Re: [gmx-users] How to obtain a approperiate PDB file of DNA?
Check the program Biomer. I allows you to create any type of DNA molecule: http://casegroup.rutgers.edu/Biomer/index.html You will also need the amber forcefield for DNA. Gerrit Message: 7 Date: Fri, 10 Apr 2009 12:21:33 +0800 From: li ming mingli1...@gmail.com Subject: Re: [gmx-users] How to obtain a approperiate PDB file of DNA? To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 114aa2a90904092121m58c2eceaq42ce8731c9aa...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Hi, Mark: I want to check the chain length of DNA on the translocation time through a nanopore. So the DNA chains with different polymerization but the same monomer structure is necessary. How can I solve this problem? Does anybody has a optimized DNA pdb file for GMX simulation? Thanks a lot!! Ming 2009/4/10 Mark Abraham mark.abra...@anu.edu.au li ming wrote: Hi, all... I have a question on the pdb files of DNA: How can I obtain an appropriate DNA pdb file for GMX simulation? I just download some pdb files from Internet, but it is not compatible for GMX, saying that the residue was not found in rtp file. How can I solve this problem? Are the references available on this problem? Perhaps you should start by searching for some tutorial material with emphasis on these types of simulation. Furthermore, if I want to get several DNA pdb files with increasing degree of polymerization (such as 10, 20, 50 etc.). How can I achieve this goal? This may or may not be easy to achieve, but you should start by describing it more fully. What are you wanting to polymerize, and what do you mean by that word? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Ming Li Institute of Chemistry,Chinese Academy of Sciences Zhongguancun, Beijing, 100080, P. R. China Tel: +86-10-13811601014 / 62564829 E-mail: lim...@iccas.ac.cn / mingli1...@gmail.com ... Knowledge is a city to the building of which every human being brought a stone. -- next part -- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20090410/937f6a4a/attachment.html -- ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! End of gmx-users Digest, Vol 60, Issue 65 * -- Gerrit Groenhof MPI biophysical chemistry Goettingen Germany http://wwwuser.gwdg.de/~ggroenh/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] LINCS warnings generated in NPT ensemble and not in NVT
Lee Soin wrote: Hello! I'm using COM pulling with distance constraint between two domains of a protein. The energy minimization and a 100-ps equilibrating process in the NPT ensemble with position restraints on protein atoms all passed OK. Then I applied a distance constraint between COM of two domains and performed the simulaiton in the NPT ensemble. But after the first few steps I received such warnings: restraints and constraints are different phenomena in GROMACS, and it's not clear from this description you're aware of that. Perhaps you could describe better how you implemented your effects. :-) Step 7 Warning: pressure scaling more than 1%, mu: 1.03819 1.03819 1.03819 Step 8 Warning: pressure scaling more than 1%, mu: 0.98123 0.98123 0.98123 Step 9 Warning: pressure scaling more than 1%, mu: 0.746615 0.746615 0.746615 Step 10 Warning: pressure scaling more than 1%, mu: 1.34141 1.34141 1.34141 Step 10, time 0.02 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.017756, max 0.670789 (between atoms 3187 and 3188) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 4334 4336 41.30.0813 0.1101 0.1090 4334 4335 39.20.0813 0.1090 0.1090 4332 4334 32.10.1139 0.1548 0.1529 4325 4326 34.50.0813 0.1091 0.1090 4299 4301 31.10.1077 0.1468 0.1449 4293 4296 34.50.0814 0.1086 0.1090 4284 4285 30.60.0812 0.1093 0.1090 4225 4226 64.80.0812 0.1144 0.1090 4208 4210 31.00.1140 0.1522 0.1529 and then the program exited for too many LINCS warnings. The following two changes lead to no problem: (1) distance constraint between COM of two domains is applied, but the simulation is done in the NVT ensemble; (2) distance restraint using an umbrella potential instead of distance constraint is applied, and the simulation is done in NPT. So can anyone tell me what the problem is? Maybe, if they were confident of your nomenclature. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] questions regarding Replica Exchange
Hi, I have few queries regarding Replica Exchange MD. 1) I have 17 replicas , and the files are named as md_0.trr,..,.md_16.trr.Replica exchange is attempted every 100ps. Thus starting from 0, upto 100ps, the coordinates, velocities etc. that are written in md_0.trr files corresspond to the simulation at the lowest temperature say 313K. At 100ps, if there is a successful exchange between replica 0 and 1, then the coordinates and boxes are exchanged and the coordinates,etc. of replica 1 at 100 ps are written in md_0.trr files. Have I understood the process correctly ? 2) Once the simulation is over I have to use demux.pl to get the replica_index.xvg and replica_temp.xvg file. The replica_temp.xvg file has 18 columns, the first one being the time and 17 columns. Thus the 2nd column gives me the record regarding which replica occupies the lowest temp. ie. 313 K every 100ps. Is this correct? 3) Using replica_index. xvg , I will have to use trjcat to make the trajectories continous. when I give the command- trjcat -f md_*.trr -demux replica_index.xvg ,it attempts to write just one file trajout.xtc and gives a bus error. But i give the command trjcat -f md_*.trr -demux replica_index.xvg -o new_md_0.trr new_md_1.trr ..new_md_16.trr ,the command runs fine. What coordinates are written in the new_md_0.trr( ie. the new continous trajectory file) ? Does this continous file contain the information about the replica 0 over the time? It will be of great help if I get any suggestions regarding my queries. Thanking You, Sarbani ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] questions regarding Replica Exchange
sarbani chattopadhyay wrote: Hi, I have few queries regarding Replica Exchange MD. 1) I have 17 replicas , and the files are named as md_0.trr,..,.md_16.trr.Replica exchange is attempted every 100ps. Thus starting from 0, upto 100ps, the coordinates, velocities etc. that are written in md_0.trr files corresspond to the simulation at the lowest temperature say 313K. At 100ps, if there is a successful exchange between replica 0 and 1, then the coordinates and boxes are exchanged and the coordinates,etc. of replica 1 at 100 ps are written in md_0.trr files. Have I understood the process correctly ? yes. 2) Once the simulation is over I have to use demux.pl to get the replica_index.xvg and replica_temp.xvg file. The replica_temp.xvg file has 18 columns, the first one being the time and 17 columns. Thus the 2nd column gives me the record regarding which replica occupies the lowest temp. ie. 313 K every 100ps. Is this correct? yes. 3) Using replica_index. xvg , I will have to use trjcat to make the trajectories continous. when I give the command- trjcat -f md_*.trr -demux replica_index.xvg ,it attempts to write just one file trajout.xtc and gives a bus error. But i give the command trjcat -f md_*.trr -demux replica_index.xvg -o new_md_0.trr new_md_1.trr ..new_md_16.trr ,the command runs fine. What coordinates are written in the new_md_0.trr( ie. the new continous trajectory file) ? Does this continous file contain the information about the replica 0 over the time? yes. you can verify this by plotting e.g. RMSD as a function of time for each replica, these should be continuous functions of time, even at exchange times. It will be of great help if I get any suggestions regarding my queries. Thanking You, Sarbani http://sigads.rediff.com/RealMedia/ads/click_nx.ads/www.rediffmail.com/signatureline@middle? ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] LINCS warnings generated in NPT ensemble and not in NVT
The difference between restraints and constraints is indeed something I'm aware of :-) Even though distance restraint between COM of two domains worked just OK for me, I would prefer to use distance constraint since that will introduce fewer artifacts and can fix the distance between two domains exactly at the desired distance. So now everything I'm going to ask is under the assumption that I'm using distance constraint in COM pulling. The protein I'm using consists of two domains, and the problem is as follows: After energy minimization and a 100-ps equilibration in NPT, I applied a distance constraint between COM of two domains and performed COM pulling in the NPT ensemble. But after the first few steps I received such warnings: Step 7 Warning: pressure scaling more than 1%, mu: 1.03819 1.03819 1.03819 Step 8 Warning: pressure scaling more than 1%, mu: 0.98123 0.98123 0.98123 Step 9 Warning: pressure scaling more than 1%, mu: 0.746615 0.746615 0.746615 Step 10 Warning: pressure scaling more than 1%, mu: 1.34141 1.34141 1.34141 Step 10, time 0.02 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.017756, max 0.670789 (between atoms 3187 and 3188) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 4334 4336 41.30.0813 0.1101 0.1090 4334 4335 39.20.0813 0.1090 0.1090 4332 4334 32.10.1139 0.1548 0.1529 4325 4326 34.50.0813 0.1091 0.1090 4299 4301 31.10.1077 0.1468 0.1449 4293 4296 34.50.0814 0.1086 0.1090 4284 4285 30.60.0812 0.1093 0.1090 4225 4226 64.80.0812 0.1144 0.1090 4208 4210 31.00.1140 0.1522 0.1529 .. and then the program exited for too many LINCS warnings. If I change the ensemble to NVT, everything is OK. So I think I have made everything clear, haven't I? And thank you if you can help me again :-) -- SUN Li Department of Physics Nanjing University, China ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] define atoms
Dear mark excuse me. I attempt it again.in analysis result of md peptide I have the table t consist of atoms number column and the other column rmsd(nm).I want to know what is thename of atom which define number 12 in backbone group ?Is it NCC for example related to ser or another aminoacid ? Do I have to by hand or software spdbv. which program is define number of atoms?in topology top number of atom is defined but it is not compatible in backbone group. thanks again -- sh-karbalaee ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Release of R.E.D. Server
Quoting Joe Joe ilcho...@gmail.com: What about use for commercial purposes? So far, commercial users can use the R.E.D.-III.2 tools which are distributed in the standalone version. A specific license agreement has to be signed in this case. regards, Francois On Thu, Apr 9, 2009 at 1:31 AM, FyD f...@q4md-forcefieldtools.org wrote: Dear All, I am pleased to announce the release of R.E.D. Server available @ http://q4md-forcefieldtools.org/REDS/. R.E.D. Server provides the software and hardware (i. e. a cluster of computers) required for the derivation of highly effective and reproducible RESP and ESP atomic charge values embedded in force field libraries suitable for molecular dynamics simulations. R.E.D. Server interfaces the last stable version of the RESP ESP charge Derive program (R.E.D. IV April 2009 so far) developed by the q4md force field tools team, and provides the binaries for the last versions of the Gaussian, GAMESS-US, or the PC-GAMESS/Firefly program, and for the RESP program. More generally, the last developments in term of RESP and ESP charge derivation carried out by the q4md force field tools team will be provided through R.E.D. Server. The release of these new developments will be carried out from time to time, and the description of those last features released in R.E.D. Server is available at the R.E.D. Server news web page. By involving multiple molecules, multiple conformations and multiple orientations in charge derivation and by handling specific charge constraints during the fitting step, R.E.D. IV allows building complex force field topology database or FFTopDB corresponding to the simultaneous generation of numerous molecular fragments (N-terminal, C-terminal and central amino acid fragments, 5'- or Y'-terminal, 3'- or X'-terminal and central nucleotide fragments as well as monosaccharide and metal complex fragments) in a single execution. The all atom or united-carbon force field library model can be in-differentially generated. A procedure to study the impact of the various charge constraints required during the fitting step of a molecular fragment has been implemented allowing users to compare charge values, and thus to validate or reject charge sets. The use of R.E.D. Server and R.E.D. IV is described in Frequently Asked Questions http://q4md-forcefieldtools.org/REDS/faq.php as well as in a specific tutorial http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php. Academic users involved in non-profit research are authorized to use R.E.D. Server. The use of R.E.D. Server is provided at no cost after signing a license agreement. The PI (principal investigator or Director of a laboratory) and the PU (R.E.D. Server principal user) have to register and sign a license agreement to be authorized to use R.E.D. Server. A general public help is provided with the q4md-forcefieldtools mailing list. Any researcher can participate in this mailing list by answering and/or sending queries at q4md-...@q4md-forcefieldtools.org after registration at sy...@q4md-forcefieldtools.org. Archives of the q4md-fft mailing list are public. A private assistance is also available for registered users from the Assistance Service available at the R.E.D. Server Home page. We are registered in the AMBER and CCL mailing lists, and we will answer to the queries about the q4md force field tools in these mailing lists as well. The R.E.D. III.2 tools distributed in a standalone version at http://q4md-forcefieldtools.org/RED/, the RESP ESP charge DDataBase (or R.E.DD.B. http://q4md-forcefieldtools.org/REDDB/) which allows freely storing and distributing RESP and ESP charges embedded in force field libraries in the scientific community and R.E.D. Server constitute to the best of our knowledge unique tools. regards, F.-Y. Dupradeau --- http://q4md-forcefieldtools.org/FyD/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] define atoms
shahrbanoo karbalaee wrote: Dear mark excuse me. I attempt it again.in analysis result of md peptide I have the table t consist of atoms number column and the other column rmsd(nm).I want to know what is thename of atom which define number 12 in backbone group ?Is it NCC for example related to ser or another aminoacid ? Do I have to by hand or software spdbv. which program is define number of atoms?in topology top number of atom is defined but it is not compatible in backbone group. thanks again RMSD or RMSF? RMSD should not be broken down by atom, I think. In any case, atom 12 in the analysis should be whatever atom 12 is in the topology/structure. If you can provide a copy-paste example of where you think the problem is occurring, that may help; I am still not entirely clear what the problem is. -Justin -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Re: Free energy with Gromacs.
You may also want to look at www.alchemistry.org, as it has some general information about how these should be set up. On Wed, Mar 18, 2009 at 8:02 PM, Justin A. Lemkul jalem...@vt.edu wrote: Again, *please keep all Gromacs-related correspondence on the mailing list* The type of information that you have posted is important to share with others who may know how to help. I do not know the answer to your problem. I would suggest contacting the list again with the following information: 1. The relevant contents of your .mdp file(s) 2. What each figure in your image represents (main image vs. inset) -Justin Eudes Fileti wrote: Justin thanks for the reply. Sorry, 16 refers to the value of dg / dl for lambda = 0. I am sending you a link for you see the profile of the curve. http://cromo.ufabc.edu.br/~fileti/web/dgdl-transfer2.jpg This case is for solute in benzene. The peak in lambda=0 is around 3. For sc-power=1 I got a peak much higher than for sc-power=2, and therefore the integration in this case (sc-power=1) could lead me to a much greater error. In both cases (ethanol and benzene) the curves coincide for values of lambda beyond 0.4. bests eef P.S.: I am using the 3.3.3 version. ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC Rua Santa Adélia, 166 - Bloco B, Sala 1048 09210-170 Santo André - SP Brasil +55.11.4437-8408 skype: eefileti http://cromo.ufabc.edu.br/~fileti/ On Wed, Mar 18, 2009 at 7:13 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Eudes Fileti wrote: Hello Justin, I am facing a very similar problem to that you experienced and described in (http://www.gromacs.org/pipermail/gmx-users/2008-February/032429.html). I throw this question in the GMX forum and Berk has kindly helped me. But reading the forum I realized that you already could be solved the problem so that maybe I could help more directly. Please keep Gromacs-related discussions on the list. If you had followed the rest of the thread you reference, you will find that my calculations were falling victim to a bug in Gromacs-3.3.1. If you are using a newer version, then my situation is not applicable, since the problem has been fixed (IIRC) as of Gromacs-3.3.3. If you are using version 3.3.1, re-run your simulations with a newer version. I have tried to calculate the free energy of transfer from benzene to ethanol for a polyhydroxylated (24 OH's). This system has 24 hydroxyl groups, and in ethanol, there should be more than 20 solute-solvent hydrogen bonds being erased simultaneously (not to mention the possible intramolecular HB's). The Dg/dlambda plot, for both, benzene and ethanol shows a very high and narrow peak near lambda=0. In the case of ethanol is worse due to the solute-solvent hydrogen bonds. I performed two sets of simulations, one for sc-power=1 and another for sc-power=2, using the following protocol: 1) I made disappear the electrostatic interactions turning off the charges (by 200ps), 2) At the sequence I made disappear the LJ interactions (for more 200ps) 3) Finally I performed a run of 0.5ns. Correct me i this procedure is inappropriate. To start, Berk said me that the use of sc-power=2 never is recommended. Ok! Secondly, then he gave me a good tip that I was not taking into account: Disappear the electrostatic interactions using hard-core instead soft-core. I did this and actually work (only in part). When I used softcore to desappear the electrostatic interations, the value of dg/dlambda for lambda = 0 was ~16. Following the tip of Berk, wiht hardcore I got ~2000! Right, you should only need soft-core for the LJ component. However when I needed to use softcore again, now to remove the LJ interactions, the value returned back to ~16.` I don't understand what you mean. Is the total area under the curve 16? That is ridiculously high. I don't know that I have the expertise to help you much more. I am not entirely familiar with your methodology. What I have done in my own work is run 21 independent simulations at lambda points between 0 and 1 (5 ns each after equilibration), and integrated the resulting curve. None of my dV/dl points ever approached that magnitude, but I can't comment on your specific case, because I don't know what you're doing. -Justin Could you gimme some insigths to solve this problem? Best eef P.S.: You can solve your problem of polyphenolic compound? ___ Eudes Eterno Fileti
[gmx-users] Pressure Coupling Problem
Alright, sorry that I wasn't able to help. I'm confused by some apparent contradictions in your posts and I'm not sure that I'm going to be useful to you here. Quoting http://www.gromacs.org/pipermail/gmx-users/2009-April/041173.html: No matter how much minimization I do the volume of the box expands when run it using berendsen pressure coupling with a tau_p -f .1. Quoting http://www.gromacs.org/pipermail/gmx-users/2009-April/041159.html: So I got my small water box (800 waters) to behave stably with pressure coupling after more minimization ... Good luck. Chris. -- original message -- Nope not an A/nm problem. As a simple test I take spc.gro from share/top. I reconfigure the box (i.e. editconf -f spc.gro -d 1.0 -c -bt cubic -o water_center. I then solvate with genbox, minimize and run using the mdp file I provided earlier. No matter how much minimization I do the volume of the box expands when run it using berendsen pressure coupling with a tau_p -f .1. Ilya On Thu, Apr 9, 2009 at 11:22 AM, Chris Neale chris.ne...@utoronto.cawrote: [Hide Quoted Text] So your problem with the small water box was solved simply by adding more minimization? I then suspect that all of your problems are simply related to a bad starting structure -- and by the sound of it is really is very bad. Are you sure that you don't have an angstrom / nm problem here? Chris. -- original message -- So I got my small water box (800 waters) to behave stably with pressure coupling after more minimization but I still can't get my large system to work with pressure coupling. I tried minimizing but I can never get the Fmax to be less 102, which is pretty normal for protein/water simulations of large proteins, at least from my experience. I have since run 400 ps NVT as ... ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Query
Hi, i am running MD on a system where a protien and a small peptide chain are placed closely. After running the simulation when i was analyzing the system, i got a rmsd plot with numerous bumps. For creating the xtc file i tried different options like -pbc nojump/whole etc and also -center tric, still i am getting the rmsd plot with those bumps. Further i analysed the rmsd for the protein and peptides seperatley which come up well. I request all the members to please provide me guidanceor possible pathway to solve this issue. Your help will be highly appreciated. Amit Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
RE: [gmx-users] What's the max number of pull groups?
Thanks so much, Berk. I have another question regarding the pull code. Can I define a pull group that contains more than one molecules? I tried to define some lipid molecules as a single pull group and pull them out of a bilayer. But I couldn't see the lipids out. If I try one lipid as a pull group, I got what I expected. Lanyuan From: g...@hotmail.com To: gmx-users@gromacs.org Subject: RE: [gmx-users] What's the max number of pull groups? Date: Fri, 10 Apr 2009 23:04:32 +0200 Hi, There is no maximum. Berk From: lulany...@msn.com To: gmx-users@gromacs.org Date: Fri, 10 Apr 2009 16:04:18 -0400 Subject: [gmx-users] What's the max number of pull groups? Hello, Could anyone tell me what the maximum number of COM pulling groups is in GMX 4? Thanks very much. Lanyuan Lu 立刻下载 MSN 保护盾，保障 MSN 安全稳定！ 现在就下载！ What can you do with the new Windows Live? Find out _ Live Search视频搜索，快速检索视频的利器！ http://www.live.com/?scope=video___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] mdrun_mpi error Signal: Segmentation fault
I have segmentation fault error while running mdrun_mpi( gromacs 4.0.4). I have installed gromacs 4.0.4 two month ago and been working fine. Today, I just got Segment errors. Rebooting does not much help. Here is log: [rd:06790] *** Process received signal *** [d:06790] Signal: Segmentation fault (11) [rd:06790] Signal code: (128) [rd:06790] Failing at address: (nil) [rd:06790] [ 0] /lib64/tls/libpthread.so.0 [0x36bc30c430] [rd:06790] [ 1] /lib64/ld-linux-x86-64.so.2 [0x36bb607496] [rd:06790] [ 2] /lib64/ld-linux-x86-64.so.2 [0x36bb60789e] [rd:06790] [ 3] /lib64/ld-linux-x86-64.so.2 [0x36bb60a68a] [rd:06790] [ 4] /lib64/ld-linux-x86-64.so.2 [0x36bb60a552] [rd:06790] [ 5] /usr/local/topspin/lib64/libvapi.so(vipul_cleanup+0x50) [0x2a984472b0] [rd:06790] [ 6] /usr/local/topspin/lib64/libvapi.so [0x2a98440c32] [rd:06790] *** End of error message *** Thanks ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] mdrun_mpi error Signal: Segmentation fault
nam kim wrote: I have segmentation fault error while running mdrun_mpi( gromacs 4.0.4). I have installed gromacs 4.0.4 two month ago and been working fine. Today, I just got Segment errors. Rebooting does not much help. Here is log: [rd:06790] *** Process received signal *** [d:06790] Signal: Segmentation fault (11) [rd:06790] Signal code: (128) [rd:06790] Failing at address: (nil) [rd:06790] [ 0] /lib64/tls/libpthread.so.0 [0x36bc30c430] [rd:06790] [ 1] /lib64/ld-linux-x86-64.so.2 [0x36bb607496] [rd:06790] [ 2] /lib64/ld-linux-x86-64.so.2 [0x36bb60789e] [rd:06790] [ 3] /lib64/ld-linux-x86-64.so.2 [0x36bb60a68a] [rd:06790] [ 4] /lib64/ld-linux-x86-64.so.2 [0x36bb60a552] [rd:06790] [ 5] /usr/local/topspin/lib64/libvapi.so(vipul_cleanup+0x50) [0x2a984472b0] [rd:06790] [ 6] /usr/local/topspin/lib64/libvapi.so [0x2a98440c32] [rd:06790] *** End of error message *** Are there any other messages from mdrun? Anything printed to the screen (LINCS warnings, etc)? -Justin Thanks ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] x2top: duplicate bond, angle, dihedral parameters; missing VdW parameters
Dear All, I ran the x2top command and successfully generated a topology. However, the topology file has duplicate bond, angle, and dihedral parameters and missing Van der Waals parameters. I am including sections of my topology file for your perusal. Please let me know why this is occurring and how to solve this problem? Much thanks. Darrell Command issued (Note: I selected the oplsaa option): x2top -ff select -f graphene_nm.gro -o graphene_nm.top Selected segments from graphene_nm.top file: [ bonds ] ; aiaj functc0c1c2c3 1 2 1 1.42e-01 4.00e+05 1.42e-01 4.00e+05 [ pairs ] ; aiaj functc0c1c2c3 111 1 [ angles ] ; aiajak functc0c1c2 c3 2 1 3 1 1.20e+02 4.00e+02 1.20e+02 4.00e+02 [ dihedrals ] ; aiajakal functc0c1c2 c3c4c5 3 1 2 5 3 3.60e+02 5.00e+00 3.00e+00 3.60e+02 5.00e+00 3.00e+00 Selected segments from graphene_nm.top file(for reference): MD of Graphene, t=0.0 270 2Grph C1 0.000 0.000 0.000 0. 0. 0. 2Grph C2 0.071 -0.123 0.000 0. 0. 0. 2Grph C3 0.071 0.123 0.000 0. 0. 0. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Replica Exchange Error
Hi All, I get the following error when running replica exchange. I have 32 replica's with each replica running on 4 processors (128 total). How do I decrease the domain decomposition cell size, -dss? What should I set it to? Thanks, Ilya DD cell 2 0 0: Neighboring cells do not have atoms: 22217 20764 20762 21782 21780 22244 22249 21863 21734 21739 3 22240 DD cell 3 0 0: Neighboring cells do not have atoms: 21856 21868 DD cell 4 0 0: Neighboring cells do not have atoms: 21807 21809 DD cell 5 0 0: Neighboring cells do not have atoms: 22240 21765 20764 20762 21253 21250 21863 21860 22246 22251 21771 21789 DD cell 7 0 0: Neighboring cells do not have atoms: 21858 1 21736 DD cell 0 0 0: Neighboring cells do not have atoms: 21789 21811 21253 21769 21742 21724 DD cell 7 0 0: Neighboring cells do not have atoms: 1 21742 DD cell 1 0 0: Neighboring cells do not have atoms: 3 22240 DD cell 2 0 0: Neighboring cells do not have atoms: DD cell 4 0 0: Neighboring cells do not have atoms: 21807 21809 20764 20762 21782 21780 21739 21745 21722 21727 DD cell 5 0 0: Neighboring cells do not have atoms: 21765 20764 20762 21253 21250 21863 21860 21771 21789 --- Program mdrun_mpi, VERSION 4.0.4 Source code file: domdec_con.c, line: 679 Fatal error: DD cell 5 0 0 could only obtain 96 of the 108 atoms that are connected via vsites from the neighboring cells. This probably means your vsite lengths are too long compared to the domain decomposition cell size. Decrease the number of domain decomposition grid cells or use the -rcon option of mdrun. --- Live for Liposuction (Robbie Williams) Error on node 45, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 45 out of 128 --- Program mdrun_mpi, VERSION 4.0.4 Source code file: domdec_con.c, line: 679 Fatal error: DD cell 0 0 0 could only obtain 40 of the 45 atoms that are connected via vsites from the neighboring cells. This probably means your vsite lengths are too long compared to the domain decomposition cell size. Decrease the number of domain decomposition grid cells or use the -rcon option of mdrun. --- Live for Liposuction (Robbie Williams) Error on node 40, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 40 out of 128 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Replica Exchange Error
Joe Joe wrote: Hi All, I get the following error when running replica exchange. I have 32 replica's with each replica running on 4 processors (128 total). How do I decrease the domain decomposition cell size, -dss? What should I set it to? snip You're getting some hints from mdrun, I'd start there: --- Program mdrun_mpi, VERSION 4.0.4 Source code file: domdec_con.c, line: 679 Fatal error: DD cell 5 0 0 could only obtain 96 of the 108 atoms that are connected via vsites from the neighboring cells. This probably means your vsite lengths are too long compared to the domain decomposition cell size. Decrease the number of domain decomposition grid cells or use the -rcon option of mdrun. --- ...So manually set -dd and/or -rcon. -Justin -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Replica Exchange Error
How do I determine what those values should be? How does it affect the simulation? thanks, Ilya On Fri, Apr 10, 2009 at 8:00 PM, Justin A. Lemkul jalem...@vt.edu wrote: Joe Joe wrote: Hi All, I get the following error when running replica exchange. I have 32 replica's with each replica running on 4 processors (128 total). How do I decrease the domain decomposition cell size, -dss? What should I set it to? snip You're getting some hints from mdrun, I'd start there: --- Program mdrun_mpi, VERSION 4.0.4 Source code file: domdec_con.c, line: 679 Fatal error: DD cell 5 0 0 could only obtain 96 of the 108 atoms that are connected via vsites from the neighboring cells. This probably means your vsite lengths are too long compared to the domain decomposition cell size. Decrease the number of domain decomposition grid cells or use the -rcon option of mdrun. --- ...So manually set -dd and/or -rcon. -Justin -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
