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<P><FONT SIZE=2>Hi XAvier,<BR>
<BR>
Yes, now it makes sense.<BR>
<BR>
Thank you very much for making it clear.<BR>
<BR>
<BR>
Abu Naser<BR>
<BR>
School Of Life Sciences<BR>
Heriot-Watt University<BR>
Edinburgh EH14 4AS<BR>
Email: mn2@hw.ac.uk<BR>
Phone: +44(0)1314518265<BR>
Fax : +44(0) 131 451 3009<BR>
<BR>
<BR>
<BR>
<BR>
<BR>
<BR>
-----Original Message-----<BR>
From: gmx-users-bounces@gromacs.org on behalf of Xavier Periole<BR>
Sent: Tue 25/09/2007 8:12 PM<BR>
To: Discussion list for GROMACS users<BR>
Subject: Re: [gmx-users] g_dist<BR>
<BR>
<BR>
The output of g_dist gives:<BR>
<BR>
time distance DeltaX DeltaY DeltaZ<BR>
<BR>
distance = sqrt(DeltaX**2+DeltaY**2+DeltaZ**2)<BR>
<BR>
DeltaX, Y or Z are the differences of the atomic (COM)<BR>
positions in each direction. A negative value simply means<BR>
that one of the atoms (COM) has a value larger than the<BR>
other one in the corresponding direction.<BR>
<BR>
The negative value is not a distance yet! Just the<BR>
difference between the two atoms (COM) positions<BR>
on one direction.<BR>
<BR>
Would that make sense?<BR>
<BR>
> hi XAvier,<BR>
><BR>
> Thanks for your response.<BR>
> It was a question more of about how you would interpret the<BR>
> negative values(distance) in a particular component.<BR>
><BR>
> With thanks,<BR>
><BR>
> Abu Naser<BR>
><BR>
> School Of Life Sciences<BR>
> Heriot-Watt University<BR>
> Edinburgh EH14 4AS<BR>
> Email: mn2@hw.ac.uk<BR>
> Phone: +44(0)1314518265<BR>
>Fax : +44(0) 131 451 3009<BR>
><BR>
><BR>
><BR>
><BR>
><BR>
><BR>
> -----Original Message-----<BR>
>From: gmx-users-bounces@gromacs.org on behalf of Xavier Periole<BR>
> Sent: Tue 25/09/2007 10:13 AM<BR>
> To: Discussion list for GROMACS users<BR>
> Subject: Re: [gmx-users] g_dist<BR>
><BR>
> On Tue, 25 Sep 2007 10:03:30 +0100<BR>
> "Naser, Md Abu" <mn2@hw.ac.uk> wrote:<BR>
>> Hi David,<BR>
>><BR>
>> Yes, it should be a vector as it is a difference between the center of mass<BR>
>>of two groups in<BR>
>> x,y, and z directions. Then, negative means an opposite direction. Is that<BR>
>>right?<BR>
><BR>
> g_dist gives the distance and the component in each direction.<BR>
> The components been the difference between the atomic (or COM)<BR>
> positions there is no problem in having a negative value.<BR>
><BR>
>><BR>
>> Abu Naser<BR>
>><BR>
>> School Of Life Sciences<BR>
>> Heriot-Watt University<BR>
>> Edinburgh EH14 4AS<BR>
>> Email: mn2@hw.ac.uk<BR>
>> Phone: +44(0)1314518265<BR>
>>Fax : +44(0) 131 451 3009<BR>
>><BR>
>><BR>
>><BR>
>><BR>
>><BR>
>><BR>
>> -----Original Message-----<BR>
>>From: gmx-users-bounces@gromacs.org on behalf of David van der Spoel<BR>
>> Sent: Tue 25/09/2007 9:42 AM<BR>
>> To: Discussion list for GROMACS users<BR>
>> Subject: Re: [gmx-users] g_dist<BR>
>><BR>
>> Naser, Md Abu wrote:<BR>
>>><BR>
>>><BR>
>>> Hi all user,<BR>
>>><BR>
>>> I have just calculated a distance between backbone and side chain of the<BR>
>>> same protein. I get<BR>
>>> negative distance along x and y direction. What dose negative distance mean?<BR>
>>><BR>
>> please be more specific. is that a vector?<BR>
>><BR>
>>> Thanks in advance.<BR>
>>><BR>
>>><BR>
>>> Abu Naser<BR>
>>><BR>
>>> School Of Life Sciences<BR>
>>> Heriot-Watt University<BR>
>>> Edinburgh EH14 4AS<BR>
>>> Email: mn2@hw.ac.uk<BR>
>>> Phone: +44(0)1314518265<BR>
>>> Fax : +44(0) 131 451 3009<BR>
>>><BR>
>>><BR>
>>><BR>
>>><BR>
>>><BR>
>>> ------------------------------------------------------------------------<BR>
>>><BR>
>>> _______________________________________________<BR>
>>> gmx-users mailing list gmx-users@gromacs.org<BR>
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>><BR>
>><BR>
>> --<BR>
>> David van der Spoel, Ph.D.<BR>
>> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.<BR>
>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.<BR>
>> spoel@xray.bmc.uu.se spoel@gromacs.org <A HREF="http://folding.bmc.uu.se">http://folding.bmc.uu.se</A><BR>
>> _______________________________________________<BR>
>> gmx-users mailing list gmx-users@gromacs.org<BR>
>> <A HREF="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</A><BR>
>> Please search the archive at <A HREF="http://www.gromacs.org/search">http://www.gromacs.org/search</A> before posting!<BR>
>> Please don't post (un)subscribe requests to the list. Use the<BR>
>> www interface or send it to gmx-users-request@gromacs.org.<BR>
>> Can't post? Read <A HREF="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</A><BR>
>><BR>
><BR>
> -----------------------------------------------------<BR>
> XAvier Periole - PhD<BR>
><BR>
> 1- Institute of Molecular Assemblies<BR>
> City University of New York - USA<BR>
> 2- Molecular Dynamics-Group<BR>
> University of Groningen - The Netherlands<BR>
> <A HREF="http://md.chem.rug.nl/~periole">http://md.chem.rug.nl/~periole</A><BR>
> -----------------------------------------------------<BR>
> _______________________________________________<BR>
> gmx-users mailing list gmx-users@gromacs.org<BR>
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> Please search the archive at <A HREF="http://www.gromacs.org/search">http://www.gromacs.org/search</A> before posting!<BR>
> Please don't post (un)subscribe requests to the list. Use the<BR>
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><BR>
<BR>
-----------------------------------------------------<BR>
XAvier Periole - PhD<BR>
<BR>
1- Institute of Molecular Assemblies<BR>
City University of New York - USA<BR>
2- Molecular Dynamics-Group<BR>
University of Groningen - The Netherlands<BR>
<A HREF="http://md.chem.rug.nl/~periole">http://md.chem.rug.nl/~periole</A><BR>
-----------------------------------------------------<BR>
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Please don't post (un)subscribe requests to the list. Use the<BR>
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