[gmx-users] order parameter for UAFF model

[afsaneh maleki]

thanks for your reply

i have got output file,i used the following options:
# g_order -f md.xtc -s md.tpr  -n sn1.ndx   -o order-sn1.xvg   -od
deuter-sn1.xvg    -d z

whatever deuter-sn1.xvg get me is the same Sc-c (the vector Ci-1,Ci,Ci+1 is
considered as molecule vector)? where i used the united atoms force field
for my system.

thanks very much,
Afsaneh

On Sun, Feb 7, 2010 at 7:14 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> afsaneh maleki wrote:
>
>> Hi all,
>>
>> i used united the atom force field model for the membrane lipids . to
>> calculate order parameter i used :
>> g_order  -od   -d
>>   i know united atom force field doesn't  have hydrogen atoms in
>> hydrocarbons chains .
>>  i want to know gromacs calculates order parameter * Sc-c* or *Sc-d*
>> (Deuterium) ?
>>
>
> Simple geometry.
>
>
>
>>  in the output is written:  title "Deuterium order parameters"
>>
>>
> Is that it?  If you've got an empty output, then your index file probably
> wasn't prepared correctly.  There is a how-to on the g_order page on the
> Gromacs website:
>
> http://www.gromacs.org/Documentation/Gromacs_Utilities/g_order
>
> -Justin
>
>  thanks in advance,
>> Afsaneh
>>
>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>



-
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100207/a83c82de/attachment.html>