Re: [gmx-users] constraining multiple types of bonds
thanks a lot Justin I'll try to follow this protocol. On Sun, Nov 11, 2012 at 8:59 AM, Justin Lemkul jalem...@vt.edu wrote: On 11/10/12 10:27 PM, tarak karmakar wrote: Thanks Justin If I want to constrain all the bonds in the substrate molecule present inside the enzyme cavity then along with SHAKE what I need to use ? Set constraints = none in the .mdp file and add an explicit [constraints] section in the ligand topology. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 listgmx-users@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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tarak -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] About periodic image of system.......
Hi justin , Thank you a lot for your explaination. My opinion on the working of g_mindist -pi is that when it shows the distance between two atom of the protein is less than vdw cut off ( 1.4 nm ) , then protein see it periodic image, and it is the violation of pbc. Is these is right??? ( That is the shortest Periodic distance should be larger than vdw cut off 1.4 ) If it is right, g_mindist say that The shortest periodic distance is 0.154938 (nm) at time 16162 (ps), between atoms 223 and 3270 This is less than 1.4 then Why it is not problem..??? As per your previous reply, The confusion likely arises from the fact that you're selecting Protein, which actually contains multiple molecules, rather than a single protein molecule. Atoms can come pretty close during a simulation, especially if they are involved in, for instance, hydrogen bonds. These means whenever I have to check the protein pbc , I have to make the index file for each chain, and have to select the pbc for that??? Please accept my apology if I repiting the same questions. but it is really confusing to me.. With best Wishes and Regards.. Rama david On Sun, Nov 11, 2012 at 12:47 AM, Justin Lemkul jalem...@vt.edu wrote: On 11/10/12 10:22 AM, rama david wrote: Thank you justin, I actually check these file in vmd by seeing its periodic image , but I not seen any problem in PBC. As per you, If protein contain multiple chain, I have to make the index group for each one. Then I have to check each one by g_mindist -pi Is these right??? I suspect that would be more appropriate. But what wiil be the problem if I used the whole group Still I not get the your explanation..Pardon me, but please explain it again?? I don't know how to say it differently. The minimum image convention, periodicity, and neighbor searching are all covered in almost every simulation textbook, and some elements are described on gromacs.org and in the manual. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re:Ka/Kd
Dear Justin, Thanks, Just a normal delta G then. I wondered if it also was doing a matrices from 2 columns if you supply something like just the 2d output from covar/anaeig (PCA). I did find a simple python 6 liner for just doing PCA with the first (or any 2) derivatives just using numpy, and some module written by tsjerk Wassenaar posted a few years ago (a Gromacs plugin called g_entropy) which all together seem to meet my needs. Also (the above person) has a number of small python scripts for Gromacs for matirces, PCA, and just turning .xpm data from g_sham into a number matrices to put into a plotting tool (such as Scidavis or something). There on a web page, and a few dozen just scattered in older gromacs postings. If I had a request for Gromacs dev though it would be to multithread the vector portions of the analytical tools. A single Intel i7 or AMD only uses one of the 8 cores, so it takes several hours, for each component times each of however trajectories are looked at. Most everything else is a minute or two only using a single core. Sincerely, Stephan Watkins Original-Nachricht Datum: Fri, 09 Nov 2012 14:44:31 -0500 Von: Justin Lemkul jalem...@vt.edu An: Discussion list for GROMACS users gmx-users@gromacs.org Betreff: Re: [gmx-users] Re:Ka/Kd On 11/9/12 1:02 PM, lloyd riggs wrote: Dear All, Reguarding a question I asked below. Does anyone know what the formulei, etc...are for g_sham taking in 2 columns (or 3 with time) and turning it into a density matrix. Is it just a count, summation on x-y or other? Values are divided into histograms and calculated by dG = -RT ln (P - P0), where P0 is the histogram bin with the largest probability such that the value of dG is set to zero here and all other values are relative to it. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 listgmx-users@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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] problem with simulation of freezing of water
On 11/11/12 9:53 AM, Ali Alizadeh wrote: Dear All users I did simulation of water freezind at low temperature(260 k) so that i was hoped to see regular structure of ice, I used OPLS-AA force field, SPC and 100ns, But i can not see the regular structure of ice(i used vmd for representation of my simulation)? In your opinion, Where did i mistake in my simulation? Where did i mistake in my simulation? The freezing point of a water model for MD simulation is not necessarily equal to the actual freezing point of water. See, for instance http://iopscience.iop.org/0953-8984/17/45/013/pdf/cm5_45_013.pdf. There are probably other papers, as well, but one can find this easily by Googling freezing point of SPC water. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 listgmx-users@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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re:Ka/Kd
On 11/11/12 7:47 AM, lloyd riggs wrote: Dear Justin, Thanks, Just a normal delta G then. I wondered if it also was doing a matrices from 2 columns if you supply something like just the 2d output from covar/anaeig (PCA). I did find a simple python 6 liner for just doing PCA with the first (or any 2) derivatives just using numpy, and some module written by tsjerk Wassenaar posted a few years ago (a Gromacs plugin called g_entropy) which all together seem to meet my needs. Also (the above person) has a number of small python scripts for Gromacs for matirces, PCA, and just turning .xpm data from g_sham into a number matrices to put into a plotting tool (such as Scidavis or something). There on a web page, and a few dozen just scattered in older gromacs postings. If I had a request for Gromacs dev though it would be to multithread the vector portions of the analytical tools. A single Intel i7 or AMD only uses one of the 8 cores, so it takes several hours, for each component times each of however trajectories are looked at. Most everything else is a minute or two only using a single core. Framework for parallelizing analysis tools is in the works, with a target of version 5.0 for implementation, since the code is undergoing a major overhaul for that release, anyway. It will be a long time before that release, though, but it's in the works. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 listgmx-users@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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] About periodic image of system.......
On 11/11/12 4:51 AM, rama david wrote: Hi justin , Thank you a lot for your explaination. My opinion on the working of g_mindist -pi is that when it shows the distance between two atom of the protein is less than vdw cut off ( 1.4 nm ) , then protein see it periodic image, and it is the violation of pbc. Is these is right??? ( That is the shortest Periodic distance should be larger than vdw cut off 1.4 ) This is correct, when considering a single molecule, i.e. it can't see itself. If you have two proteins, and you choose the blanket Protein group, you haven't determined anything, because now the calculation involves multiple molecules. If it is right, g_mindist say that The shortest periodic distance is 0.154938 (nm) at time 16162 (ps), between atoms 223 and 3270 This is less than 1.4 then Why it is not problem..??? Because they're in separate molecules. Did you ever do as I suggested and visualize this frame? It will be immediately apparent that there is no problem. Please refer to textbooks or even simple Google searching for explanations of the minimum image convention. As I said, it is described in almost every reference text. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 listgmx-users@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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re:problem with simulation of freezing of water
On 11/11/12 11:22 AM, Ali Alizadeh wrote: Dear Justin Thank you for reply, I want to simulation of water freezing, my condition: pressure=300 bar and T=240 k , number 1656, run time= 100ns, I can not see regular structure of ice by MD simulation or by gromacs? In your opinion, if i want this structure of ice for my simulation, What can i do? Start by searching the literature for a suitable protocol. Ice simulations have been done before. As I said before, each water model has a different melting point, and hardly any of them correspond to the actual experimental value. See if you can produce a suitable simulation with a pressure of 1 bar (proof of concept) and then change conditions. What you have to keep in mind is that most water models were designed to work at ambient conditions for normal simulations. They do not necessarily work under extremes or produce useful results under those conditions. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 listgmx-users@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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re:problem with simulation of freezing of water
On 2012-11-11 17:26, Justin Lemkul wrote: On 11/11/12 11:22 AM, Ali Alizadeh wrote: Dear Justin Thank you for reply, I want to simulation of water freezing, my condition: pressure=300 bar and T=240 k , number 1656, run time= 100ns, I can not see regular structure of ice by MD simulation or by gromacs? In your opinion, if i want this structure of ice for my simulation, What can i do? Start by searching the literature for a suitable protocol. Ice simulations have been done before. As I said before, each water model has a different melting point, and hardly any of them correspond to the actual experimental value. See if you can produce a suitable simulation with a pressure of 1 bar (proof of concept) and then change conditions. What you have to keep in mind is that most water models were designed to work at ambient conditions for normal simulations. They do not necessarily work under extremes or produce useful results under those conditions. -Justin Try TIP4P/Ice -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re:problem with simulation of freezing of water
Hi, Also note that it is difficult to simulate the right structure of ice (Ih). You didn't write what you want to study, but search the literature carefully. You may need to use an ab-initio model. Ran Message: 7 Date: Sun, 11 Nov 2012 11:26:19 -0500 From: Justin Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Re:problem with simulation of freezing of water To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 509fd1ab.50...@vt.edu Content-Type: text/plain; charset=UTF-8; format=flowed On 11/11/12 11:22 AM, Ali Alizadeh wrote: Dear Justin Thank you for reply, I want to simulation of water freezing, my condition: pressure=300 bar and T=240 k , number 1656, run time= 100ns, I can not see regular structure of ice by MD simulation or by gromacs? In your opinion, if i want this structure of ice for my simulation, What can i do? Start by searching the literature for a suitable protocol. Ice simulations have been done before. As I said before, each water model has a different melting point, and hardly any of them correspond to the actual experimental value. See if you can produce a suitable simulation with a pressure of 1 bar (proof of concept) and then change conditions. What you have to keep in mind is that most water models were designed to work at ambient conditions for normal simulations. They do not necessarily work under extremes or produce useful results under those conditions. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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@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 103, Issue 52 ** -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] problem with simulation of freezing of water
The phase transition of water from liquid to ice is very hard to observe in MD simulations. In the lab you can in fact supercool water for minutes without ice forming until you trigger the phase transition by e.g. knocking the beaker or add nucleating agents. An MD simulation takes place on timescales that are many orders of magnitude shorter, so obtaining ice in simulations when starting form a liquid system seem as likely as winning a billion dollars and getting struck by lightning at the same time. There are water models that nucleate much more easy than in experiments, which may be useful for you. Best, Erik 11 nov 2012 kl. 15.53 skrev Ali Alizadeh: Dear All users I did simulation of water freezind at low temperature(260 k) so that i was hoped to see regular structure of ice, I used OPLS-AA force field, SPC and 100ns, But i can not see the regular structure of ice(i used vmd for representation of my simulation)? In your opinion, Where did i mistake in my simulation? Where did i mistake in my simulation? -- Sincerely Ali Alizadeh -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] problem with MPI
FYI: If you are planning to run single-node, you don't need MPI. Just compile with default settings and you'll get a thread-parallel version that supports MPI parallelization within mdrun based on multi-threading (using the library thread-MPI). In practice his means that: $ mdrun -nt 2 will use two CPU cores and if you omit the -nt option it will use all cores available. -- Szilárd On Sat, Nov 10, 2012 at 11:48 AM, Bahar Mehrpuyan baharmehrpu...@yahoo.comwrote: hi gmx users I installed gromacs 4.5.5 on my Ubuntu system , and every thing was OK, but when i try to run mpirun, the following error appears: $ mpirun -np 2 mdrun -v -deffnm md_0_1 mpiexec_bahar-laptop: cannot connect to local mpd (/tmp/mpd2.console_bahar); possible causes: 1. no mpd is running on this host 2. an mpd is running but was started without a console (-n option) In case 1, you can start an mpd on this host with: mpd and you will be able to run jobs just on this host. here is the detailed description of installing: 1) installing openmpi-1.4.1 from package manager 2)fftw3 ./configure --prefix=/home/bahar/program --enable-threads --enable-float --enable-sse make make istall 3)gromacs exportCPPFLAGS=-I/home/bahar/program/include export LDFLAGS=-L/home/bahar/program/lib ./configure --prefix=/home/bahar/4-5-5 --enable-mpi make make mdrun make install make install-mdrun Any suggestion would be greatly appreciated. -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] how to restart a stopped simulation
Hi all, my simulation has stopped due to power failure, can anyone tell me how to restart it from the same point. -- Ananya Chatterjee, -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] how to restart a stopped simulation
Hi Ananya, You can refer this. http://www.gromacs.org/Documentation/How-tos/Doing_Restarts?highlight=restarting bye kavya On Mon, Nov 12, 2012 at 11:27 AM, ananyachatterjee ananyachatter...@iiserkol.ac.in wrote: Hi all, my simulation has stopped due to power failure, can anyone tell me how to restart it from the same point. -- Ananya Chatterjee, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] how to restart a stopped simulation
Hi all, I have restarted my simulation stopped due to power failure by using the command: mdrun -s md.tpr -cpi state.cpt -append And now I am getting the following error: Program mdrun, VERSION 4.0.7 Source code file: ../../../../src/gmxlib/checkpoint.c, line: 547 Fatal error: The checkpoint file is empty/corrupted, or maybe you are out of quota? can any one help in this regards. I have two .cpt files one state.cpt (0 bytes) and another state_prev.cpt file(5.4 MB). Should I have to use state_prev.cpt file to restart the simulation? On Mon, 12 Nov 2012 11:37:02 +0530, Kavyashree M wrote: Hi Ananya, You can refer this. http://www.gromacs.org/Documentation/How-tos/Doing_Restarts?highlight=restarting bye kavya On Mon, Nov 12, 2012 at 11:27 AM, ananyachatterjee ananyachatter...@iiserkol.ac.in wrote: Hi all, my simulation has stopped due to power failure, can anyone tell me how to restart it from the same point. -- Ananya Chatterjee, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Ananya Chatterjee, Senior Research Fellow (SRF), Department of biological Science, IISER-Kolkata. -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Continuous mdrun vs step-by-step mdrun
Dear gromacs users, I have a very basic doubt regarding mdrun. Is there any difference between doing final MD for 100 ns at a stretch and doing the same with a 10 ns step size (*i.e., 10ns20ns30ns100ns*) on a cluster of 256 processors. I have read some where that continuous MD of longer simulations will cause spurious drifts in velocity and energy, errors in velocity correlationetc. Please advise me in this regard. Thank you and Happy DIWALI -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] how to restart a stopped simulation
State_prev.cpt is the previous check point file to state.cpt. Usually the check point file generates for every 15 mins. You can use the state_prev.cpt because your state.cpt has no data (0 bytes) On Mon, Nov 12, 2012 at 11:54 AM, ananyachatterjee ananyachatter...@iiserkol.ac.in wrote: Hi all, I have restarted my simulation stopped due to power failure by using the command: mdrun -s md.tpr -cpi state.cpt -append And now I am getting the following error: Program mdrun, VERSION 4.0.7 Source code file: ../../../../src/gmxlib/**checkpoint.c, line: 547 Fatal error: The checkpoint file is empty/corrupted, or maybe you are out of quota? can any one help in this regards. I have two .cpt files one state.cpt (0 bytes) and another state_prev.cpt file(5.4 MB). Should I have to use state_prev.cpt file to restart the simulation? On Mon, 12 Nov 2012 11:37:02 +0530, Kavyashree M wrote: Hi Ananya, You can refer this. http://www.gromacs.org/**Documentation/How-tos/Doing_** Restarts?highlight=restartinghttp://www.gromacs.org/Documentation/How-tos/Doing_Restarts?highlight=restarting bye kavya On Mon, Nov 12, 2012 at 11:27 AM, ananyachatterjee ananyachatter...@iiserkol.ac.**in ananyachatter...@iiserkol.ac.in wrote: Hi all, my simulation has stopped due to power failure, can anyone tell me how to restart it from the same point. -- Ananya Chatterjee, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Ananya Chatterjee, Senior Research Fellow (SRF), Department of biological Science, IISER-Kolkata. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] do_dssp Segmentation fault
Hi all, I am meeting the following error in Gromacs 4.5.5 with do_dssp Here is the command do_dssp -f md.xtc -s md.tpr -o dssp.xpm give me the following error segmentation fault I have downloaded the executable DSSP form http://swift.cmbi.ru.nl/gv/dssp/ and set the environment variable, but do_dssp did not work. How can I fix it? Thanks a lot -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
