style='font-size:12.0pt'>-----Original
Message-----<br>
From: gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org] On
Behalf Of Vitaly Chaban<br>
Sent: Friday, August 22, 2008 14:05 PM<br>
To: gmx-users@gromacs.org<br>
Subject: [gmx-users] groups to write to trr</span></font></p>
<p class=MsoPlainText dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span style='font-size:12.0pt'>Hi</span></font><span
dir=RTL></span><span lang=HE dir=RTL><span dir=RTL></span>,<o:p></o:p></span></p>
<p class=MsoPlainText dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span lang=HE dir=RTL style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span style='font-size:12.0pt'>Is it possible to
write only the specified groups to the TRR</span></font><span lang=HE dir=RTL><o:p></o:p></span></p>
<p class=MsoPlainText dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span style='font-size:12.0pt'>trajectory like
using xtc-grps key for XTC</span></font><span dir=RTL></span><span lang=HE
dir=RTL><span dir=RTL></span>?<o:p></o:p></span></p>
<p class=MsoPlainText dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span lang=HE dir=RTL style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span style='font-size:12.0pt'>We calculate
VACFs and so need velocities to be written but only the</span></font><span
lang=HE dir=RTL><o:p></o:p></span></p>
<p class=MsoPlainText dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span style='font-size:12.0pt'>velocity of some
groups are of interest, not of all the particles. The</span></font><span
lang=HE dir=RTL><o:p></o:p></span></p>
<p class=MsoPlainText dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span lang=HE dir=RTL style='font-size:12.0pt'>"</span>full"
TRRs take extremely huge space</font><span dir=RTL></span><span lang=HE
dir=RTL><span dir=RTL></span>...<o:p></o:p></span></p>
<p class=MsoPlainText dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span lang=HE dir=RTL style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span lang=HE dir=RTL style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span style='font-size:12.0pt'>Thanks</span></font><span
dir=RTL></span><span lang=HE dir=RTL><span dir=RTL></span>.<o:p></o:p></span></p>
<p class=MsoPlainText dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span lang=HE dir=RTL style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span lang=HE dir=RTL style='font-size:12.0pt'>--
<o:p></o:p></span></font></p>
<p class=MsoPlainText dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span style='font-size:12.0pt'>Vitaly V. Chaban</span></font><span
lang=HE dir=RTL><o:p></o:p></span></p>
<p class=MsoPlainText dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><st1:place w:st="on"><st1:PlaceType w:st="on"><font size=3 face=Arial><span
style='font-size:12.0pt'>School</span></font></st1:PlaceType> of <st1:PlaceName
w:st="on">Chemistry</st1:PlaceName></st1:place><span lang=HE dir=RTL><o:p></o:p></span></p>
<p class=MsoPlainText dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><st1:place w:st="on"><st1:PlaceName w:st="on"><font size=3 face=Arial><span
style='font-size:12.0pt'>National</span></font></st1:PlaceName> <st1:PlaceType
w:st="on">University</st1:PlaceType></st1:place> of Kharkiv<span lang=HE
dir=RTL><o:p></o:p></span></p>
<p class=MsoPlainText dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span style='font-size:12.0pt'>Svoboda sq., 4, <st1:place
w:st="on"><st1:City w:st="on">Kharkiv</st1:City> <st1:PostalCode w:st="on">61077</st1:PostalCode>,
<st1:country-region w:st="on">Ukraine</st1:country-region></st1:place></span></font><span
lang=HE dir=RTL><o:p></o:p></span></p>
<p class=MsoPlainText dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span style='font-size:12.0pt'>email: chaban@univer.kharkov.ua</span></font><span
lang=HE dir=RTL><o:p></o:p></span></p>
<p class=MsoPlainText dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span style='font-size:12.0pt'>skype: vvchaban</span></font><span
lang=HE dir=RTL><o:p></o:p></span></p>
<p class=MsoPlainText dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span lang=HE dir=RTL style='font-size:12.0pt'>_______________________________________________<o:p></o:p></span></font></p>
<p class=MsoPlainText dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span style='font-size:12.0pt'>gmx-users mailing
list gmx-users@gromacs.org</span></font><span lang=HE
dir=RTL><o:p></o:p></span></p>
<p class=MsoPlainText dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span style='font-size:12.0pt'>http://www.gromacs.org/mailman/listinfo/gmx-users</span></font><span
lang=HE dir=RTL><o:p></o:p></span></p>
<p class=MsoPlainText dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span style='font-size:12.0pt'>Please search the
archive at http://www.gromacs.org/search before posting</span></font><span
dir=RTL></span><span lang=HE dir=RTL><span dir=RTL></span>!<o:p></o:p></span></p>
<p class=MsoPlainText dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span style='font-size:12.0pt'>Please don't post
(un)subscribe requests to the list. Use the</span></font><span dir=RTL></span><span
dir=RTL><span dir=RTL></span> <span lang=HE><o:p></o:p></span></span></p>
<p class=MsoPlainText dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span style='font-size:12.0pt'>www interface or send
it to gmx-users-request@gromacs.org</span></font><span dir=RTL></span><span
lang=HE dir=RTL><span dir=RTL></span>.<o:p></o:p></span></p>
<p class=MsoPlainText dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span style='font-size:12.0pt'>Can't post? Read
http://www.gromacs.org/mailing_lists/users.php<o:p></o:p></span></font></p>
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