[gmx-users] Re: gmx-users Digest, Vol 91, Issue 119

Saba Ferdous saba.bsbi154 at iiu.edu.pk
Thu Nov 17 17:49:16 CET 2011 

Dear Justin,

I have set 1.5 dodecahedron. i centered the complex in box.
complex.gro, complexsol.gro and complex_sol_ions.gro seems inside in box. I
m using VMD for visualization. i have rotated it in 3D
while when after EM step, i visualize em.gro then half complex seems
outside the box. is there any way to center em.gro after energy
minimization?

I have attached the snapshots. Kindly see and suggest me that is it correct
and should I continue with equilibrium step?

Kindly help me out...

On Thu, Nov 17, 2011 at 6:21 PM, <gmx-users-request at gromacs.org> wrote:

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> Today's Topics:
>
>   1. Regarding cosine content (bipin singh)
>   2. Re: Strange problem.complex out of Box after EM (Justin A. Lemkul)
>   3. Re: Umbrella Sampling - Justin tutorial (Steven Neumann)
>   4. Re: Regarding cosine content (Tsjerk Wassenaar)
>   5. Re: Regarding cosine content (bipin singh)
>   6. Cuda not detected (Andrzej Rzepiela)
>   7. Re: Regarding TIP4P structure (Justin A. Lemkul)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 17 Nov 2011 16:52:48 +0530
> From: bipin singh <bipinelmat at gmail.com>
> Subject: [gmx-users] Regarding cosine content
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
>        <CAKb2Z-FhAfSZ6KCRmLsQVQJqwbA0c_iNQdCgQAh2huOxGGwrMQ at mail.gmail.com
> >
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hello all,
>
> I have done PCA from 50ns long trajectory for two similar proteins
> (length 180 aa and RMSD 0.2 A).
> The equilibration time and final simulation condition were identical
> for both the protein.
> But when I checked the cosine content for PC1 for both proteins they
> were 0.9 and 0.5 respectively.
> What can be the reason for this huge difference in cosine content of
> the two proteins ?
>
>
> --
> -----------------------
> Regards,
> Bipin Singh
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 17 Nov 2011 06:51:43 -0500
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Strange problem.complex out of Box after EM
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4EC4F54F.6060800 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> Saba Ferdous wrote:
> > Dear Gromacs users
> >
> > I am trying to simulate a protein complex. That complex has been
> > obtained after protein-protein docking.
> >
> > I have geneated topology, defined box and solvate, added ions
> > successfully. My complex is centered in box.
> >
> > but when I performed Energy minimization then my protein complex comes
> > out of box from one side.
> >
> > can any body help me in fixing this problem so that i could proceed
> > towards equilibrium steps..
> >
>
> There is no problem.  It is odd that EM would cause periodicity issues, but
> suggests that your protein is not centered properly or that your box is not
> large enough to accommodate it.  There may be some inconvenience for
> visualization (which can be fixed), but there is no such thing as
> "outside" in a
> periodic system.
>
>
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
>
> -Justin
>
> --
> ========================================
>
> 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
>
> ========================================
>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 17 Nov 2011 11:55:31 +0000
> From: Steven Neumann <s.neumann08 at gmail.com>
> Subject: [gmx-users] Re: Umbrella Sampling - Justin tutorial
> To: jalemkul at vt.edu, Discussion list for GROMACS users
>        <gmx-users at gromacs.org>
> Message-ID:
>        <CAKZJqQG+oGcdDWLUPtNoONK=4igAZDJW518hP7=zB2CND97PPw at mail.gmail.com
> >
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Justin,
>
> I am sorry for so many questions but I do not understand something.
> First we run the simulation of pulling Chain A from ChainB with constant
> force (pull_k1=1000) and constant velocity of pulling (pull_rate1=0.01) We
> extract windows as we discussed and then run simulations with those
> configurations as a starting point. I saw the trajectory of one of these
> simulations and it looks like normal MD simulation. My question is: Why do
> we have in mdp file still pull code as we do not pull protein chain any
> more? Pull rate is set to zero but force is still applied... why? Is this
> code just used to extract pullf.xvg and pullx.xvg which does not change too
> much?
> I would appreciate the explanation as without undesratnding the basics its
> not good to do any simulation like this.
>
> Thank you
>
> Steven
>
>
>
>
> Are my questions to trivial or noones knows? Please, help!
>
> On Wed, Nov 16, 2011 at 9:31 AM, Steven Neumann <s.neumann08 at gmail.com
> >wrote:
>
> > Hi GMX Users,
> >
> > I am doing Justin tutorial of Umbrella sampling. I have just finished
> > continous pulling of chainA from the reference chainB. I have some
> > questions. I looked at the trajectory of pulling and it has began with
> > dissociating residue 27Alanine from the ChainB following 26, 25, 24...1.
> My
> > question is why? As you apply pulling with the constant force to the COM
> of
> > the whole chain why does it start with terminal residue following then
> one
> > by one? Why not the middle one or any other?
> >
> > The second thing I would like to extract starting configurations from
> from
> > my pulling. Till frame 189 the COM varies from 0.49 to 0.56 - makes sense
> > as the ChainA is still within ChainB. I would like to use configurations:
> >
> > 0 - 0.50
> > 50 - 0.52
> > 100 - 0.51
> > 150 - 0.51
> > 200 - 0.62
> > 250 - 2.21
> > ....
> > 500 - 5.48
> >
> > My question is: Do I have to use exactly the same e.g. 0.2 nm spacing or
> > this configuration above is ok? Can the spacing in nm vary?
> > And the last thing - is it required to use frames till 189 as the COM
> > varies in this area?
> >
> > Thank you!
> >
> > Steven
> >
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> ------------------------------
>
> Message: 4
> Date: Thu, 17 Nov 2011 13:04:14 +0100
> From: Tsjerk Wassenaar <tsjerkw at gmail.com>
> Subject: Re: [gmx-users] Regarding cosine content
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
>        <CABzE1Si4jcNfj-gaN6QaRo-TOAcA1M72vpj36rd+JJRVosgnrQ at mail.gmail.com
> >
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi Bipin,
>
> It seems one of the proteins is taking longer to reach an equilibrium.
> Maybe it is undergoing a conformational change?
> Did you calculate the principal components per protein, or for the
> joint trajectories? It would have been better to echo the commands you
> used on the list, because it might result in a different
> interpretation. I also made some comments on the list a short while
> ago regarding the interpretation of projections and cosine content.
> Maybe they can help you form a picture of what is happening :)
>
> Hope it helps,
>
> Tsjerk
>
>
> On Thu, Nov 17, 2011 at 12:22 PM, bipin singh <bipinelmat at gmail.com>
> wrote:
> > Hello all,
> >
> > I have done PCA from 50ns long trajectory for two similar proteins
> > (length 180 aa and RMSD 0.2 A).
> > The equilibration time and final simulation condition were identical
> > for both the protein.
> > But when I checked the cosine content for PC1 for both proteins they
> > were 0.9 and 0.5 respectively.
> > What can be the reason for this huge difference in cosine content of
> > the two proteins ?
> >
> >
> > --
> > -----------------------
> > Regards,
> > Bipin Singh
> > --
> > 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/Support/Mailing_Lists/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/Support/Mailing_Lists
> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
>
>
> ------------------------------
>
> Message: 5
> Date: Thu, 17 Nov 2011 18:07:44 +0530
> From: bipin singh <bipinelmat at gmail.com>
> Subject: Re: [gmx-users] Regarding cosine content
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
>        <CAKb2Z-FCCwxBRw69qFefRmyTeJsqq4iz35cOO+hOJzBCmhUJ9g at mail.gmail.com
> >
> Content-Type: text/plain; charset=ISO-8859-1
>
> Thanks for the reply...
> I calculated principal components per protein using the command
> g_anaeig -f md.xtc -s md.tpr -v eigenvec.trr -eig eigenval.xvg -comp
> eigcomp.xvg -rmsf eigrmsf.xvg -2d 2dproj.xvg -proj proj.xvg -tu ns
> -extr extr.pdb -filt filt.xtc -first 1 -last 2
>
> Also please suggest how one can differentiate between the two
> scenarios, when the high cosine content is due to random diffusion or
> conformational changes ?
>
>
> On Thu, Nov 17, 2011 at 17:34, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> > Hi Bipin,
> >
> > It seems one of the proteins is taking longer to reach an equilibrium.
> > Maybe it is undergoing a conformational change?
> > Did you calculate the principal components per protein, or for the
> > joint trajectories? It would have been better to echo the commands you
> > used on the list, because it might result in a different
> > interpretation. I also made some comments on the list a short while
> > ago regarding the interpretation of projections and cosine content.
> > Maybe they can help you form a picture of what is happening :)
> >
> > Hope it helps,
> >
> > Tsjerk
> >
> >
> > On Thu, Nov 17, 2011 at 12:22 PM, bipin singh <bipinelmat at gmail.com>
> wrote:
> >> Hello all,
> >>
> >> I have done PCA from 50ns long trajectory for two similar proteins
> >> (length 180 aa and RMSD 0.2 A).
> >> The equilibration time and final simulation condition were identical
> >> for both the protein.
> >> But when I checked the cosine content for PC1 for both proteins they
> >> were 0.9 and 0.5 respectively.
> >> What can be the reason for this huge difference in cosine content of
> >> the two proteins ?
> >>
> >>
> >> --
> >> -----------------------
> >> Regards,
> >> Bipin Singh
> >> --
> >> 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/Support/Mailing_Lists/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/Support/Mailing_Lists
> >>
> >
> >
> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
> >
> > post-doctoral researcher
> > Molecular Dynamics Group
> > * Groningen Institute for Biomolecular Research and Biotechnology
> > * Zernike Institute for Advanced Materials
> > University of Groningen
> > The Netherlands
> > --
> > 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/Support/Mailing_Lists/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/Support/Mailing_Lists
> >
>
>
>
> --
> -----------------------
> Regards,
> Bipin Singh
>
>
> ------------------------------
>
> Message: 6
> Date: Thu, 17 Nov 2011 13:23:15 +0100
> From: Andrzej Rzepiela <Andrzej.Rzepiela at physik.uni-freiburg.de>
> Subject: [gmx-users] Cuda not detected
> To: gmx-users at gromacs.org
> Message-ID:
>        <F2E137B5-6631-4588-8F18-ECB451C46D96 at physik.uni-freiburg.de>
> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>
> Hey,
>
> I am playing with the gpu version of mdrun and could make it run with:
>
> ~/gromacs/gpu/bin/mdrun-gpu -s topol.tpr -device
> "OpenMM:platform=Cuda,memtest=15,deviceid=0,force-device=yes"
>
> However after reboot of the machine ( which is a testing machine)
>
> I get the following error:
>
>
> -------------------------------------------------------
> Program mdrun-gpu, VERSION 4.5.5
> Source code file: /home/weber/gromacs/gromacs-4.5.5_gpu/src/kernel/
> openmm_wrapper.cpp, line: 1272
>
> Fatal error:
> The requested platform "Cuda" could not be found.
>
>
> echo $LD_LIBRARY_PATH:/opt/software/ganglia-3.1.7/lib64:/opt/software/
> htop-0.8.3:/usr/local/cuda/lib64:/usr/local/cuda/lib:/home/weber/
> OpenMM3.1.1-Linux64/lib
>
> echo $PATH/usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin:/usr/games:/usr/
> lib64/jvm/jre/bin:/opt/software/nvidia/3.2.16/cuda/bin:/opt/software/
> ganglia-3.1.7/bin:/opt/software/htop-0.8.3/bin:/usr/lib/mit/bin:/usr/
> lib/mit/sbin:.:/usr/local/cuda/bin:/home/weber/cmake-2.8.6/bin
>
>
> I run a simple gpu test program and it  works.
>
> I believe something is not linked correctly, maybe someone can give me
> a hint.
>
> Thank You
>
> Andrzej
>
>
>
> ------------------------------
>
> Message: 7
> Date: Thu, 17 Nov 2011 08:19:44 -0500
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Regarding TIP4P structure
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4EC509F0.1030103 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> Ravi Kumar Venkatraman wrote:
> > Dear all,
> >              Could anybody send me the link for getting the tip4p tip3p
> > and tip5p single water structure in gro/pdb or in anyother format.
> >
>
> A single water molecule?  Copy and paste the coordinates from the existing
> .gro
> files in $GMXLIB.
>
> -Justin
>
> --
> ========================================
>
> 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/Support/Mailing_Lists/Search before posting!
>
> End of gmx-users Digest, Vol 91, Issue 119
> ******************************************
>



-- 
Saba Ferdous
Research Scholar (M. Phil)
National Center for Bioinformatics
Quaid-e-Azam University, Islamabad
Pakistan
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