Re: [gmx-users] x2top
danilo gonzalez wrote: hi gmx-users i was reading , in other post, the posibillity to run a new molecule without create new .rtp file , but when i run that program, he gives me the next error message Program x2top, VERSION 3.3.3 Source code file: ../../../../src/kernel/x2top.c, line: 206 Try one of the other programs available on the download pages of gromacs instead. Fatal error: Could only find a forcefield type for 654 out of 834 atoms i read that in this file http://oldwww.gromacs.org/pipermail/gmx-users/2006-September/024068.html I really apreciate your help best regards ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 sp...@xray.bmc.uu.sesp...@gromacs.org http://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/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] Re: Some questions about OPLS/Berger combination]
Thank you Chris for your answer. It didn't though clarify the things to me, so I'll try to explain again where my objection is. The method is sound. A key realization is that the [ pairs ] section defines both the LJ and the Q pairs, so we will have double of each. We actually want double Q, since it was cut to 0.5 and 0.5*2=1.0. What we don't actually want is double epsilon, since the epsilon in question is already a special pairtypes epsilon that has been properly modified for 1-4 interactions. We thus cut epsilon in half to counteract the fact that we are forced to add it again twice in the pairs section. But why should the epsilons be doubled? For OPLS-AA both the FudgeLJ and FudgeQQ parameters are set to 0.5, so both the Coulombic and LJ 1-4 interactions are cut by 50%. We want them both to be 100% so, to counteract this reduction, one can put a second copy of [ pairs ] section to make GROMACS calculate both potentials twice. Dividing the epsilons by 2 will excessively reduce the 1-4 LJ potential (see below) Another point concerns the 1-4 Coulombic interaction; you state that dividing the Berger epsilons by 2 will modify both the 1-4 interactions types, the LJ and the Coulombic ones. I don't believe that I do say that anywhere. Ok, I misinterpreted what you wrote in http://lists.gromacs.org/pipermail/gmx-users/2006-September/023761.html 1. Divide the epsilon entries in the [ pairtypes ] of lipid.itp by 2.0. Now the LJ and coulombic 1-4 interactions are both exactly half of what they should be. While I am always open to the possibility that I have made a mistake, I actually put a lot of time into developing this and distributing it, so I'm not very motivated to go look into it again before I see a bit of data or perhaps a proper mathematical derivation of whatever problem you propose. I still believe that the method is properly derived and implemented. Chris. All right, I'll try to explain what I mean with the exact formulas. I understand the OPLS-AA LJ potential for 1-4 interaction between atoms A and B is calculated as: V(OPLS) = 0.5*4*epsilon*[(sigma/r)^12 - (sigma/r)^6] = 0.5*V(Berger) where 0.5 is the scaling factor as defined by FudgeLJ and the epsilon and sigma values are taken from the [ pairtypes ] section, if the pair A-B has been specified there, otherwise they are calculated from the epsilons and sigmas for the A and B atoms by the combination rule. So, if you put into this formula the Berger epsilon for a given pair of atoms, as taken from the [ pairtypes ], you get V(OPLS) which is a half of what the potential should be. What you need is to double this value, which may be achieved by putting a second copy of [ pairs ]. Now, if you divide the Berger epsilons by 2, the calculated OPLS potential will be V(OPLS) = 0.5*4*(epsilon/2)*[(sigma/r)^12 - (sigma/r)^6]=0.25*V(Berger) Putting a second copy of [ pairs ] will double this value, so you end with 50% of the proper potential value instead of 100%. So, where is the flaw in my reasoning? All my best, Dorota ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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] How to obtain the .gro and .top files for dendrimers
Dear gmx users, On current, I plan to study a dendrimer (like PAMAM) using MD simulations available in GROMACS. As is well-known, the .gro and .top files are the start points for running MD simulations in GROMACS. However, the question how to obtain the files for dendrimers puzzles me too much, since the dendrimers have a complex dendritic structure. The mail-list and the manual seem not give helpful clues on doing it. Are there someone that have the experiences to do so? Could you share these experiences with us? Any suggesstion would be acknowledged greatly. Chaofu Wu, Dr. _ Messenger10年嘉年华，礼品大奖等你拿！ http://10.msn.com.cn___ gmx-users mailing listgmx-users@gromacs.org http://lists.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] How to obtain the .gro and .top files for dendrimers
wuxiao wrote: Dear gmx users, On current, I plan to study a dendrimer (like PAMAM) using MD simulations available in GROMACS. As is well-known, the .gro and .top files are the start points for running MD simulations in GROMACS. However, the question how to obtain the files for dendrimers puzzles me too much, since the dendrimers have a complex dendritic structure. The mail-list and the manual seem not give helpful clues on doing it. Are there someone that have the experiences to do so? Could you share these experiences with us? Any suggesstion would be acknowledged greatly. Chaofu Wu, Dr. You will need to write your own rtp entries. Terminating chains may be a problem, but I don't know the structure and composition of these molecules, so it is hard to judge. 立刻下载 MSN 保护盾，保障Messenger 安全稳定！ 现在就下载！ http://im.live.cn/safe/ ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 sp...@xray.bmc.uu.sesp...@gromacs.org http://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/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] How to obtain the .gro and .top files for dendrimers
wuxiao wrote: Dear gmx users, On current, I plan to study a dendrimer (like PAMAM) using MD simulations available in GROMACS. As is well-known, the .gro and .top files are the start points for running MD simulations in GROMACS. However, the question how to obtain the files for dendrimers puzzles me too much, since the dendrimers have a complex dendritic structure. The mail-list and the manual seem not give helpful clues on doing it. Are there someone that have the experiences to do so? Could you share these experiences with us? Any suggesstion would be acknowledged greatly. Unfortunately the main topology builder for GROMACS (pdb2gmx) is fairly specific for head-to-tail polymers like protein and DNA. If you have an existing generator for coordinates in some suitable format (PDB, .gro, etc.), then you can probably make pdb2gmx work with careful use of specbond.dat and appropriate .rtp file entries. You will probably need to make versions of your residues that are terminated, since the pdb2gmx termination methods won't cope with more than two termini. A detailed knowledge of much of chapter 5 of the manual will be required. There is no existing GROMACS tool for generating coordinate files, so you are on your own here. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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] Re: How to obtain the .gro and .top files for dendrimers
Dear gmx users, In order to get more direct help, some words need to be added to the question for the first time. The dendrimer I want to study is just PAMAM, ethylenediamine (EDA) cored and amine surface poly(amidoamine). The pdb file for the PAMAM has assumed to be obtained, and I want to generate the .gro and .top files from the pdb file using pdb2gmx. According to the advice, some files need to be modified to make it implement successfully. so my question becomes: How to modify those files? Thanks a lot. Chaofu Wu, Dr. _ 上Windows Live 中国首页，下载最新版Messenger！ http://www.windowslive.cn___ gmx-users mailing listgmx-users@gromacs.org http://lists.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] Parallel computation in Gromacs 3.2.1 Reg.
Dear Gromacs users We are interested in doing long time MD using parallel computation.Can we use the Gromacs 3.2.1 version in the parallel computation system. We would appreciate if you suggest what type of parallel computing system to be bought to implement in Gromacs. Thank you Dr C.Karunakaran ***+ Dr.Karunakaran Chandran+ Biophysics Department + Medical College of Wisconsin + Milwaukee, WI-53226+ Resi.: 414-443-0085+ Off : 414-456-4034+ ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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: How to obtain the .gro and .top files for dendrimers
wuxiao wrote: Dear gmx users, In order to get more direct help, some words need to be added to the question for the first time. That's a good idea. The dendrimer I want to study is just PAMAM, ethylenediamine (EDA) cored and amine surface poly(amidoamine). The pdb file for the PAMAM has assumed to be obtained, and I want to generate the .gro and .top files from the pdb file using pdb2gmx. You don't need a .gro file. It's a by-product of pdb2gmx, however. According to the advice, some files need to be modified to make it implement successfully. so my question becomes: How to modify those files? Thanks a lot. As I said last time, you'll need to read and understand chapter 5 in detail. You need .rtp file entries for all of your monomeric units and half-capped monomeric units. This will require picking a MM forcefield, looking at how the existing .rtp file entries work for it, and adapting that knowledge to your own needs. You will also need to understand the specbond.dat mechanism to facilitate branching. This is probably not well-travelled territory, so you will have to do a lot of work. Doing some protein-specific GROMACS tutorials is also wise - particularly ones that use disulfide links, since that will teach you about specbond.dat. In general, you stand a better chance of getting useful answers to focussed questions that show you've tried to get your own information and solve your own problems. How to modify these files sounds like you want someone to do it all for you :-) Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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] Parallel computation in Gromacs 3.2.1 Reg.
chandran karunakaran wrote: Dear Gromacs users We are interested in doing long time MD using parallel computation.Can we use the Gromacs 3.2.1 version in the parallel computation system. We would appreciate if you suggest what type of parallel computing system to be bought to implement in Gromacs. Lacking a strong scientific reason (e.g. continuity with previous work) you should not be planning to use a version that's 3 or 4 years old. GROMACS 4.x is much faster. That said, pretty much anything will be reasonable, but don't skimp on your network. Even gigabit ethernet is not very useful. Search the archives for posts recommending Infiniband. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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] problem in grompp -broken charge
hi, Justin, i have completed upto the genion step of that simulation. One error is creeping in this step which is nonzero system charge. my system is said to have a charge 1.69. now how to neutralize this kind of broken charge? another thing is that how this kind of broken chage is being developed? i think something was wrong in previous steps. but can't recognise which step to account for this anomalous behavior? waiting for your valuable suggestions... Thanks again.. Shamik Love Cricket? Check out live scores, photos, video highlights and more. Click here http://cricket.yahoo.com___ gmx-users mailing listgmx-users@gromacs.org http://lists.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] problem in grompp -broken charge
Samik Bhattacharya wrote: hi, Justin, i have completed upto the genion step of that simulation. One error is creeping in this step which is nonzero system charge. my system is said to have a charge 1.69. now how to neutralize this kind of broken charge? another thing is that how this kind of broken chage is being developed? i think something was wrong in previous steps. but can't recognise which step to account for this anomalous behavior? waiting for your valuable suggestions... Probably you have broken termini. Go and read all of the output from pdb2gmx carefully. If that doesn't clue you in, look at the [atoms] section of your .top file. There's a running count of the total charge... whenever that first becomes non-integral for the last atom in a residue, you have a broken residue there. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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] make install 'only suffix append binaries'
Hi List, I would like to know if there's an option in gromacs Makefile that would allow me to once did: ./configure --disable-float --program-suffix=_d --enable-shared make Then install only the binaries created with suffix _d. I am not sure if 'make install-exec' would do it or if there's something else. The reason is I want to create a Fink package for 'gromacs-double', but if doing a normal 'make install' I will have conflict with files like '/sw/bin/GMXRC' that are essentially the same for both gromacs-simple or gromacs-double. I hope you can understand me. Many thanks in advance, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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] make install 'only suffix append binaries'
Alan wrote: Hi List, I would like to know if there's an option in gromacs Makefile that would allow me to once did: ./configure --disable-float --program-suffix=_d --enable-shared make Then install only the binaries created with suffix _d. I am not sure if 'make install-exec' would do it or if there's something else. I've no idea if that works, but it's straightforward to make a dummy install location and use configure --prefix=/that/dummy/location and see what gets put there. The reason is I want to create a Fink package for 'gromacs-double', but if doing a normal 'make install' I will have conflict with files like '/sw/bin/GMXRC' that are essentially the same for both gromacs-simple or gromacs-double. Fair enough. How about listing gromacs-single and gromacs-double in the other's Conflicts and Replaces fink fields? http://www.finkproject.org/doc/packaging/reference.php?phpLang=en#fields That might just work and have no problems. Also, I suggest making a bugzilla with your fink scripts attached when you have them working, since they may as well get put in the GROMACS admin subdirectory for future use. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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] Re: Re: protein in SDS/water
Dear Justin, AAARRRGGGHH! The last case indicated in the wiki section about 0 topology was MY case: probably I was using a .mdp file that was created with Windows. When I re-wrote my em.mdp file using vi, it worked!! I'm sorry for all this waste of time, but as I told some days ago, I've problems in seeing the contents of the GROMACS site (old and new), and I could access to this information only through the link you sent me... A little suggestion for developers: would it be possible to insert an error message more indicative for this problem? I don't pretend that computers do everything I need, but it would be nice that they could at least suggest me a solution in a less cryptic way when I have such a trivial problem, so I can avoid boring the developers themselves...;-) Thank you to all for collaboration and best regards Anna Anna Marabotti wrote: Dear all, as requested, I'm copying here the SDS.itp file (it should be not too big): ; This file was generated by PRODRG version AA081006.0504 ; PRODRG written/copyrighted by Daan van Aalten ; and Alexander Schuettelkopf ; ; Questions/comments to d...@davapc1.bioch.dundee.ac.uk ; ; When using this software in a publication, cite: ; A. W. Schuettelkopf and D. M. F. van Aalten (2004). ; PRODRG - a tool for high-throughput crystallography ; of protein-ligand complexes. ; Acta Crystallogr. D60, 1355--1363. [ moleculetype ] ; Name nrexcl SDS 3 OK, as I thought, if you #include SDS.itp you should NOT specify a separate [moleculetype] directive in your system .top file. snip As I told sometimes ago, I obtained this file from PRODRG starting from a SDS.pdb file that I created using SDS coordinates found in another .pdb file (I simply copied and pasted the SDS coordinates in a new file and called it SDS.pdb). For my simulations, however, I used the SDS.gro file and SDS.itp file generated by PRODRG. I notice that the section [ moleculetype] is present in SDS.itp, but nothing changes if I erase the [ moleculetype ] section for SDS in my_prot.top: in all cases it doesn't work... I also copied and pasted the entire topology of SDS explicitly into my_prot.top instead of typing #include SDS.itp, and nothing changed again... Well, the .itp file itself seems to have been properly generated. Concerning the order of molecules in the last [ molecules ] section, I changed it several times, and nothing changed... I'm still with an unclarified question: why genbox did not create by itself all corrections necessary to the original .top file when I used the -ci -nmol options? I added the -p flag but it doesn't change the topology by itself (as it should do, in my opinion). It would be nice if the computers did everything for us, wouldn't it? :) Maybe one day. It looks like automated updates only work for addition of water. Perhaps this can be a future improvement to genbox. Have you read the error page for your problem: http://oldwiki.gromacs.org/index.php/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology There is a specific section on the case where grompp detects 0 coordinates in the .top that might be relevant. -Justin Thank you again Anna __ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science, CNR Via Roma 64 83100 Avellino (Italy) Phone: +39 0825 299651 Fax: +39 0825 781585 Skype: annam1972 E-mail: amarabo...@isa.cnr.it Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm If you think you are too small to make a difference, try sleeping with a mosquito ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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] make install 'only suffix append binaries'
Dear Mark, Thank you very much for your reply. Indeed, reading more about Fink I can see several alternative. For now I guess I got a good solution. I have a package called 'gromacs-all' which installs gromacs single and double and now I want to make too with mpi, but first I need to solve a problem with openmpi in my Fink here. Cheers, Alan On Thu, Jun 18, 2009 at 16:43, gmx-users-requ...@gromacs.org wrote: Alan wrote: Hi List, I would like to know if there's an option in gromacs Makefile that would allow me to once did: ./configure --disable-float --program-suffix=_d --enable-shared make Then install only the binaries created with suffix _d. I am not sure if 'make install-exec' would do it or if there's something else. I've no idea if that works, but it's straightforward to make a dummy install location and use configure --prefix=/that/dummy/location and see what gets put there. The reason is I want to create a Fink package for 'gromacs-double', but if doing a normal 'make install' I will have conflict with files like '/sw/bin/GMXRC' that are essentially the same for both gromacs-simple or gromacs-double. Fair enough. How about listing gromacs-single and gromacs-double in the other's Conflicts and Replaces fink fields? http://www.finkproject.org/doc/packaging/reference.php?phpLang=en#fields That might just work and have no problems. Also, I suggest making a bugzilla with your fink scripts attached when you have them working, since they may as well get put in the GROMACS admin subdirectory for future use. Mark -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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] mpi mdrun
Hi! Thanks for your reply. So I suppose I need to have a hostfile in my directory and call it during the mpirun command. I have one clarification, since I am using a quad core how am I to list the processors on the host file? would it need to open a file name \d hostfile and have a list for example like some thing below? processor1 processor 2 processor 3 processor 4 or is getting to the hostfile an automated process (i.e.,) results from executing a program? I just put a search for host file and saw a folder by that name in the directory below ~/software/open-mpi-1.2.8/orte/mca/rds/hostfile Thanks JJ On Wed, Jun 17, 2009 at 9:42 PM, Mark Abraham mark.abra...@anu.edu.auwrote: jayant james wrote: Hi! Oh!! I see that nnodes: 1. So does that mean that the job I gave is not running on four processors? If so how am I to solve this problem? You haven't configured your MPI system with a suitable hostfile/whatever for your machine, probably. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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] mpi mdrun
On Thu, 2009-06-18 at 10:03 -0700, jayant james wrote: Hi! Thanks for your reply. So I suppose I need to have a hostfile in my directory and call it during the mpirun command. I have one clarification, since I am using a quad core how am I to list the processors on the host file? would it need to open a file name \d hostfile and have a list for example like some thing below? If you're using openmpi on a quad core computer you just need to $ mpirun -np 4 mdrun_mpi (options) -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632 -- Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of Physics, University of Helsinki, Finland jussi.leht...@helsinki.fi -- ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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] mpi mdrun
jayant james wrote: Hi! Thanks for your reply. So I suppose I need to have a hostfile in my directory and call it during the mpirun command. I have one clarification, since I am using a quad core how am I to list the processors on the host file? would it need to open a file name \d hostfile and have a list for example like some thing below? processor1 processor 2 processor 3 processor 4 or is getting to the hostfile an automated process (i.e.,) results from executing a program? I just put a search for host file and saw a folder by that name in the directory below ~/software/open-mpi-1.2.8/orte/mca/rds/hostfile This is a GROMACS mailing list, not a how-to-configure-your-MPI list :-) Read its documentation! Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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: Re: protein in SDS/water
Anna Marabotti wrote: Dear Justin, AAARRRGGGHH! The last case indicated in the wiki section about 0 topology was MY case: probably I was using a .mdp file that was created with Windows. When I re-wrote my em.mdp file using vi, it worked!! I'm sorry for all this waste of time, but as I told some days ago, I've problems in seeing the contents of the GROMACS site (old and new), and I could access to this information only through the link you sent me... A little suggestion for developers: would it be possible to insert an error message more indicative for this problem? I don't pretend that computers do everything I need, but it would be nice that they could at least suggest me a solution in a less cryptic way when I have such a trivial problem, so I can avoid boring the developers themselves...;-) It's actually an extremely rare cause for the problem, and adding text about DOS line endings there would confuse people, I think. Future releases of GROMACS are supposed to have links to the Errors wiki page, and this kind of information belongs there. Preventing this problem is simple - even when working on a Windows machine, don't use its tools for editing files! Use Cygwin, or tunnel emacs out over X, or use emacs -nw, or vi. In extremis run everything through dos2unix. You were unlucky to have been compounding the problem with other mistakes, though :-) Mark Thank you to all for collaboration and best regards Anna Anna Marabotti wrote: Dear all, as requested, I'm copying here the SDS.itp file (it should be not too big): ; This file was generated by PRODRG version AA081006.0504 ; PRODRG written/copyrighted by Daan van Aalten ; and Alexander Schuettelkopf ; ; Questions/comments to d...@davapc1.bioch.dundee.ac.uk ; ; When using this software in a publication, cite: ; A. W. Schuettelkopf and D. M. F. van Aalten (2004). ; PRODRG - a tool for high-throughput crystallography ; of protein-ligand complexes. ; Acta Crystallogr. D60, 1355--1363. [ moleculetype ] ; Name nrexcl SDS 3 OK, as I thought, if you #include SDS.itp you should NOT specify a separate [moleculetype] directive in your system .top file. snip As I told sometimes ago, I obtained this file from PRODRG starting from a SDS.pdb file that I created using SDS coordinates found in another .pdb file (I simply copied and pasted the SDS coordinates in a new file and called it SDS.pdb). For my simulations, however, I used the SDS.gro file and SDS.itp file generated by PRODRG. I notice that the section [ moleculetype] is present in SDS.itp, but nothing changes if I erase the [ moleculetype ] section for SDS in my_prot.top: in all cases it doesn't work... I also copied and pasted the entire topology of SDS explicitly into my_prot.top instead of typing #include SDS.itp, and nothing changed again... Well, the .itp file itself seems to have been properly generated. Concerning the order of molecules in the last [ molecules ] section, I changed it several times, and nothing changed... I'm still with an unclarified question: why genbox did not create by itself all corrections necessary to the original .top file when I used the -ci -nmol options? I added the -p flag but it doesn't change the topology by itself (as it should do, in my opinion). It would be nice if the computers did everything for us, wouldn't it? :) Maybe one day. It looks like automated updates only work for addition of water. Perhaps this can be a future improvement to genbox. Have you read the error page for your problem: http://oldwiki.gromacs.org/index.php/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology There is a specific section on the case where grompp detects 0 coordinates in the .top that might be relevant. -Justin Thank you again Anna __ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science, CNR Via Roma 64 83100 Avellino (Italy) Phone: +39 0825 299651 Fax: +39 0825 781585 Skype: annam1972 E-mail: amarabo...@isa.cnr.it Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm If you think you are too small to make a difference, try sleeping with a mosquito ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting!
Re: [gmx-users] The Cut-off for coulombtype heat up the water system?
Dear Justin: Thanks for your response. The reason I am doing this is that I wanted to test what the different electrostatics treatments will affect my results. So the heating up is normal by using a plain cut-off and the results can not be trusted, right? On Wed, Jun 17, 2009 at 5:20 PM, Justin A. Lemkul jalem...@vt.edu wrote: Yanmei Song wrote: Dear Users: I was running a system by non-equilibrium MD using a plain Cut-off for the electrostatics: title = water cpp = /lib/cpp constraints = all_bonds integrator = md dt = 0.004 ; ps ! nsteps = 50 ; total 8ns. nstcomm = 1 nstxout = 5 nstvout = 5 nstfout = 0 nstlog = 5000 nstenergy = 5000 nstxtcout = 25000 nstlist = 10 ns_type = grid pbc = xyz coulombtype = Cut-off rlist = 0.8 rcoulomb= 0.9 rvdw= 0.8 fourierspacing = 0.12 ewald_rtol = 1e-5 ;nemd cos_acceleration= 0.005 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc_grps = SOL tau_t = 0.1 ref_t = 300 ; Energy monitoring energygrps = SOL ; Isotropic pressure coupling is now on Pcoupl = berendsen pcoupltype = isotropic ;pc-grps= SOL tau_p = 1.0 ref_p = 1.0 compressibility = 4.5e-5 ; Generate velocites is off at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 10 I can not figure out where I did wrong, the temperature of the system is 303.54 after 5ns run ( the temperature turns to 303 in 500ps). Thanks for the help in advance! Why are you using cutoff for coulombtype? It is the reason for the heating you are seeing: http://oldwww.gromacs.org/pipermail/gmx-users/2009-February/039505.html -Justin -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 Ph.D. Candidate 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://lists.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 -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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] The Cut-off for coulombtype heat up the water system?
Yanmei Song wrote: Dear Justin: Thanks for your response. The reason I am doing this is that I wanted to test what the different electrostatics treatments will affect my results. So the heating up is normal by using a plain cut-off and the results can not be trusted, right? On Wed, Jun 17, 2009 at 5:20 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: That is correct. Check J. Chem. Theor. Comp. 2 (2006) p. 1-11. Yanmei Song wrote: Dear Users: I was running a system by non-equilibrium MD using a plain Cut-off for the electrostatics: title = water cpp = /lib/cpp constraints = all_bonds integrator = md dt = 0.004 ; ps ! nsteps = 50 ; total 8ns. nstcomm = 1 nstxout = 5 nstvout = 5 nstfout = 0 nstlog = 5000 nstenergy = 5000 nstxtcout = 25000 nstlist = 10 ns_type = grid pbc = xyz coulombtype = Cut-off rlist = 0.8 rcoulomb= 0.9 rvdw= 0.8 fourierspacing = 0.12 ewald_rtol = 1e-5 ;nemd cos_acceleration= 0.005 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc_grps = SOL tau_t = 0.1 ref_t = 300 ; Energy monitoring energygrps = SOL ; Isotropic pressure coupling is now on Pcoupl = berendsen pcoupltype = isotropic ;pc-grps= SOL tau_p = 1.0 ref_p = 1.0 compressibility = 4.5e-5 ; Generate velocites is off at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 10 I can not figure out where I did wrong, the temperature of the system is 303.54 after 5ns run ( the temperature turns to 303 in 500ps). Thanks for the help in advance! Why are you using cutoff for coulombtype? It is the reason for the heating you are seeing: http://oldwww.gromacs.org/pipermail/gmx-users/2009-February/039505.html -Justin -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,
Re: [gmx-users] The Cut-off for coulombtype heat up the water system?
Yanmei Song wrote: Dear Justin: Thanks for your response. The reason I am doing this is that I wanted to test what the different electrostatics treatments will affect my results. So the heating up is normal by using a plain cut-off and the results can not be trusted, right? That is one of the known problems with using cut-off, yes. -Justin On Wed, Jun 17, 2009 at 5:20 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Yanmei Song wrote: Dear Users: I was running a system by non-equilibrium MD using a plain Cut-off for the electrostatics: title = water cpp = /lib/cpp constraints = all_bonds integrator = md dt = 0.004 ; ps ! nsteps = 50 ; total 8ns. nstcomm = 1 nstxout = 5 nstvout = 5 nstfout = 0 nstlog = 5000 nstenergy = 5000 nstxtcout = 25000 nstlist = 10 ns_type = grid pbc = xyz coulombtype = Cut-off rlist = 0.8 rcoulomb= 0.9 rvdw= 0.8 fourierspacing = 0.12 ewald_rtol = 1e-5 ;nemd cos_acceleration= 0.005 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc_grps = SOL tau_t = 0.1 ref_t = 300 ; Energy monitoring energygrps = SOL ; Isotropic pressure coupling is now on Pcoupl = berendsen pcoupltype = isotropic ;pc-grps= SOL tau_p = 1.0 ref_p = 1.0 compressibility = 4.5e-5 ; Generate velocites is off at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 10 I can not figure out where I did wrong, the temperature of the system is 303.54 after 5ns run ( the temperature turns to 303 in 500ps). Thanks for the help in advance! Why are you using cutoff for coulombtype? It is the reason for the heating you are seeing: http://oldwww.gromacs.org/pipermail/gmx-users/2009-February/039505.html -Justin -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University -- Justin A. Lemkul Ph.D. Candidate 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://lists.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
Re: [gmx-users] The Cut-off for coulombtype heat up the water system?
Dear Justin: Thank you so much for your answer. That helps a lot! On Thu, Jun 18, 2009 at 10:35 AM, Justin A. Lemkul jalem...@vt.edu wrote: Yanmei Song wrote: Dear Justin: Thanks for your response. The reason I am doing this is that I wanted to test what the different electrostatics treatments will affect my results. So the heating up is normal by using a plain cut-off and the results can not be trusted, right? That is one of the known problems with using cut-off, yes. -Justin On Wed, Jun 17, 2009 at 5:20 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Yanmei Song wrote: Dear Users: I was running a system by non-equilibrium MD using a plain Cut-off for the electrostatics: title = water cpp = /lib/cpp constraints = all_bonds integrator = md dt = 0.004 ; ps ! nsteps = 50 ; total 8ns. nstcomm = 1 nstxout = 5 nstvout = 5 nstfout = 0 nstlog = 5000 nstenergy = 5000 nstxtcout = 25000 nstlist = 10 ns_type = grid pbc = xyz coulombtype = Cut-off rlist = 0.8 rcoulomb= 0.9 rvdw= 0.8 fourierspacing = 0.12 ewald_rtol = 1e-5 ;nemd cos_acceleration= 0.005 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc_grps = SOL tau_t = 0.1 ref_t = 300 ; Energy monitoring energygrps = SOL ; Isotropic pressure coupling is now on Pcoupl = berendsen pcoupltype = isotropic ;pc-grps= SOL tau_p = 1.0 ref_p = 1.0 compressibility = 4.5e-5 ; Generate velocites is off at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 10 I can not figure out where I did wrong, the temperature of the system is 303.54 after 5ns run ( the temperature turns to 303 in 500ps). Thanks for the help in advance! Why are you using cutoff for coulombtype? It is the reason for the heating you are seeing: http://oldwww.gromacs.org/pipermail/gmx-users/2009-February/039505.html -Justin --Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University -- Justin A. Lemkul Ph.D. Candidate 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://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post
[gmx-users] g_order and the tpr file
Dear GROMACS users, I've simulated a membrane system with AMBER 9.0, and now I'm trying to calculate order parameters for the carbon atoms in the fatty acid tails with the help of g_order. I've converted my AMBER trajectory to gromacs xtc and gro files. How can I obtain the tpr file needed as input for g_order? Thanks in advance. Best regards, Åge A. Skjevik, University of Bergen, Norway ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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] g_order and the tpr file
age.skje...@biomed.uib.no wrote: Dear GROMACS users, I've simulated a membrane system with AMBER 9.0, and now I'm trying to calculate order parameters for the carbon atoms in the fatty acid tails with the help of g_order. I've converted my AMBER trajectory to gromacs xtc and gro files. How can I obtain the tpr file needed as input for g_order? That will require the generation of a suitable topology; this may or may not involve pdb2gmx, depending on if you have a protein present in your system. If you have a pure membrane, you will have to make the topology by hand to include the proper .itp files, if you have them. Chapter 5 of the manual is your friend here, as are the various tutorials that are available on the web. -Justin Thanks in advance. Best regards, Åge A. Skjevik, University of Bergen, Norway ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 thewww 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 Ph.D. Candidate 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://lists.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] Final Temp = 303 K ?
Hi I was running the MD simulation and you the Berendsen method. Here is my .mdp file. ; Temperature coupling Tcoupl = Berendsen tc-grps = Protein Non-Protein tau_t= 0.1 0.1 ref_t= 300 300 But the final Temp = 303 K No matter I extend the simulation time, the final Temp = 303 K and it can not reach the ref_t = 300 K Does it make sense? The simulation system is protein + ligand + counter ions. ligand is the 33-atom molecule. force field ffG45a3. Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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] mpi mdrun
Hi! After installing GMX without the mpi Igive the following commands make clean ./configure --enable-mpi --disable-nice --program-suffix=_mpi I am getting this problem when I give the --enable-mpi option checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/local/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking how to create a ustar tar archive... gnutar checking for cc... cc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of cc... gcc3 checking dependency style of cc... gcc3 checking for mpxlc... no checking for mpicc... mpicc checking whether the MPI cc command works... yes checking for catamount... no checking how to run the C preprocessor... mpicc -E checking whether mpicc accepts -O3... yes checking whether mpicc accepts -funroll-all-loops... yes checking whether mpicc accepts -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops... yes checking for grep that handles long lines and -e... /usr/local/bin/grep checking for egrep... /usr/local/bin/grep -E checking for ANSI C header files... no checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking whether byte ordering is bigendian... no checking for int... yes checking size of int... configure: error: cannot compute sizeof (int) See `config.log' for more details. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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] Final Temp = 303 K ?
Chih-Ying Lin wrote: Hi I was running the MD simulation and you the Berendsen method. Here is my .mdp file. ; Temperature coupling Tcoupl = Berendsen tc-grps = Protein Non-Protein tau_t= 0.1 0.1 ref_t= 300 300 But the final Temp = 303 K No matter I extend the simulation time, the final Temp = 303 K and it can not reach the ref_t = 300 K Does it make sense? If this is the entirety of your .mdp file, then all the other options are defaults, including coulombtype = cutoff, which, as was just discussed today, leads to heating of the system of the magnitude that you are seeing. -Justin The simulation system is protein + ligand + counter ions. ligand is the 33-atom molecule. force field ffG45a3. Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 Ph.D. Candidate 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://lists.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] g_energy
Hi I have read the manual , Appendix C. After the command g_energy = Energy Average RMSD Fluct. Drift Tot-Drift --- Potential -196428372.215340.8525.18038518.043 Kinetic En. 37754.5219.122219.116 0.0585484 5.8549 Total Energy-158674302.504261.9855.23893523.899 Temperature 301.8141.751691.75164 0.000468047 0.0468051 Pressure (bar) 346.087165.538165.471 0.16298416.2986 Heat Capacity Cv: 12.4724 J/mol K (factor = 3.36849e-05) What is the definition of RMSD, Fluct. Drift, Tot-Drift? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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] g_energy
Chih-Ying Lin wrote: Hi I have read the manual , Appendix C. After the command g_energy = Energy Average RMSD Fluct. Drift Tot-Drift --- Potential -196428372.215340.8525.18038518.043 Kinetic En. 37754.5219.122219.116 0.0585484 5.8549 Total Energy-158674302.504261.9855.23893523.899 Temperature 301.8141.751691.75164 0.000468047 0.0468051 Pressure (bar) 346.087165.538165.471 0.16298416.2986 Heat Capacity Cv: 12.4724 J/mol K (factor = 3.36849e-05) What is the definition of RMSD, Fluct. Drift, Tot-Drift? Quoted from the manual, section D.28: Average and RMSD are calculated with full precision from the simulation (see printed manual). Drift is calculated by performing a LSQ fit of the data to a straight line. Total drift is drift multiplied by total time. The term fluctuation gives the RMSD around the LSQ fit. -Justin Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 Ph.D. Candidate 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://lists.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] mpi mdrun
jayant james wrote: Hi! After installing GMX without the mpi Igive the following commands make clean ./configure --enable-mpi --disable-nice --program-suffix=_mpi I am getting this problem when I give the --enable-mpi option snip checking size of int... configure: error: cannot compute sizeof (int) See `config.log' for more details. Usually config.log has something useful. Also, use the search page to look for cannot compute sizeof (int) http://oldwww.gromacs.org/swish-e/search/search2.php or use Google. This error has come up before several times, and there are a few possible solutions. -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/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 Ph.D. Candidate 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://lists.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] more digits
Hi, all, I need more digits to input information. But the default format of pdb file for coordinate is %8.3f. Can I modify the pdbio.c file to achive this goal? Or is there any other direct ways to input more digits coordinate information in Gromacs? Thanks in advance. Shuangxing Dai___ gmx-users mailing listgmx-users@gromacs.org http://lists.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] Final Temp = 303 K ?
Hi Here is my whole md.mdp. But the final Temp = 303 K No matter I extend the simulation time, the final Temp = 303 K and it can not reach the ref_t = 300 K Does it make sense? The simulation system is protein + ligand + counter ions. ligand is the 33-atom molecule. force field ffG45a3. Thank you Lin ; VARIOUS PREPROCESSING OPTIONS title= Lysozyme cpp = /lib/cpp ; RUN CONTROL PARAMETERS integrator = md tinit= 0 ; Starting time dt = 0.002 ; 2 femtosecond time step for integration nsteps = 25 ; 500 picoseconds total simulation time comm_mode= Linear ; Removing overall translations from the system nstcomm = 1 ; ... and doing so every step ; OUTPUT CONTROL OPTIONS nstxout = 1000 ; Writing full precision coordinates every nanosecond nstvout = 0 ; Writing velocities every nanosecond nstfout = 0 ; Not writing forces nstlog = 0 ; Writing to the log file every step nstenergy= 1000 ; Writing out energy information every step nstxtcout= 1000 ; Writing coordinates every step xtc_precision= 1000 ; Floating point number to integer scaling xtc-grps = System energygrps = Protein Non-Protein ; NEIGHBORSEARCHING PARAMETERS nstlist = 5 ns-type = Grid pbc = xyz rlist= 0.9 ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = Reaction-Field rcoulomb = 1.4 epsilon_rf = 78 epsilon_r= 1 vdw-type = Cut-off rvdw = 1.4 ; Temperature coupling Tcoupl = Berendsen tc-grps = Protein Non-Protein tau_t= 0.1 0.1 ref_t= 300 300 ; Pressure coupling Pcoupl = Berendsen Pcoupltype = Isotropic tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = no gen_temp = 300.0 gen_seed = 173529 ; OPTIONS FOR BONDS constraints = all-bonds constraint-algorithm = Lincs unconstrained-start = yes lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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] Final Temp = 303 K ?
Chih-Ying Lin wrote: Hi Here is my whole md.mdp. But the final Temp = 303 K No matter I extend the simulation time, the final Temp = 303 K and it can not reach the ref_t = 300 K Does it make sense? Yes, and I explained why. Specify options yourself, don't rely on defaults! -Justin The simulation system is protein + ligand + counter ions. ligand is the 33-atom molecule. force field ffG45a3. Thank you Lin ; VARIOUS PREPROCESSING OPTIONS title= Lysozyme cpp = /lib/cpp ; RUN CONTROL PARAMETERS integrator = md tinit= 0 ; Starting time dt = 0.002 ; 2 femtosecond time step for integration nsteps = 25 ; 500 picoseconds total simulation time comm_mode= Linear ; Removing overall translations from the system nstcomm = 1 ; ... and doing so every step ; OUTPUT CONTROL OPTIONS nstxout = 1000 ; Writing full precision coordinates every nanosecond nstvout = 0 ; Writing velocities every nanosecond nstfout = 0 ; Not writing forces nstlog = 0 ; Writing to the log file every step nstenergy= 1000 ; Writing out energy information every step nstxtcout= 1000 ; Writing coordinates every step xtc_precision= 1000 ; Floating point number to integer scaling xtc-grps = System energygrps = Protein Non-Protein ; NEIGHBORSEARCHING PARAMETERS nstlist = 5 ns-type = Grid pbc = xyz rlist= 0.9 ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = Reaction-Field rcoulomb = 1.4 epsilon_rf = 78 epsilon_r= 1 vdw-type = Cut-off rvdw = 1.4 ; Temperature coupling Tcoupl = Berendsen tc-grps = Protein Non-Protein tau_t= 0.1 0.1 ref_t= 300 300 ; Pressure coupling Pcoupl = Berendsen Pcoupltype = Isotropic tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = no gen_temp = 300.0 gen_seed = 173529 ; OPTIONS FOR BONDS constraints = all-bonds constraint-algorithm = Lincs unconstrained-start = yes lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 Ph.D. Candidate 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://lists.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] g_energy = both instantaneous and average
Hi I have read throught the Appendix C. The following is the .mdp file. Type the command g_energy -f abc-NVT500.edr -o abc-NVT500.xvg choose Pressure Based on my understanding of the Appendix C = g_energy will print out the instantaneous Pressure every 1000 step and save it into abc-NVT500.xvg. There are overall 250 instantaneous Pressure recorded. (overall steps = 25= 25/1000=250) And, the average pressure is shown on the screen. the average pressure = (sum of the 250 instantanous pressure) / 250 Also , the value of RMSD Fluct. Drift Tot-Drift are also calculated from the 250 instantaneous pressure? Is anything wrong above ? Thank you Lin ; RUN CONTROL PARAMETERS integrator = md tinit= 0 ; Starting time dt = 0.002 ; 2 femtosecond time step for integration nsteps = 25 ; 500 picoseconds total simulation time comm_mode= Linear ; Removing overall translations from the system nstcomm = 1 ; ... and doing so every step ; OUTPUT CONTROL OPTIONS nstxout = 1000 ; Writing full precision coordinates every nanosecond nstvout = 0 ; Writing velocities every nanosecond nstfout = 0 ; Not writing forces nstlog = 0 ; Writing to the log file every step nstenergy= 1000 ; Writing out energy information every step nstxtcout= 1000 ; Writing coordinates every step xtc_precision= 1000 ; Floating point number to integer scaling xtc-grps = System energygrps = Protein Non-Protein ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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] coulombtype = Reaction-Field = heat up the system
Hi I set up Tcoupl = Berendsen. ref_t = 300 K the final Temp = 303 K No matter I extend the simulation time, the final Temp = 303 K and it can not reach the ref_t = 300 K Does it make sense? the final Temp = 303 K and stable. Can I analyze the data from this simulation? The simulation system is protein + ligand + counter ions. ligand is the 33-atom molecule. force field ffG45a3. ; Temperature coupling Tcoupl = Berendsen tc-grps = Protein Non-Protein tau_t= 0.1 0.1 ref_t= 300 300 ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = Reaction-Field rcoulomb = 1.4 epsilon_rf = 78 epsilon_r= 1 vdw-type = Cut-off rvdw = 1.4 Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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] g_energy = RMSD = Standard Deviation?
HI After the command g_energy = the value of RMSD is shown, I can not find the math definition of RMSD from manual. Is the math definition of RMSD = Standard Deviation in Statistics? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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] g_energy = RMSD = Standard Deviation?
Chih-Ying Lin wrote: HI After the command g_energy = the value of RMSD is shown, I can not find the math definition of RMSD from manual. Is the math definition of RMSD = Standard Deviation in Statistics? First Google result for root mean square deviation: http://en.wikipedia.org/wiki/Root_mean_square_deviation -Justin Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 Ph.D. Candidate 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://lists.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] trjconv -pbc -center
Hi I have a protein+several ligand in the simulation box. After 5ns, the protein drift to the right edge of the box and the ligand drift to the left edge of the box. I supposed that the ligands dock/attach on the protein. I want to center the protein and see if the ligands dock/attach on the protein. The command trjconv is used. I have tried different option -pbc and -center. Even though I center the protein, but the ligand is still away from the protein. It seems not make sense. with option -pbc cluster the computer was running and never end. so, how can i use trjconv command to center protein and to see the ligand attaching on the protein? Thank you Lin Option -pbc sets the type of periodic boundary condition treatment: * mol puts the center of mass of molecules in the box. * res puts the center of mass of residues in the box. * atom puts all the atoms in the box. * nojump checks if atoms jump across the box and then puts them back. * cluster clusters all the atoms in the selected index such that they are all closest to the center of mass of the cluster which is iteratively updated. Note that this will only give meaningful results if you in fact have a cluster. Luckily that can be checked afterwards using a trajectory viewer. Note also that if your molecules are broken this will not work either. * whole only makes broken molecules whole. Option -center centers the system in the box. The user can select the group which is used to determine the geometrical center. The location of the center is set with -boxcenter: tric: half of the sum of the box vectors, rect: half of the box diagonal, zero: zero. Use option -pbc mol in addition to -center when you want all molecules in the box after the centering. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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] trjconv -pbc -center
Chih-Ying Lin wrote: Hi I have a protein+several ligand in the simulation box. After 5ns, the protein drift to the right edge of the box and the ligand drift to the left edge of the box. I supposed that the ligands dock/attach on the protein. I want to center the protein and see if the ligands dock/attach on the protein. The command trjconv is used. I have tried different option -pbc and -center. Even though I center the protein, but the ligand is still away from the protein. It seems not make sense. with option -pbc cluster the computer was running and never end. so, how can i use trjconv command to center protein and to see the ligand attaching on the protein? Well, does the association you expect actually occur? It seems to me that if you center the protein in the box, and the ligands do not associate, then you can't force it to happen with trjconv. -Justin Thank you Lin Option -pbc sets the type of periodic boundary condition treatment: * mol puts the center of mass of molecules in the box. * res puts the center of mass of residues in the box. * atom puts all the atoms in the box. * nojump checks if atoms jump across the box and then puts them back. * cluster clusters all the atoms in the selected index such that they are all closest to the center of mass of the cluster which is iteratively updated. Note that this will only give meaningful results if you in fact have a cluster. Luckily that can be checked afterwards using a trajectory viewer. Note also that if your molecules are broken this will not work either. * whole only makes broken molecules whole. Option -center centers the system in the box. The user can select the group which is used to determine the geometrical center. The location of the center is set with -boxcenter: tric: half of the sum of the box vectors, rect: half of the box diagonal, zero: zero. Use option -pbc mol in addition to -center when you want all molecules in the box after the centering. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 Ph.D. Candidate 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://lists.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] trjconv -pbc -center
Hi, I answered a very similar question last week but it appears that gmx-users is not online by now: try to use this script. And be aware to re-wrap code lines as my mail splits it. Please comment if it actually works for you. Best. Daniel *** Usage notes: - Just copy/and/paste the code on a textfile and make it executable with chmod 700, !!!take care of broken/split lines by email/post artifacts!!! - I use mdrun with -deffnm for the outputs; therefore this script is made to work when all the output files have the same name. - Do not forget to replace the *** field for the GROBIN variable on the code. - On the code 0 and 1 are the index groups for system and protein respectively. However, for any complex the trick to have a nice representation is to center the system only on one of the proteins, for example, for me: echo -e del 1-14\n r 1-238\n r 1-239\n q\n | $GROBIN/make_ndx -f pre1_$NAME.gro -o pre1_$NAME.ndx makes the trick, since it erases all the groups from my index, except system, and then creates the group 1 only for one of my proteins (residues 1-238) and additionally the group 2 used to output my complex in the absence of waters (residues 1-239). To run use: ./scriptname PATH-TO-DINAMIC/MDOUTPUT-NAME-WITHOUT-DOT-OR-EXTENSIONS OUTPUT-NAME Example: ./filterscript /home/dsilva/dynamic/production/md filteredmd *** CODE: *** #!/bin/bash #Daniel Silva, script to filter trajectories PATH=$1 NAME=$2 GROBIN=/usr/local/gromacs/bin #MODIFY THIS LINE TO POINT TO YOUR GROMACS BINARIES PATH /bin/cp $PATH.tpr ./$NAME-filtered.tpr echo -e 0\n| $GROBIN/trjconv -f $PATH -s $NAME-filtered.tpr -pbc whole -o pre1_$NAME echo -e 0\n| $GROBIN/trjconv -f $PATH -s $NAME-filtered.tpr -pbc whole -o pre1_$NAME.gro -e 0 ### Modify the next line if you have any kind of complex, in order to make group 1 pointing only to one of proteins in the complex. (Example: echo -e del 1-14\n r 1-238\n r 1-239\n q\n | $GROBIN/make_ndx -f pre1_$NAME.gro -o pre1_$NAME.ndx) echo -e q\n | $GROBIN/make_ndx -f pre1_$NAME.gro -o pre1_$NAME.ndx echo -e 1\n0\n | $GROBIN/trjconv -f pre1_$NAME -s $NAME-filtered.tpr -pbc atom -ur compact -center -n pre1_$NAME.ndx -o pre2_$NAME echo -e 1\n0\n | $GROBIN/trjconv -f pre2_$NAME -s $NAME-filtered.tpr -fit rot+trans -n pre1_$NAME.ndx -o $NAME-filtered echo -e 0\n| $GROBIN/trjconv -f $NAME-filtered -s $NAME-filtered.tpr -e 0 -n pre1_$NAME.ndx -o $NAME-filtered.gro ### If you also want to output trajectories without waters uncomment the next two lines. Also, if you have complexes take care of the group that you are sending to the output (Example, for me it needs to be group 2 not 1; echo -e 1\n2\n and echo -e 2\n, respectively for the next two lines) # echo -e 1\n1\n | $GROBIN/trjconv -f pre2_$NAME -s $NAME-filtered.tpr -fit rot+trans -n pre1_$NAME.ndx -o $NAME-filtered-NoHOH # echo -e 1\n| $GROBIN/trjconv -f $NAME-filtered -s $NAME-filtered.tpr -e 0 -n pre1_$NAME.ndx -o $NAME-filtered-NoHOH.gro /bin/rm ./pre*_$NAME.* ###CODE END 2009/6/18 Justin A. Lemkul jalem...@vt.edu: Chih-Ying Lin wrote: Hi I have a protein+several ligand in the simulation box. After 5ns, the protein drift to the right edge of the box and the ligand drift to the left edge of the box. I supposed that the ligands dock/attach on the protein. I want to center the protein and see if the ligands dock/attach on the protein. The command trjconv is used. I have tried different option -pbc and -center. Even though I center the protein, but the ligand is still away from the protein. It seems not make sense. with option -pbc cluster the computer was running and never end. so, how can i use trjconv command to center protein and to see the ligand attaching on the protein? Well, does the association you expect actually occur? It seems to me that if you center the protein in the box, and the ligands do not associate, then you can't force it to happen with trjconv. -Justin Thank you Lin Option -pbc sets the type of periodic boundary condition treatment: * mol puts the center of mass of molecules in the box. * res puts the center of mass of residues in the box. * atom puts all the atoms in the box. * nojump checks if atoms jump across the box and then puts them back. * cluster clusters all the atoms in the selected index such that they are all closest to the center of mass of the cluster which is iteratively updated. Note that this will only give meaningful results if you in fact have a cluster. Luckily that can be checked afterwards using a trajectory viewer. Note also that if your molecules are broken this will not work either. * whole only makes broken molecules whole. Option -center centers the system in the box. The user can select the group which is used to determine the geometrical center.
[gmx-users] trjconv -pbc atom -center rect
Hi I have a protein+several ligand in the simulation box. After 5ns, the protein drift to the right edge of the box and the ligand drift to the left edge of the box. with this command = trjconv -pbc atom -center rect the most part of the protein is still in the right edge of the box the small part of the protein is shifted in the left edge of the box and i can clearly see that the ligand attach onto the protein. but, the protein is NOT in the center of the box ??? so, how can i use trjconv command to center protein and to see the ligand attaching on the protein? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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] more digits
Shuangxing Dai wrote: Hi, all, I need more digits to input information. But the default format of pdb file for coordinate is %8.3f. Can I modify the pdbio.c file to achive this goal? Or is there any other direct ways to input more digits coordinate information in Gromacs? Use a .g96 file for input. Virtually all GROMACS tools accept many possible formats when a coordinate file is required. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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] The Cut-off for coulombtype heat up the water system?
Hi People conclude that the heating up is normal by using a plain cut-off. So, how to fix the problem? 1. From Berk = use multiple groups. = how ??? = I have been thinking that it is better to group the molecule = such as: protein , non-protein 2. change the coulombtype without the coulomb cut-off rcoulomb ? = such as PME, PPPM ? = what's the suggestion about this? 3. Normally, how do people fix this problem? Thank you Lin http://oldwww.gromacs.org/pipermail/gmx-users/2009-February/039505.html No, this problem is not due to the Berendsen thermostat. The integrations errors in the electrostatics have much more effect on the water than on the protein, because the water has higher charges and is far more mobile. No thermostat can correct for these errors, unless you use multiple groups. In addition the Berendsen thermostat will move energy from fast to slow motions. This effects becomes much stronger when the thermostat has to do a lot of scaling due to the heat generated by cut-off's. Inaccurate constraining will remove heat from the system, but this effect is orders of magnitude smaller than the Coulomb cut-off heating. Berk Dear Justin: Thanks for your response. The reason I am doing this is that I wanted to test what the different electrostatics treatments will affect my results. So the heating up is normal by using a plain cut-off and the results can not be trusted, right? On Wed, Jun 17, 2009 at 5:20 PM, Justin A. Lemkul jalem...@vt.edu wrote: Yanmei Song wrote: Dear Users: I was running a system by non-equilibrium MD using a plain Cut-off for the electrostatics: title = water cpp = /lib/cpp constraints = all_bonds integrator = md dt = 0.004 ; ps ! nsteps = 50 ; total 8ns. nstcomm = 1 nstxout = 5 nstvout = 5 nstfout = 0 nstlog = 5000 nstenergy = 5000 nstxtcout = 25000 nstlist = 10 ns_type = grid pbc = xyz coulombtype = Cut-off rlist = 0.8 rcoulomb= 0.9 rvdw= 0.8 fourierspacing = 0.12 ewald_rtol = 1e-5 ;nemd cos_acceleration= 0.005 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc_grps = SOL tau_t = 0.1 ref_t = 300 ; Energy monitoring energygrps = SOL ; Isotropic pressure coupling is now on Pcoupl = berendsen pcoupltype = isotropic ;pc-grps= SOL tau_p = 1.0 ref_p = 1.0 compressibility = 4.5e-5 ; Generate velocites is off at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 10 I can not figure out where I did wrong, the temperature of the system is 303.54 after 5ns run ( the temperature turns to 303 in 500ps). Thanks for the help in advance! Why are you using cutoff for coulombtype? It is the reason for the heating you are seeing: http://oldwww.gromacs.org/pipermail/gmx-users/2009-February/039505.html -Justin -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 Ph.D. Candidate 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://lists.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 -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20090618/08853d93/attachment.html ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users
[gmx-users] Re: x2top (David van der Spoel)
mr spoel, i have the .top for my system using PRODRG, but when I try run this .top with the next command editconf -bt cubic –f DRGFIN.gro –o poli12.pdb –d 0.9, the program gives me the next error message __- Program editconf, VERSION 3.3.3 Source code file: ../../../../src/gmxlib/statutil.c, line: 797 Invalid command line argument: –f __ Why??, what is the problem?, please help me I add the .top file generated by PRODRG PRODRG COORDS 143 1DRG CAG 1 -0.354 -0.675 -1.939 1DRG CAH 2 -0.265 -0.690 -2.047 1DRG CAI 3 -0.164 -0.593 -2.067 1DRG CAJ 4 -0.151 -0.482 -1.981 1DRG CAK 5 -0.242 -0.469 -1.874 1DRG CAF 6 -0.345 -0.564 -1.850 1DRG CAD 7 -0.447 -0.550 -1.732 1DRG CAC 8 -0.489 -0.686 -1.672 1DRG CAB 9 -0.608 -0.704 -1.602 1DRG CAA 10 -0.639 -0.841 -1.540 1DRG CAE 11 -0.398 -0.471 -1.610 1DRG CAL 12 -0.372 -0.321 -1.624 1DRG CAM 13 -0.264 -0.302 -1.540 1DRG CAN 14 -0.239 -0.181 -1.479 1DRG CAO 15 -0.145 -0.173 -1.357 1DRG CAQ 16 -0.131 -0.028 -1.303 1DRG CAR 17 -0.028 -0.002 -1.210 1DRG CAS 18 -0.016 0.126 -1.151 1DRG CAT 19 -0.109 0.227 -1.186 1DRG CAU 20 -0.212 0.203 -1.279 1DRG CAV 21 -0.223 0.075 -1.337 1DRG CAP 22 -0.200 -0.267 -1.245 1DRG CAW 23 -0.328 -0.212 -1.181 1DRG CAX 24 -0.420 -0.298 -1.124 1DRG CAY 25 -0.489 -0.238 -1.019 1DRG CAZ 26 -0.618 -0.281 -0.945 1DRG CBB 27 -0.722 -0.164 -0.954 1DRG CBC 28 -0.717 -0.061 -1.053 1DRG CBD 29 -0.810 0.045 -1.055 1DRG CBE 30 -0.911 0.049 -0.955 1DRG CBF 31 -0.919 -0.051 -0.856 1DRG CBG 32 -0.825 -0.156 -0.856 1DRG CBA 33 -0.673 -0.419 -0.989 1DRG CBH 34 -0.778 -0.476 -0.892 1DRG CBI 35 -0.850 -0.593 -0.923 1DRG CBJ 36 -0.954 -0.622 -1.013 1DRG CBK 37 -1.023 -0.547 -1.130 1DRG CBM 38 -1.175 -0.524 -1.112 1DRG CBN 39 -1.261 -0.595 -1.200 1DRG CBO 40 -1.400 -0.572 -1.197 1DRG CBP 41 -1.453 -0.479 -1.106 1DRG CBQ 42 -1.369 -0.408 -1.017 1DRG CBR 43 -1.230 -0.431 -1.020 1DRG CBL 44 -0.959 -0.413 -1.170 1DRG CBS 45 -0.997 -0.363 -1.309 1DRG CBT 46 -1.054 -0.238 -1.293 1DRG CBU 47 -1.025 -0.142 -1.389 1DRG CBV 48 -1.078 0.003 -1.397 1DRG CBX 49 -1.127 0.030 -1.544 1DRG CBY 50 -1.063 -0.033 -1.655 1DRG CBZ 51 -1.103 -0.008 -1.787 1DRG CCA 52 -1.210 0.082 -1.810 1DRG CCB 53 -1.276 0.146 -1.703 1DRG CCC 54 -1.233 0.120 -1.571 1DRG CBW 55 -1.184 0.035 -1.288 1DRG CCD 56 -1.175 0.182 -1.247 1DRG CCE 57 -1.260 0.231 -1.147 1DRG CCF 58 -1.354 0.329 -1.182 1DRG CCG 59 -1.414 0.426 -1.078 1DRG CCI 60 -1.428 0.565 -1.147 1DRG CCJ 61 -1.552 0.620 -1.189 1DRG CCK 62 -1.558 0.747 -1.249 1DRG CCL 63 -1.439 0.819 -1.269 1DRG CCM 64 -1.314 0.767 -1.229 1DRG CCN 65 -1.309 0.640 -1.168 1DRG CCH 66 -1.546 0.378 -1.012 1DRG CCO 67 -1.579 0.462 -0.887 1DRG CCP 68 -1.713 0.465 -0.851 1DRG CCQ 69 -1.792 0.579 -0.875 1DRG CCR 70 -1.938 0.595 -0.827 1DRG CCT 71 -2.006 0.728 -0.871 1DRG CCU 72 -1.952 0.816 -0.968 1DRG CCV 73 -2.020 0.935 -1.003 1DRG CCW 74 -2.142 0.966 -0.940 1DRG CCX 75 -2.198 0.880 -0.842 1DRG CCY 76 -2.129 0.762 -0.808 1DRG CCS 77 -2.031 0.475 -0.860 1DRG CCZ 78 -2.050 0.432 -1.006 1DRG CDA 79 -2.152 0.492 -1.080 1DRG CDB 80 -2.268 0.421 -1.112 1DRG CDC 81 -2.372 0.462 -1.220 1DRG CDE 82 -2.519 0.462 -1.170 1DRG CDF 83 -2.618 0.412 -1.259 1DRG CDG 84 -2.755 0.415 -1.224 1DRG CDH 85 -2.792 0.469 -1.099 1DRG CDI 86 -2.695 0.519 -1.009 1DRG CDJ 87 -2.558 0.515 -1.045 1DRG CDD 88 -2.346 0.598 -1.286 1DRG CDK 89 -2.390 0.600 -1.433 1DRG CDL 90 -2.425 0.728 -1.473 1DRG CDM 91 -2.559 0.765 -1.486 1DRG CDN 92 -2.599 0.910 -1.515 1DRG CDP 93 -2.751 0.928 -1.538 1DRG CDQ 94 -2.793 1.025 -1.633 1DRG CDR 95 -2.931 1.049 -1.654 1DRG CDS 96 -3.026 0.975 -1.581 1DRG CDT 97 -2.986 0.878 -1.486 1DRG CDU 98 -2.849 0.855 -1.465 1DRG CDO 99 -2.559 0.994 -1.393
Re: [gmx-users] The Cut-off for coulombtype heat up the water system?
Chih-Ying Lin wrote: Hi People conclude that the heating up is normal by using a plain cut-off. So, how to fix the problem? 0. Do more background reading. :-) 1. From Berk = use multiple groups. = how ??? = I have been thinking that it is better to group the molecule = such as: protein , non-protein 2. change the coulombtype without the coulomb cut-off rcoulomb ? = such as PME, PPPM ? = what's the suggestion about this? 3. Normally, how do people fix this problem? These days, PME will tend to be the easiest to defend in a publication. You will have lower heating problems with various modified forms of cut-offs and/or longer cut-offs, but then you have the problem of justifying the use of the force field, which was probably parametrized for some other coulomb scheme. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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] g_energy = RMSD vs Fluctuation
Hi The definition of the Fluctuation is shown on the Manual, Appendix C, eqn (C.1) The definition of the RMSD is as shown from the link. http://en.wikipedia.org/wiki/Root_mean_square_deviation The definition of the estimators is unclear though. So, what is the definition of the estimators? The following is showing one set of the results from g_energy. = The RMSD of Temp, Pressure, Kinetic En. correspond to their Fluct. = The RMSD of Potential and Total Energy do NOT correspond to their Fluct. I think that the definition of the estimators of Temp, Pressure, Kinetic En. are their average values, am I right? How about the definition of the estimators of Potential and Total Energy ? Thank you Lin Energy Average RMSD Fluct. Drift Tot-Drift --- Potential -196428372.215340.8525.18038518.043 Kinetic En. 37754.5219.122219.116 0.0585484 5.8549 Total Energy-158674302.504261.9855.23893523.899 Temperature 301.8141.751691.75164 0.000468047 0.0468051 Pressure (bar) 346.087165.538165.471 0.16298416.2986 Heat Capacity Cv: 12.4724 J/mol K (factor = 3.36849e-05) ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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
