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, <[email protected]> wrote: > Send gmx-users mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > 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 <[email protected]> > Subject: [gmx-users] Regarding cosine content > To: Discussion list for GROMACS users <[email protected]> > Message-ID: > <cakb2z-fhafsz6kcrmlsqvqjqwba0c_inqdcgqah2huoxggw...@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" <[email protected]> > Subject: Re: [gmx-users] Strange problem.complex out of Box after EM > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[email protected]> > 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 <[email protected]> > Subject: [gmx-users] Re: Umbrella Sampling - Justin tutorial > To: [email protected], Discussion list for GROMACS users > <[email protected]> > Message-ID: > <CAKZJqQG+oGcdDWLUPtNoONK=4igAZDJW518hP7=zb2cnd97...@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 <[email protected] > >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 > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20111117/8b9ec4a6/attachment-0001.html > > ------------------------------ > > Message: 4 > Date: Thu, 17 Nov 2011 13:04:14 +0100 > From: Tsjerk Wassenaar <[email protected]> > Subject: Re: [gmx-users] Regarding cosine content > To: Discussion list for GROMACS users <[email protected]> > Message-ID: > <cabze1si4jcnfj-gan6qaro-toaca1m72vpj36rd+jjrvosg...@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 <[email protected]> > 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 [email protected] > > 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 [email protected]. > > 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 <[email protected]> > Subject: Re: [gmx-users] Regarding cosine content > To: Discussion list for GROMACS users <[email protected]> > Message-ID: > <cakb2z-fccwxbrw69qfefrmytejsqq4iz35coo+hojzbcmhu...@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 <[email protected]> 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 <[email protected]> > 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 [email protected] > >> 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 [email protected]. > >> 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 [email protected] > > 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 [email protected]. > > 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 <[email protected]> > Subject: [gmx-users] Cuda not detected > To: [email protected] > Message-ID: > <[email protected]> > 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" <[email protected]> > Subject: Re: [gmx-users] Regarding TIP4P structure > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[email protected]> > 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 > [email protected] > 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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