Thank you sooo much Tsjerk,<br>I've been struggling for 3 days to understand how g_rmsf works.<br>Thank you, your explanation is very clear.<br><br>Cheers,<br>Carla<br><br><div class="gmail_quote">On Wed, Feb 17, 2010 at 3:18 PM, Tsjerk Wassenaar <span dir="ltr"><<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Hi Carla,<br>
<br>
What g_rmsf does is calculate the first (average) and second<br>
(fluctuation) central moments. For that, it is required that the<br>
conformational space is defined, which is done by fitting each frame<br>
to the reference structure. The reference is only used for that. The<br>
fluctuation is calculated about the mean position. It doesn't make<br>
sense to most people to calculate a non-central second moment, so be<br>
assured that that's not what g_rmsf does (for the few people<br>
interested, it can be done with g_covar :p).<br>
<br>
g_rmsf does what you want.<br>
<br>
Cheers,<br>
<font color="#888888"><br>
Tsjerk<br>
</font><div><div></div><div class="h5"><br>
On Wed, Feb 17, 2010 at 3:06 PM, Carla Jamous <<a href="mailto:carlajamous@gmail.com">carlajamous@gmail.com</a>> wrote:<br>
> Thank you Tsjerk,<br>
> but one more question:<br>
> if I do the following: g_rmsf -f a.xtc -s b.tpr -o rmsf.xvg -ox average.pdb<br>
> -n c.ndx<br>
><br>
> does gromacs claculate the rmsf after fitting to b.tpr or to average.pdb?<br>
> & if I want it to calculatefluctuations between the position of<br>
> particle i and the time-averaged position of the same particle i, do I have<br>
> to do:<br>
><br>
> g_rmsf -f a.xtc -s average.pdb -o rmsf.xvg?????<br>
><br>
> Thank you & sorry to bother. I'm just trying to understand what g_rmsf<br>
> really does, to help me analyze my results.<br>
><br>
> Carla<br>
><br>
> On Wed, Feb 17, 2010 at 10:25 AM, Tsjerk Wassenaar <<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>><br>
> wrote:<br>
>><br>
>> Hi Carla,<br>
>><br>
>> Justin's recipe should've worked. As he suggested, maybe the ligand is<br>
>> not with the protein. You can check by multiplying your system with<br>
>> genconf:<br>
>><br>
>> genconf -f in.pdb -o out.pdb -nbox 2 2 2<br>
>><br>
>> If the ligand is with the protein, one copy will be located in one of<br>
>> the copies of the protein.<br>
>><br>
>> g_rmsf does write the average structure, if requested. Use the option -ox<br>
>><br>
>> Cheers,<br>
>><br>
>> Tsjerk<br>
>><br>
>> On Wed, Feb 17, 2010 at 10:08 AM, Carla Jamous <<a href="mailto:carlajamous@gmail.com">carlajamous@gmail.com</a>><br>
>> wrote:<br>
>> > Hi Justin,<br>
>> > I'm still trying to figure out what happened with my ligand.<br>
>> > Meanwhile, I have another question: I can't figure out how to calculate<br>
>> > an<br>
>> > average structure in gromacs.<br>
>> > And does g_rmsf calculate the average structure automatically?<br>
>> ><br>
>> > Thanks again<br>
>> > Carla<br>
>> ><br>
>> > On Tue, Feb 16, 2010 at 5:44 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
>> > wrote:<br>
>> >><br>
>> >><br>
>> >> Carla Jamous wrote:<br>
>> >>><br>
>> >>> Hi Justin,<br>
>> >>> Thank you for your answer but I'm still not getting my ligand to stay<br>
>> >>> in<br>
>> >>> the box.<br>
>> >>><br>
>> >>> I tried the following(after taking a look at the mailing list<br>
>> >>> archive):<br>
>> >>><br>
>> >>> trjconv -s a.tpr -f b.xtc -o c.xtc -center -ur compact -pbc mol<br>
>> >>> (centering on "Protein")<br>
>> >>> trjconv -s d.tpr -f c.xtc -o f.xtc -fit rot+trans<br>
>> >>><br>
>> >>> So please do you have another advise to give me?<br>
>> >>><br>
>> >><br>
>> >> If that's not working, then I wonder if your ligand is still actually<br>
>> >> bound to your protein :) The above sequence always works for me, as<br>
>> >> long as<br>
>> >> there actually is a complex. You can also try -pbc cluster, but I know<br>
>> >> that<br>
>> >> algorithm can hang.<br>
>> >><br>
>> >> -Justin<br>
>> >><br>
>> >>> Thanks<br>
>> >>> Carla<br>
>> >>><br>
>> >>> On Mon, Feb 15, 2010 at 4:32 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a><br>
>> >>> <mailto:<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>>> wrote:<br>
>> >>><br>
>> >>><br>
>> >>><br>
>> >>> Carla Jamous wrote:<br>
>> >>><br>
>> >>> Hi everyone,<br>
>> >>> I'm using this command to extract my protein and my ligand from<br>
>> >>> the trajectory.<br>
>> >>><br>
>> >>> trjconv -f prot_md60ns.xtc -s prot_md50.tpr -fit rot+trans -pbc<br>
>> >>> whole -n prot_wat.ndx -o prot_ligand_60ns.xtc < grps >& outtrj<br>
>> >>><br>
>> >>> Before, I had a problem with residues of my protein showing at<br>
>> >>> the other end of the box, when I display my .xtc with VMD.<br>
>> >>> the "-pbc whole" fixed it.<br>
>> >>><br>
>> >>> However, now I have another issue: my ligand is at the other<br>
>> >>> end<br>
>> >>> of the box. So please can anyone tell me what can I do to fix<br>
>> >>> that and get a reasonable RMSD value?<br>
>> >>><br>
>> >>><br>
>> >>> You may need several more iterations of trjconv (one rarely does<br>
>> >>> the<br>
>> >>> trick), employing -pbc nojump, -pbc cluster, and/or -center. For<br>
>> >>> protein-ligand complexes, I have often found that the combination<br>
>> >>> of:<br>
>> >>><br>
>> >>> trjconv -pbc mol -ur compact -center<br>
>> >>><br>
>> >>> (centering on "Protein")<br>
>> >>><br>
>> >>> does the trick. And it makes molecules whole, as well :) I think<br>
>> >>> there are also some breakdowns (documented somewhere in the list<br>
>> >>> archive) when applying -fit and -pbc in the same step. I believe<br>
>> >>> it<br>
>> >>> is recommended to fix PBC first, then applying any sort of fitting<br>
>> >>> in a separate, subsequent step.<br>
>> >>><br>
>> >>> -Justin<br>
>> >>><br>
>> >>> Thank you<br>
>> >>> Carla<br>
>> >>><br>
>> >>><br>
>> >>> -- ========================================<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> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<br>
>> >>> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
>> >>><br>
>> >>> ========================================<br>
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>> >>><br>
>> >>><br>
>> >><br>
>> >> --<br>
>> >> ========================================<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.vt.edu/Pages/Personal/justin</a><br>
>> >><br>
>> >> ========================================<br>
>> >> --<br>
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>> ><br>
>> ><br>
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>> ><br>
>><br>
>><br>
>><br>
>> --<br>
>> Tsjerk A. Wassenaar, Ph.D.<br>
>><br>
>> Computational Chemist<br>
>> Medicinal Chemist<br>
>> Neuropharmacologist<br>
>> --<br>
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<br>
<br>
<br>
--<br>
Tsjerk A. Wassenaar, Ph.D.<br>
<br>
Computational Chemist<br>
Medicinal Chemist<br>
Neuropharmacologist<br>
--<br>
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</div></div></blockquote></div><br>