<br><br><div class="gmail_quote">2011/6/22 <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
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Today's Topics:<br>
<br>
1. Re: PMF and appending simulation: -pf and -px flags (gromacs<br>
4.0.7) (Justin A. Lemkul)<br>
2. Re: DPPC temperatur setting (Justin A. Lemkul)<br>
3. in preparation for 4.5.5 and 4.6 releases (Rossen Apostolov)<br>
4. plateau in msd (glass transition); ref_t (Anja Kuhnhold)<br>
5. Re: Programs to add residues (Michael Lerner)<br>
6. Re: Autocorrelation of dipole moment (Andr? Farias de Moura)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Wed, 22 Jun 2011 06:14:06 -0400<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] PMF and appending simulation: -pf and -px<br>
flags (gromacs 4.0.7)<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4E01C06E.9080800@vt.edu">4E01C06E.9080800@vt.edu</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
<br>
<br>
Shay Teaching wrote:<br>
> Hi everyone,<br>
><br>
> Does the appending option also work when doing PMF?<br>
> I have a simulation that crashed in the middle (not-gromacs-related),<br>
> and now I want to continue from where it stopped.<br>
> But using the -append option does not seem to continue writing to the<br>
> files specified in -px and -pf.<br>
><br>
<br>
Appending can be done, but without seeing your actual series of commands, no one<br>
can offer you any useful advice or insight as to why it isn't working in your case.<br>
<br>
-Justin<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>
<br>
------------------------------<br>
<br>
Message: 2<br>
Date: Wed, 22 Jun 2011 06:16:52 -0400<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] DPPC temperatur setting<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4E01C114.20709@vt.edu">4E01C114.20709@vt.edu</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
<br>
<br>
marco miele wrote:<br>
> Hi everybody<br>
> I am starting to analyze the membrane system composed with DPPC lipids,<br>
> I saw both MD membrane paper and KALP-15 tutorial to setting a 323K.<br>
> My question is That<br>
> in this way we working around 50 C, which is not body temperature 37 C,<br>
> this is not realistic approach,<br>
> If my interest is to obtain data that respects the human body condition<br>
> can I to setting the temperature at 310 = 37 C or a make mistake and<br>
> obtain artefacts data.<br>
><br>
<br>
The reason for using 323 K in the case of DPPC is that (1) it is a common<br>
experimental temperature and (2) it is above the phase-transition temperature<br>
for this lipid. Anywhere below 315 K or so and your membrane will enter a gel<br>
phase, which is not representative of the membrane properties in vivo. Working<br>
with DPPC thus involves a tradeoff - you can either produce a liquid phase (like<br>
in vivo) or physiological temperature (while losing the physical properties<br>
associated with cellular membranes). The latter is often disfavored, but the<br>
end result is that DPPC is simply a poor choice to represent cell membranes, but<br>
is often a useful in vitro model, depending on your aims and available data.<br>
<br>
-Justin<br>
<br><br></blockquote><div> <br>My aim is to obtain a good model for analyzing a receptor protein (not channel).<br>I prepared a system with DPPC CHOL and Protein, but I am not sure fore only temperature.<br><br><span style="color: rgb(153, 51, 153);">"The latter is often disfavored, but the</span> <span style="color: rgb(153, 51, 153);">end result is that DPPC is simply a poor choice to represent cell membranes,<br>
but </span><span style="color: rgb(153, 51, 153);">is often a useful in vitro model, depending on your aims and available da<span style="color: rgb(102, 51, 102);">ta.</span></span><span style="color: rgb(102, 51, 102);">"</span><br style="color: rgb(153, 51, 153);">
<br>What kind of lipid you suggest me, in vision of system indicated before DPPC CHOL PROTEIN.<br>I am interesting to understand if the conformation of protein is mantained in diff % of CHOL.<br></div><div><br></div><div>
</div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
--<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>
<br>
------------------------------<br>
<br>
Message: 3<br>
Date: Wed, 22 Jun 2011 13:10:12 +0200<br>
From: Rossen Apostolov <<a href="mailto:rossen@kth.se">rossen@kth.se</a>><br>
Subject: [gmx-users] in preparation for 4.5.5 and 4.6 releases<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>>,<br>
Discussion list for GROMACS development <<a href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a>>,<br>
<a href="mailto:gmx-announce@gromacs.org">gmx-announce@gromacs.org</a><br>
Message-ID: <<a href="mailto:4E01CD94.8050205@kth.se">4E01CD94.8050205@kth.se</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi,<br>
<br>
We are preparing for a new maintenance release 4.5.5. It will fix<br>
critical open issues with previous releases, so please file your reports<br>
in <a href="http://redmine.gromacs.org" target="_blank">redmine.gromacs.org</a> by the end of June.<br>
<br>
After the 4.5.5 release, the stable branch will be frozen for bugfixes<br>
only, and new functionality will be added to a new release-4-6-patches<br>
branch, a fork of release-4-5-patches right after 4.5.5.<br>
<br>
Currently the plan is to have in 4.6:<br>
<br>
* faster native GPU implementation supporting most of current<br>
Gromacs features<br>
* collective I/O<br>
* lambda dynamics and other free energy extensions<br>
* AdResS (<a href="http://www.mpip-mainz.mpg.de/%7Epoma/multiscale/adress.php" target="_blank">http://www.mpip-mainz.mpg.de/~poma/multiscale/adress.php</a>)<br>
* advanced rotational pulling<br>
* file history<br>
* several new tools<br>
* autoconf removed - support for building only with CMake<br>
<br>
Code from contributors will be considered for inclusion also but it's<br>
necessary that<br>
<br>
* comes with support for the code in future releases, e.g. port it<br>
to the completely new C++ structure in the 5.0 release and<br>
maintain it after<br>
* builds against 4.5.5<br>
* produces scientifically reliable results<br>
* works in parallel and doesn't affect the performance<br>
* comes with regression test sets for the new features<br>
* has the necessary documentation for usage<br>
<br>
After 4.5.5 bug fixes need to be applied as:<br>
<br>
* bugs in 4.5.5:<br>
o fix in 4.5.5 -> fix in 4.6 -> fix in master<br>
* bugs in the new features introduced in 4.6:<br>
o fix in 4.6 -> fix in master<br>
<br>
<br>
The plan is to have 4.5.5 around end of July, and 4.6-gamma a month later.<br>
<br>
Rossen<br>
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Message: 4<br>
Date: Wed, 22 Jun 2011 13:34:58 +0200<br>
From: Anja Kuhnhold <<a href="mailto:anja.kuhnhold@physik.uni-halle.de">anja.kuhnhold@physik.uni-halle.de</a>><br>
Subject: [gmx-users] plateau in msd (glass transition); ref_t<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID: <<a href="mailto:fac78671a57f.4e01ef82@uni-halle.de">fac78671a57f.4e01ef82@uni-halle.de</a>><br>
Content-Type: text/plain; charset=us-ascii<br>
<br>
Hi everyone,<br>
<br>
I'm simulating a bead-spring polymer model (1600 chains and 10 beads per chain in a 26.6^3 box with pbc) with LJ and FENE potentials.<br>
I calculate the mean-square-displacement for different temperatures. For T=0.46 (in LJ units) I expected to get a plateau in the msd curve (glass transition)- but there is none. The curve for T=0.46 is similar to the one for T=1.0 (above glass transition) with only a small shift to lower values- but no plateau.<br>
<br>
My .mdp-files look as follows:<br>
<br>
integrator = md-vv<br>
dt = 0.0035<br>
nsteps = 100<br>
nstxout = 1<br>
nstvout = 1<br>
nstfout = 1<br>
nstlog = 1<br>
ns_type = grid<br>
pbc = xyz<br>
periodic_molecules = yes<br>
rvdw = 1.12<br>
rlist = 1.3<br>
tcoupl = nose-hoover<br>
tc-grps = System<br>
tau_t = 20<br>
ref_t = 55.32<br>
vdwtype = Shift<br>
rcoulomb = 1.12<br>
coulombtype = Reaction-Field-zero<br>
epsilon_rf = 0<br>
<br>
I have 6 of these files, where only nsteps and nst*out are changed by multiplying them by 10 (so I get overlapping intervals for the msd).<br>
<br>
<br>
Is the ref_t correct? The results in the md.log file say T is about 89.<br>
Why do I not get a plateau? What did I not consider?<br>
<br>
Thanks in advance.<br>
Anja<br>
<br>
<br>
------------------------------<br>
<br>
Message: 5<br>
Date: Wed, 22 Jun 2011 08:52:32 -0400<br>
From: Michael Lerner <<a href="mailto:mglerner@gmail.com">mglerner@gmail.com</a>><br>
Subject: Re: [gmx-users] Programs to add residues<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:BANLkTim7dbY4uwefcc38HiPJw8TZ7jZeVA@mail.gmail.com">BANLkTim7dbY4uwefcc38HiPJw8TZ7jZeVA@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
On Tue, Jun 21, 2011 at 4:12 PM, Chris Neale <<a href="mailto:chris.neale@utoronto.ca">chris.neale@utoronto.ca</a>>wrote:<br>
<br>
> Try "Loopy". You can get it to build termini in addition to loops.<br>
><br>
> <a href="http://wiki.c2b2.columbia.edu/**honiglab_public/index.php/**Software:Loopy" target="_blank">http://wiki.c2b2.columbia.edu/**honiglab_public/index.php/**Software:Loopy</a><<a href="http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:Loopy" target="_blank">http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:Loopy</a>><br>
><br>
><br>
I've also seen people use PyMOL's builder to do this. Either way, you'll<br>
need to take (a lot of) extra care to minimize your linker and make sure<br>
that it looks reasonable.<br>
<br>
-Michael<br>
<br>
<br>
> Nevertheless, I'd suggest simply omitting that part of the protein and<br>
> capping your new terminus to remove the charge. You will have more<br>
> difficulties converging the conformation of the unstructured terminus than<br>
> you may expect.<br>
<br>
<br>
> CHris.<br>
><br>
> -- original message --<br>
><br>
> Hi all,<br>
><br>
> Is there a program that allows the user to add residues to the N and C<br>
> terminus, without using the electron density? I would like to add a<br>
> short linker to my protein which doesn't exist in the electron<br>
> density.<br>
><br>
> Thanks a lot,<br>
><br>
> Sincerely,<br>
> Zack<br>
><br>
> --<br>
> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
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<br>
--<br>
Michael Lerner, Ph.D.<br>
IRTA Postdoctoral Fellow<br>
Laboratory of Computational Biology NIH/NHLBI<br>
5635 Fishers Lane, Room T909, MSC 9314<br>
Rockville, MD 20852 (UPS/FedEx/Reality)<br>
Bethesda MD 20892-9314 (USPS)<br>
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Message: 6<br>
Date: Wed, 22 Jun 2011 10:53:21 -0300<br>
From: Andr? Farias de Moura <<a href="mailto:moura@ufscar.br">moura@ufscar.br</a>><br>
Subject: Re: [gmx-users] Autocorrelation of dipole moment<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <BANLkTi=zdVSNcy9n7n=<a href="mailto:AVmTdHqohEd3mXQ@mail.gmail.com">AVmTdHqohEd3mXQ@mail.gmail.com</a>><br>
Content-Type: text/plain; charset=ISO-8859-1<br>
<br>
sure, the ACF for a vector gives you the average cosine between that vector<br>
at time t=0 and the same vector at a later time lag, thus negative values may<br>
be seen as an inversion of the direction to which the vector points<br>
out (-1 would<br>
be the value for a vector lying 180 degrees away from the direction at t=0).<br>
<br>
best<br>
<br>
Andre<br>
<br>
On Tue, Jun 21, 2011 at 8:29 PM, Chathurika Abeyrathne<br>
<<a href="mailto:c.abeyrathne@student.unimelb.edu.au">c.abeyrathne@student.unimelb.edu.au</a>> wrote:<br>
><br>
><br>
> Hi,<br>
><br>
> Is it possible to get negative values for normalized autocorrelation of<br>
> total dipole moment.<br>
><br>
> Thank you.<br>
><br>
><br>
> Regards,<br>
> Chathurika.<br>
><br>
> --<br>
> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
> Please search the archive at<br>
> <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
> Please don't post (un)subscribe requests to the list. Use the<br>
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><br>
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End of gmx-users Digest, Vol 86, Issue 138<br>
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</font></blockquote></div><br>