[gmx-users] (no subject)
Dear All I am learning molecular simulation using Gromacs. when I complete my simulation, How can I check that my simulation run was o.k. and the output so obtained can be trusted. Is there any easy calculation, which could be performed. Thanks in advance. msnayeem -- 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 with tabulated potentials for 3 different atoms
Hi, I don't want to get into discussions on drugs and I don't know if you already switched package, but I'l post my answer anyhow. The energy groups in each pair on your energygrp_table line should be separated by a space. The table files should contain all columns, unused columns are allowed to contain zero's, since they are simply ignored. PS: Please don't mail me directly with questions on Gromacs, apart from the good reasons already given on the list, this is a strong incentive for me not to answer your mail. Berk From: mrvartore...@gmail.com Date: Mon, 19 Apr 2010 10:05:59 -0300 To: gmx-users@gromacs.org Subject: [gmx-users] Problem with tabulated potentials for 3 different atoms I'm trying to use tabulated potentials for a very simple system: a polymer chain with only 3 kind of atoms: A, B and C, all of it with zero charge. A--(B)n--C The only interactions that accounts are AB, AC, BB and CC, so in my mdp file I have writen: coulombtype = user vdw-type= user energygrps = A B C energygrp_table = AB AC BB BC Also, I'm using tabulated bonded potentials for bonds and angles. The main questions are how to tell to mdrun that he must read my table files and can I be sure that the reading is OK? For the bonding part I have the following table files: table_b1.xvg table_a1.xvg table_a2.xvg table_a3.xvg And in the mdrun commandline I'm using the option -tableb table. But how to handle the non bonding table files? table_A_B.xvg table_A_C.xvg table_B_B.xvg table_B_C.xvg Must I write energygrps = A B C energygrp_table = AC BB BC in the mdp file and use the tables table.xvg table_A_C.xvg table_B_B.xvg table_B_C.xvg with the command line for mdrun saying -table table.xvg? Another thing, because the tables doesn't have to contain only zero columns... Can I put anything on the f and f' columns (because the charge of my atoms is zero)? Can I put (for example) 0.5 in the g and g' columns and my potential (and the force) minus 0.5 in columns h and h'? I'm using the 4.0.7 version. Again as an abstract: System: 1 chain A--(B)n--C Bonds: A-B = B-B = B-C -- only one table: table_b1.xvg Angles: A-B-B, B-B-B, B-B-C -- 3 tables: table_a1.xvg, table_a2.xvg, table_a3.xvg Charges: none VDW interactions: A-B, A-C, B-B, B-C -- 4 tables table_A_B.xvg, table_A_C.xvg, table_B_B.xvg, table_B_C.xvg *.mdp lines: coulombtype = user vdw-type= user energygrps = A B C energygrp_table = ? run commandline: mdrun -s -c -e -x -g -table ? -tableb ? Any help will be appreciated. Thank you. Martin R. Vartorelli -- 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 _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/-- 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] (no subject)
On 20/04/2010 4:39 PM, shahid nayeem wrote: Dear All I am learning molecular simulation using Gromacs. when I complete my simulation, How can I check that my simulation run was o.k. and the output so obtained can be trusted. Is there any easy calculation, which could be performed. No. These tend to be how long should a piece of string be? questions, unfortunately. The best thing to do is to have the simulation objective in mind before you touch a computer. Now you can hopefully make decisions for the right reasons, and can grapple sensibly with assessing whether you've achieved that objective. 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] CG-MD simulation of protein, always crash with protein
The representation of extended regions (b-sheets) is more stable using elastic bonds than a dihedral angle because the flexibility of the force field makes possible the occurrence of situations where the two bonds get aligned and therefore the plan used to defined the dihedral can not be calculated and the program crashes. But I am not sure that was your problem. You mentioned that the program was stopping due to too many lincs warnings. Cycles (trp, phe, his) seemed to be the cause. Do you still have lincs warnings, may be less? The other thing is that is your protein deforms as much as before, there is another way to simulate you protein with Martini: http://md.chem.rug.nl/cgmartini/index.php/tools/118-end XAvier. On Apr 20, 2010, at 7:16 AM, Trang wrote: Elastic bonds did help the system survive. I'm not really understand why do we need more robust bonds in this system. Does it mean that there exists large forces that cause my system to blow up? Would you mind giving an explanation? Thanks indeed for your taking time to help. Trang On Mon, Apr 19, 2010 at 4:26 PM, Martti Louhivuori m.j.louhivu...@rug.nl wrote: On 19 Apr 2010, at 06:49, Trang wrote: The protein topo is too large, so I put it here. http://pastie.org/926617 The protein topology is fine, but you could try also with elastic bonds instead of dihedrals in the extended regions (--elastic option). Elastic bonds are more robust than dihedrals, especially if running with a larger timestep (30fs). Here is the system topology. #include ../martini_v2.1.itp #include ../martini_v2.1_aminoacids.itp The last line is unnecessary. Use it only when simulating single aminoacids instead of a polypeptide. Minimized structure showed no close contact (with distance cutoff 1.6, even to 1.9). Production run stopped at That's only 0.16-0.19nm, so overlap is still possible. step 175552 (5266.56 ps) with Segmentation fault, preceeded with a lot of Lincs warnings (I set ring_bonds = constraints). This is the mdp file, this file goes along with the system in vaccuum that crashed. I'm not sure if What's different this time around? Last time you said you couldn't run it even in vacuum. Sounds like you are just hitting statistical limits with your combination of (extended) dihedrals + 30fs timestep. Use a smaller timestep (20fs for example) or switch to local elastic bonds for the beta-strands... and solvate the system (without overlap) so the simulation makes some sense! -martti- -- Post-doctoral research fellow Moleculaire Dynamica University of Groningen Nijenborgh 4, 9747AG Groningen, the Netherlands tel. +(31) 50 363 4339 | fax. +(31) 50 363 4398 -- 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 -- 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! 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] about H-Bonds g_hbond
Hi, Please submit a bugzilla, assign it to me, and I'll try to fix it along with heaps of other things. Erik Marklund Justin A. Lemkul skrev: babu gokul wrote: Hi all I am getting an error in g_hbond such as Program g_hbond_d, VERSION 4.0.7 Source code file: gmx_hbond.c, line: 565 Fatal error: Error in func_type Position Rest. Could anyone tell me how to solve this problem. thanks in advance If you have position restraints defined, you can't run g_hbond for some reason. The work-around is to re-generate a .tpr file that does not use position restraints and do the analysis. -Justin E R Azhagiya singam Send free SMS to your Friends on Mobile from your Yahoo! Messenger. Download Now! http://messenger.yahoo.com/download.php -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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] (no subject)
Mark Abraham skrev: On 20/04/2010 4:39 PM, shahid nayeem wrote: Dear All I am learning molecular simulation using Gromacs. when I complete my simulation, How can I check that my simulation run was o.k. and the output so obtained can be trusted. Is there any easy calculation, which could be performed. No. These tend to be how long should a piece of string be? questions, unfortunately. The best thing to do is to have the simulation objective in mind before you touch a computer. Now you can hopefully make decisions for the right reasons, and can grapple sensibly with assessing whether you've achieved that objective. Mark True. There are certain things that are fairly general though. For instance, see if the conseved thrermodynamic quantities for your simulated ensemble are converged. If not, the simulation may still be ok, but may not be long eniough. -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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] Force output
I think this one can help you: http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000306 You can download a code that gives you the forces from the following website: http://projects.eml.org/mbm/website/fda_gromacs.htm Ilona Quoting Avisek Das avi...@stanford.edu: Dear GROMACS developers and users, I have a question regarding GROMACS force output. I need the total force on each atom at every timestep in a constant temperature MD trajectory. I am using the Nose-Hoover thermostat for constant temperature simulations. I know that by using the 'nstfout' keyword in the .mdp file I can tell GROMACS to output forces in the trajectory (.trr) file. Now my question is what exactly is written in the output file as force when I use the above mentioned option. I understand that at first this question may seem a little strange and unnecessary, since everybody knows what a force is, but in the context of Nose-Hoover dynamics there is a slight chance of potential confusion as discussed below. The force information is very crucial for our subsequent analysis, that is why we wanted to make sure that we know exactly what is being printed when one uses the 'nstfout' keyword. Total force on a particle can be interpreted as either the negative gradient of the total potential energy with respect to the position of the atom in question OR the instantaneous rate of change of momentum of the atom. Now for normal Hamiltonian dynamics both of these definitions will give the same number but for the Nose-Hoover dynamics they will be different. Because in the Nose-Hoover equations the rate of change of momentum of an atom is a sum of two terms, first term is the negative gradient of total potential and the second term is momentum of the particle multiplied by a thermostat parameter. So, in Nose-Hoover equation instantaneous rate of change of momentum is NOT equal to the negative gradient of the potential with respect to the atom position. In the light of above discussion can anyone please tell me when GROMACS prints forces in the trajectory file during a Nose-Hoover dynamics, which quantity does it print? Is it the negative gradient of the total potential with respect to the atom position OR the total instantaneous rate of change of momentum which includes an extra term? Thanks a lot, Avisek -- 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! 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 with tabulated potentials for 3 different atoms
Berk: Thanks for the help, and thanks too to the other members of the list who helped me. My simulation is working now with some energy problems, but this is another problem not related to the software. The missing space characters were a typing mistake. About drugs and other subjets of your post, they are all out of my research interests. Maybe you wanted to say these to another user? Martin. -- 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 with tabulated potentials for 3 different atoms
From: mrvartore...@gmail.com Date: Tue, 20 Apr 2010 06:33:09 -0300 To: gmx-users@gromacs.org Subject: [gmx-users] Problem with tabulated potentials for 3 different atoms Berk: Thanks for the help, and thanks too to the other members of the list who helped me. My simulation is working now with some energy problems, but this is another problem not related to the software. The missing space characters were a typing mistake. About drugs and other subjets of your post, they are all out of my research interests. Maybe you wanted to say these to another user? This was intended as a subtle hint to list members in general to keep the discussions polite and constructive. Berk Martin. -- 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 _ New Windows 7: Find the right PC for you. Learn more. http://windows.microsoft.com/shop-- 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] about H-Bonds g_hbond
Erik Marklund wrote: Hi, Please submit a bugzilla, assign it to me, and I'll try to fix it along with heaps of other things. This bug has been outstanding for some time already: http://bugzilla.gromacs.org/show_bug.cgi?id=334 -Justin Erik Marklund Justin A. Lemkul skrev: babu gokul wrote: Hi all I am getting an error in g_hbond such as Program g_hbond_d, VERSION 4.0.7 Source code file: gmx_hbond.c, line: 565 Fatal error: Error in func_type Position Rest. Could anyone tell me how to solve this problem. thanks in advance If you have position restraints defined, you can't run g_hbond for some reason. The work-around is to re-generate a .tpr file that does not use position restraints and do the analysis. -Justin E R Azhagiya singam Send free SMS to your Friends on Mobile from your Yahoo! Messenger. Download Now! http://messenger.yahoo.com/download.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing 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] genbox
Hello, I want to use a file.pdb which has 8 chain of polypeptide, each chain contains 6 residues. I need to expand it to 12 chains of 6 rsidues so I need to add 4 chains or in the other word 24 residues. I think I have to use genbox, so I make another copy of file.pdb and rename it to insert.pdb and i used this command, but it doesn't work. genbox -cp file.pdb -ci insert.pdb -nmole 24 -o out.gro can anybody help me? Fahimeh _ Hotmail: Trusted email with powerful SPAM protection. https://signup.live.com/signup.aspx?id=60969-- 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] genbox
fahimeh bafti wrote: Hello, I want to use a file.pdb which has 8 chain of polypeptide, each chain contains 6 residues. I need to expand it to 12 chains of 6 rsidues so I need to add 4 chains or in the other word 24 residues. I think I have to use genbox, so I make another copy of file.pdb and rename it to insert.pdb and i used this command, but it doesn't work. genbox -cp file.pdb -ci insert.pdb -nmole 24 -o out.gro can anybody help me? The implication with genbox -ci -nmol is that the coordinate file passed to -ci contains one molecule, and an additional -nmol molecules are inserted. So if you already have 8, you need a coordinate file with one polypeptide and then: genbox -ci insert.pdb -nmol 4 Note in the documentation that -nmol refers to the number of molecules, not a number of residues, which I think is the root of your problem. -Justin Fahimeh Hotmail: Trusted email with powerful SPAM protection. Sign up now. https://signup.live.com/signup.aspx?id=60969 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing 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] Compiling Gromacs 4.0.7 on AIX 5.3
Hello again I followed your advices this time here's what I did : downloading gromacs 4.0.7 downloading fftw 2.1.5 initializing environment variables (modified to fit my configuration (pwr5) : export LDFLAGS='-L/usr/local/lib' export CPPFLAGS='-I/usr/local/include' export PATH=/usr/lpp/ppe.hpct/bin:/usr/vacpp/bin:.:/usr/bin:/etc:/usr/sbin:/usr/ucb:/usr/bin/X11:/sbin:/usr/java14/jre/bin:/usr/java14/bin:/usr/lpp/LoadL/full/bin:/usr/local/bin export F77=xlf_r export CC=xlc_r export CXX=xlc++_r export FFLAGS=-O5 -qarch=pwr5 -qtune=pwr5 export CFLAGS=-O5 -qarch=pwr5 -qtune=pwr5 export CXXFLAGS=-O5 -qarch=pwr5 -qtune=pwr5 for FFTW : ./configure --enable-threads --enable-float make make install (that's OK, installed in /usr/local/lib and /usr/local/include) for Gromacs : ./configure --with-fft=fftw2 (that's OK) make unfortunately, the result is : ... nb_kernel333.h, line 101.1: 1506-282 (S) The type of the parameters must be specified in a prototype. nb_kernel334.h, line 63.1: 1506-033 (S) Function F77_FUNC_ is not valid. Function cannot return a function. nb_kernel334.h, line 63.1: 1506-282 (S) The type of the parameters must be specified in a prototype. nb_kernel334.h, line 101.1: 1506-033 (S) Function F77_FUNC_ is not valid. Function cannot return a function. nb_kernel334.h, line 101.1: 1506-282 (S) The type of the parameters must be specified in a prototype. nb_kernel400.h, line 63.1: 1506-033 (S) Function F77_FUNC_ is not valid. Function cannot return a function. nb_kernel400.h, line 63.1: 1506-282 (S) The type of the parameters must be specified in a prototype. nb_kernel400.h, line 101.1: 1506-033 (S) Function F77_FUNC_ is not valid. Function cannot return a function. nb_kernel400.h, line 101.1: 1506-282 (S) The type of the parameters must be specified in a prototype. nb_kernel410.h, line 63.1: 1506-033 (S) Function F77_FUNC_ is not valid. Function cannot return a function. nb_kernel410.h, line 63.1: 1506-282 (S) The type of the parameters must be specified in a prototype. nb_kernel410.h, line 101.1: 1506-033 (S) Function F77_FUNC_ is not valid. Function cannot return a function. nb_kernel410.h, line 101.1: 1506-282 (S) The type of the parameters must be specified in a prototype. nb_kernel420.h, line 63.1: 1506-033 (S) Function F77_FUNC_ is not valid. Function cannot return a function. nb_kernel420.h, line 63.1: 1506-282 (S) The type of the parameters must be specified in a prototype. nb_kernel420.h, line 63.1: 1506-343 (S) Redeclaration of F77_FUNC_ differs from previous declaration on line 101 of nb_kernel410.h. nb_kernel420.h, line 63.1: 1506-050 (I) Return type void(int*,int*,int*,int*,int*,float*,float*,int*,float*,float*,float*,float*,float*,float*,float*,int*,int*,float*,float*,float*,float*,float*,float*,float*,float*,int*,int*,void*,int*,int*) in redeclaration is not compatible with the previous return type void(int*,int*,int*,int*,int*,float*,float*,int*,float*,float*,float*,float*,float*,float*,float*,int*,int*,float*,float*,float*,float*,float*,float*,float*,float*,int*,int*,void*,int*,int*,float*). nb_kernel420.h, line 100.1: 1506-033 (S) Function F77_FUNC_ is not valid. Function cannot return a function. nb_kernel420.h, line 100.1: 1506-282 (S) The type of the parameters must be specified in a prototype. nb_kernel430.h, line 63.1: 1506-033 (S) Function F77_FUNC_ is not valid. Function cannot return a function. nb_kernel430.h, line 63.1: 1506-282 (S) The type of the parameters must be specified in a prototype. nb_kernel430.h, line 101.1: 1506-033 (S) Function F77_FUNC_ is not valid. Function cannot return a function. nb_kernel430.h, line 101.1: 1506-282 (S) The type of the parameters must be specified in a prototype. make: 1254-004 The error code from the last command is 1. Stop. make: 1254-004 The error code from the last command is 2. Stop. make: 1254-004 The error code from the last command is 1. Stop. make: 1254-004 The error code from the last command is 1. Stop. make: 1254-004 The error code from the last command is 1. Stop. make: 1254-004 The error code from the last command is 2. Stop. make: 1254-004 The error code from the last command is 1. Stop. I don't really know how to do this :-( Le 16/04/2010 20:43, Chris Neale a écrit : Dear Sebastien: Perhaps it's obvious, but can you confirm that you used the compilation options that I posted? My suggestion was not so much that you should try to compile 4.0.4 but that you should try the options that I posted. So if you used your original compilation commands with gromacs version 4.0.4 then I am not surprised that it also failed to compile... please go back and attempt with the commands that I provided. If, however, you did try those options (and on v4.0.4) then I am sorry to say that I'm no expert at compilation -- a previous colleague worked out that AIX compillation for me and I'm just passing along what worked for me. Regarding the fftw question, I am sorry
Re: [gmx-users] Compiling Gromacs 4.0.7 on AIX 5.3
I've never worked with such architecture, but I do remember seeing a few posts in the past, some of which may be useful. Perhaps this one will hold some clues: http://lists.gromacs.org/pipermail/gmx-users/2007-April/027074.html Sorry I can't provide much more than this, but I thought I'd at least mention it. -Justin Sebastien Morin wrote: Hello again I followed your advices this time here's what I did : downloading gromacs 4.0.7 downloading fftw 2.1.5 initializing environment variables (modified to fit my configuration (pwr5) : export LDFLAGS='-L/usr/local/lib' export CPPFLAGS='-I/usr/local/include' export PATH=/usr/lpp/ppe.hpct/bin:/usr/vacpp/bin:.:/usr/bin:/etc:/usr/sbin:/usr/ucb:/usr/bin/X11:/sbin:/usr/java14/jre/bin:/usr/java14/bin:/usr/lpp/LoadL/full/bin:/usr/local/bin export F77=xlf_r export CC=xlc_r export CXX=xlc++_r export FFLAGS=-O5 -qarch=pwr5 -qtune=pwr5 export CFLAGS=-O5 -qarch=pwr5 -qtune=pwr5 export CXXFLAGS=-O5 -qarch=pwr5 -qtune=pwr5 for FFTW : ./configure --enable-threads --enable-float make make install (that's OK, installed in /usr/local/lib and /usr/local/include) for Gromacs : ./configure --with-fft=fftw2 (that's OK) make unfortunately, the result is : ... nb_kernel333.h, line 101.1: 1506-282 (S) The type of the parameters must be specified in a prototype. nb_kernel334.h, line 63.1: 1506-033 (S) Function F77_FUNC_ is not valid. Function cannot return a function. nb_kernel334.h, line 63.1: 1506-282 (S) The type of the parameters must be specified in a prototype. nb_kernel334.h, line 101.1: 1506-033 (S) Function F77_FUNC_ is not valid. Function cannot return a function. nb_kernel334.h, line 101.1: 1506-282 (S) The type of the parameters must be specified in a prototype. nb_kernel400.h, line 63.1: 1506-033 (S) Function F77_FUNC_ is not valid. Function cannot return a function. nb_kernel400.h, line 63.1: 1506-282 (S) The type of the parameters must be specified in a prototype. nb_kernel400.h, line 101.1: 1506-033 (S) Function F77_FUNC_ is not valid. Function cannot return a function. nb_kernel400.h, line 101.1: 1506-282 (S) The type of the parameters must be specified in a prototype. nb_kernel410.h, line 63.1: 1506-033 (S) Function F77_FUNC_ is not valid. Function cannot return a function. nb_kernel410.h, line 63.1: 1506-282 (S) The type of the parameters must be specified in a prototype. nb_kernel410.h, line 101.1: 1506-033 (S) Function F77_FUNC_ is not valid. Function cannot return a function. nb_kernel410.h, line 101.1: 1506-282 (S) The type of the parameters must be specified in a prototype. nb_kernel420.h, line 63.1: 1506-033 (S) Function F77_FUNC_ is not valid. Function cannot return a function. nb_kernel420.h, line 63.1: 1506-282 (S) The type of the parameters must be specified in a prototype. nb_kernel420.h, line 63.1: 1506-343 (S) Redeclaration of F77_FUNC_ differs from previous declaration on line 101 of nb_kernel410.h. nb_kernel420.h, line 63.1: 1506-050 (I) Return type void(int*,int*,int*,int*,int*,float*,float*,int*,float*,float*,float*,float*,float*,float*,float*,int*,int*,float*,float*,float*,float*,float*,float*,float*,float*,int*,int*,void*,int*,int*) in redeclaration is not compatible with the previous return type void(int*,int*,int*,int*,int*,float*,float*,int*,float*,float*,float*,float*,float*,float*,float*,int*,int*,float*,float*,float*,float*,float*,float*,float*,float*,int*,int*,void*,int*,int*,float*). nb_kernel420.h, line 100.1: 1506-033 (S) Function F77_FUNC_ is not valid. Function cannot return a function. nb_kernel420.h, line 100.1: 1506-282 (S) The type of the parameters must be specified in a prototype. nb_kernel430.h, line 63.1: 1506-033 (S) Function F77_FUNC_ is not valid. Function cannot return a function. nb_kernel430.h, line 63.1: 1506-282 (S) The type of the parameters must be specified in a prototype. nb_kernel430.h, line 101.1: 1506-033 (S) Function F77_FUNC_ is not valid. Function cannot return a function. nb_kernel430.h, line 101.1: 1506-282 (S) The type of the parameters must be specified in a prototype. make: 1254-004 The error code from the last command is 1. Stop. make: 1254-004 The error code from the last command is 2. Stop. make: 1254-004 The error code from the last command is 1. Stop. make: 1254-004 The error code from the last command is 1. Stop. make: 1254-004 The error code from the last command is 1. Stop. make: 1254-004 The error code from the last command is 2. Stop. make: 1254-004 The error code from the last command is 1. Stop. I don't really know how to do this :-( Le 16/04/2010 20:43, Chris Neale a écrit : Dear Sebastien: Perhaps it's obvious, but can you confirm that you used the compilation options that I posted? My suggestion was not so much that you should try to compile 4.0.4 but that you should try the options that I posted. So if you used your original compilation commands with gromacs version 4.0.4 then I am not surprised that it also
[gmx-users] Problems with g_energy
Hi folks I have recently encountered some problems with g_energy which I have not encountered before. I am running simulations for 32 molecular cages on 16 cpus in our local cluster. The maximum time for any one job is 24 hrs. Therfore after 24 hrs the jobs are killed so I countinue the job using the following script: #!/bin/bash #PBS -N mdsubhexcge #PBS -q long_eth #PBS -l nodes=2:ppn=8 #PBS -e test.e #PBS -o test.o #PBS -l walltime=23:59:59 . /etc/profile.d/modules.sh . ~/.bashrc cd /home/gmelaugh/phd/subhexyl/long600to200 cat $PBS_NODEFILE machinefile module load maui torque mpirun -machinefile machinefile -np 16 /home/gmelaugh/gromacs-4.0.7-parallel/bin/mdrun -pd -s topol.tpr -cpi state.cpt -append The bottom command as I gather continues to write the relevant information to the relevant files starting from the last checkpoint. This seems to be the case as the new data is written to both the traj and log files. I am however encountering the following errors when trying to run g_energy: Reading energy frame 4000 time 4.000 WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=-1125995535, time=0. Trying to skip frame expect a crash though --- Program g_energy, VERSION 4.0.7 Source code file: smalloc.c, line: 179 Fatal error: Not enough memory. Failed to realloc 846361600 bytes for fr-ener, fr-ener=0x7b0b40 (called from file enxio.c, line 354) --- I'd Like Monday Mornings Better If They Started Later (Garfield) : Cannot allocate memory There is ample memory space on my machine so I can't see where the problem lies. Is there a way of viewing the energy file in nonbinary format? or has anybody ever come across this problem before? Cheers Gavin -- 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] genbox
Thank you Justin but I end up with a new error. now in the insert.pdp file I have a molecule which I need to add 4 copy of that inside the solute.pdb genbox_d -ci insert.pdb -nmol 4 -cp solute.pdb but it gave me: Fatal error: more then one residue in insert molecules program terminated Fahimeh Date: Tue, 20 Apr 2010 07:10:59 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] genbox fahimeh bafti Hello, I want to use a file.pdb which has 8 chain of polypeptide, each chain contains 6 residues. I need to expand it to 12 chains of 6 rsidues so I need to add 4 chains or in the other word 24 residues. I think I have to use genbox, so I make another copy of file.pdb and rename it to insert.pdb and i used this command, but it doesn't work. genbox -cp file.pdb -ci insert.pdb -nmole 24 -o out.gro can anybody help me? The implication with genbox -ci -nmol is that the coordinate file passed to -ci contains one molecule, and an additional -nmol molecules are inserted. So if you already have 8, you need a coordinate file with one polypeptide and then: genbox -ci insert.pdb -nmol 4 Note in the documentation that -nmol refers to the number of molecules, not a number of residues, which I think is the root of your problem. -Justin Fahimeh Hotmail: Trusted email with powerful SPAM protection. Sign up now. https://signup.live.com/signup.aspx?id=60969 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing 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 _ Hotmail: Trusted email with Microsoft’s powerful SPAM protection. https://signup.live.com/signup.aspx?id=60969-- 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] about H-Bonds g_hbond
Justin A. Lemkul skrev: Erik Marklund wrote: Hi, Please submit a bugzilla, assign it to me, and I'll try to fix it along with heaps of other things. This bug has been outstanding for some time already: http://bugzilla.gromacs.org/show_bug.cgi?id=334 -Justin Ok. Thanks. I guess I was a bit sloppy. I'll look into it. Erik Marklund Justin A. Lemkul skrev: babu gokul wrote: Hi all I am getting an error in g_hbond such as Program g_hbond_d, VERSION 4.0.7 Source code file: gmx_hbond.c, line: 565 Fatal error: Error in func_type Position Rest. Could anyone tell me how to solve this problem. thanks in advance If you have position restraints defined, you can't run g_hbond for some reason. The work-around is to re-generate a .tpr file that does not use position restraints and do the analysis. -Justin E R Azhagiya singam Send free SMS to your Friends on Mobile from your Yahoo! Messenger. Download Now! http://messenger.yahoo.com/download.php -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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] Problems with g_energy
Gavin Melaugh wrote: Hi folks I have recently encountered some problems with g_energy which I have not encountered before. I am running simulations for 32 molecular cages on 16 cpus in our local cluster. The maximum time for any one job is 24 hrs. Therfore after 24 hrs the jobs are killed so I countinue the job using the following script: #!/bin/bash #PBS -N mdsubhexcge #PBS -q long_eth #PBS -l nodes=2:ppn=8 #PBS -e test.e #PBS -o test.o #PBS -l walltime=23:59:59 . /etc/profile.d/modules.sh . ~/.bashrc cd /home/gmelaugh/phd/subhexyl/long600to200 cat $PBS_NODEFILE machinefile module load maui torque mpirun -machinefile machinefile -np 16 /home/gmelaugh/gromacs-4.0.7-parallel/bin/mdrun -pd -s topol.tpr -cpi state.cpt -append The bottom command as I gather continues to write the relevant information to the relevant files starting from the last checkpoint. This seems to be the case as the new data is written to both the traj and log files. I am however encountering the following errors when trying to run g_energy: Reading energy frame 4000 time 4.000 WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=-1125995535, time=0. Trying to skip frame expect a crash though --- Program g_energy, VERSION 4.0.7 Source code file: smalloc.c, line: 179 Fatal error: Not enough memory. Failed to realloc 846361600 bytes for fr-ener, fr-ener=0x7b0b40 (called from file enxio.c, line 354) --- I'd Like Monday Mornings Better If They Started Later (Garfield) : Cannot allocate memory There is ample memory space on my machine so I can't see where the problem lies. Is there a way of viewing the energy file in nonbinary format? or has anybody ever come across this problem before? You can run both gmxcheck and gmxdump on the .edr file. What does that show? -Justin Cheers Gavin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing 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] genbox
fahimeh bafti wrote: Thank you Justin but I end up with a new error. now in the insert.pdp file I have a molecule which I need to add 4 copy of that inside the solute.pdb genbox_d -ci insert.pdb -nmol 4 -cp solute.pdb but it gave me: Fatal error: more then one residue in insert molecules program terminated Then you have two options: 1. Use the development (git) version of the code, which I believe can now deal with multi-residue molecules. 2. Use editconf to position all the components of your system. You could, I suppose, hack your insert.pdb to contain one residue (i.e., through renaming and renumbering) and then convert it back, but that sounds like a mess. Probably #2 is the easiest. -Justin Fahimeh Date: Tue, 20 Apr 2010 07:10:59 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] genbox fahimeh bafti Hello, I want to use a file.pdb which has 8 chain of polypeptide, each chain contains 6 residues. I need to expand it to 12 chains of 6 rsidues so I need to add 4 chains or in the other word 24 residues. I think I have to use genbox, so I make another copy of file.pdb and rename it to insert.pdb and i used this command, but it doesn't work. genbox -cp file.pdb -ci insert.pdb -nmole 24 -o out.gro can anybody help me? The implication with genbox -ci -nmol is that the coordinate file passed to -ci contains one molecule, and an additional -nmol molecules are inserted. So if you already have 8, you need a coordinate file with one polypeptide and then: genbox -ci insert.pdb -nmol 4 Note in the documentation that -nmol refers to the number of molecules, not a number of residues, which I think is the root of your problem. -Justin Fahimeh Hotmail: Trusted email with powerful SPAM protection. Sign up now. https://signup.live.com/signup.aspx?id=60969 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@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 Hotmail: Trusted email with Microsoft’s powerful SPAM protection. Sign up now. https://signup.live.com/signup.aspx?id=60969 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing 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] Finishing time donot showing
Hello all i got a system crash at some steps.. after creating the new .trr file using command tpbconv and running MDS by mdrun command the approximate finishing time is not showing. and also a warning is showing as WARNING: this run may generate approximately 4583292 Mb of data is there any changes that i should do while giving the command and can i continue with this warning. -- Bharath.K Ph-9535629260 -- 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] Finishing time donot showing
On Apr 20, 2010, at 9:14 AM, Bharath.K wrote: Hello all i got a system crash at some steps.. after creating the new .trr file using command tpbconv trr file with tpbconv? you mean tpr? and running MDS what is MDS? by mdrun command the approximate finishing time is not showing. and also a warning is showing as WARNING: this run may generate approximately 4583292 Mb of data That is a bit enormous is there any changes that i should do while giving the command and can i continue with this warning. Which exact command did you use? -- Bharath.K Ph-9535629260 -- 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 -- 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] Finishing time donot showing
Bharath.K wrote: Hello all i got a system crash at some steps.. after creating the new .trr file using command tpbconv and running MDS by mdrun command the approximate finishing time is not showing. and also a warning is showing as WARNING: this run may generate approximately 4583292 Mb of data is there any changes that i should do while giving the command and can i continue with this warning. Are you using the -v flag with mdrun? That's the only way I know of to get approximate completion time. If you are using -v, then it could just be that your simulation is very slow, a behavior that depends on the size of the system, available computing resources, node interconnect, etc. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing 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] Problems with g_energy
Hi justin Basically the gmxdump produces the same as below as does gmxcheck. gmxcheck also produces the following: Checking energy file ener.edr Opened ener.edr as single precision energy file frame: 0 (index 0), t: 0.000 Reading energy frame 4000 time 4.000 WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though Timesteps at t=43010 don't match (10, -43010) WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though Timesteps at t=0 don't match (-43010, 0) WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though It is at the point 43010 ps where the simulation had more than likely exceeeded the queue limit. Do you think it would be safer to use the -maxh option of mdrun ? as my jobs several days in duration. Cheers Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi folks I have recently encountered some problems with g_energy which I have not encountered before. I am running simulations for 32 molecular cages on 16 cpus in our local cluster. The maximum time for any one job is 24 hrs. Therfore after 24 hrs the jobs are killed so I countinue the job using the following script: #!/bin/bash #PBS -N mdsubhexcge #PBS -q long_eth #PBS -l nodes=2:ppn=8 #PBS -e test.e #PBS -o test.o #PBS -l walltime=23:59:59 . /etc/profile.d/modules.sh . ~/.bashrc cd /home/gmelaugh/phd/subhexyl/long600to200 cat $PBS_NODEFILE machinefile module load maui torque mpirun -machinefile machinefile -np 16 /home/gmelaugh/gromacs-4.0.7-parallel/bin/mdrun -pd -s topol.tpr -cpi state.cpt -append The bottom command as I gather continues to write the relevant information to the relevant files starting from the last checkpoint. This seems to be the case as the new data is written to both the traj and log files. I am however encountering the following errors when trying to run g_energy: Reading energy frame 4000 time 4.000 WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=-1125995535, time=0. Trying to skip frame expect a crash though --- Program g_energy, VERSION 4.0.7 Source code file: smalloc.c, line: 179 Fatal error: Not enough memory. Failed to realloc 846361600 bytes for fr-ener, fr-ener=0x7b0b40 (called from file enxio.c, line 354) --- I'd Like Monday Mornings Better If They Started Later (Garfield) : Cannot allocate memory There is ample memory space on my machine so I can't see
Re: [gmx-users] Problems with g_energy
Gavin Melaugh wrote: Hi justin Basically the gmxdump produces the same as below as does gmxcheck. gmxcheck also produces the following: Checking energy file ener.edr Opened ener.edr as single precision energy file frame: 0 (index 0), t: 0.000 Reading energy frame 4000 time 4.000 WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though Timesteps at t=43010 don't match (10, -43010) WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though Timesteps at t=0 don't match (-43010, 0) WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though It is at the point 43010 ps where the simulation had more than likely exceeeded the queue limit. Do you think it would be safer to use the -maxh option of mdrun ? as my jobs several days in duration. That's not a bad idea, if you know there's a limit. It looks like the file somehow got corrupted. You might be able to parse out meaningful data from frames before the corruption using eneconv for the .edr file and trjconv for your trajectories. Then, if you have a .cpt file from an earlier time point, you can restart. If you've been continually over-writing the .cpt files, though, you won't be able to get an exact restart. -Justin Cheers Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi folks I have recently encountered some problems with g_energy which I have not encountered before. I am running simulations for 32 molecular cages on 16 cpus in our local cluster. The maximum time for any one job is 24 hrs. Therfore after 24 hrs the jobs are killed so I countinue the job using the following script: #!/bin/bash #PBS -N mdsubhexcge #PBS -q long_eth #PBS -l nodes=2:ppn=8 #PBS -e test.e #PBS -o test.o #PBS -l walltime=23:59:59 . /etc/profile.d/modules.sh . ~/.bashrc cd /home/gmelaugh/phd/subhexyl/long600to200 cat $PBS_NODEFILE machinefile module load maui torque mpirun -machinefile machinefile -np 16 /home/gmelaugh/gromacs-4.0.7-parallel/bin/mdrun -pd -s topol.tpr -cpi state.cpt -append The bottom command as I gather continues to write the relevant information to the relevant files starting from the last checkpoint. This seems to be the case as the new data is written to both the traj and log files. I am however encountering the following errors when trying to run g_energy: Reading energy frame 4000 time 4.000 WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=-1125995535, time=0. Trying to skip frame expect a crash though --- Program
Re: [gmx-users] Problems with g_energy
Cheers Justin Just to make sure then to run the simulation with -maxh to avoid the 24hr cut off I use the command: mdrun -pd -s topol.tpr -maxh 23 (using 23 hrs to be overcautious) then to restart: mdrun -pd -cpi state.cpt Do I have to use the -append option in the above command to continue writing to the existing files ? Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi justin Basically the gmxdump produces the same as below as does gmxcheck. gmxcheck also produces the following: Checking energy file ener.edr Opened ener.edr as single precision energy file frame: 0 (index 0), t: 0.000Reading energy frame 4000 time 4.000 WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though Timesteps at t=43010 don't match (10, -43010) WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though Timesteps at t=0 don't match (-43010, 0) WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though It is at the point 43010 ps where the simulation had more than likely exceeeded the queue limit. Do you think it would be safer to use the -maxh option of mdrun ? as my jobs several days in duration. That's not a bad idea, if you know there's a limit. It looks like the file somehow got corrupted. You might be able to parse out meaningful data from frames before the corruption using eneconv for the .edr file and trjconv for your trajectories. Then, if you have a .cpt file from an earlier time point, you can restart. If you've been continually over-writing the .cpt files, though, you won't be able to get an exact restart. -Justin Cheers Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi folks I have recently encountered some problems with g_energy which I have not encountered before. I am running simulations for 32 molecular cages on 16 cpus in our local cluster. The maximum time for any one job is 24 hrs. Therfore after 24 hrs the jobs are killed so I countinue the job using the following script: #!/bin/bash #PBS -N mdsubhexcge #PBS -q long_eth #PBS -l nodes=2:ppn=8 #PBS -e test.e #PBS -o test.o #PBS -l walltime=23:59:59 . /etc/profile.d/modules.sh . ~/.bashrc cd /home/gmelaugh/phd/subhexyl/long600to200 cat $PBS_NODEFILE machinefile module load maui torque mpirun -machinefile machinefile -np 16 /home/gmelaugh/gromacs-4.0.7-parallel/bin/mdrun -pd -s topol.tpr -cpi state.cpt -append The bottom command as I gather continues to write the relevant information to the relevant files starting from the last checkpoint. This seems to be the case as the new data is written to both the traj and log files. I am however encountering the following errors when trying to run g_energy: Reading energy frame 4000 time 4.000 WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying
[gmx-users] parallel simulation in dual core PC
Hi, I want to use my dual core PC to do the simulation. The version of GROMACS installed is version 4.0.5. According the message post by others on mailing list before. I type lamboot first, and type the commend: mpirun -np 2 mdrun_mpi -s 200ns.tpr -e 200ns.edr -o 200ns.trr -g 200ns.log -c 200ns.gro. When the simulation starts, I use the commend, top, to check the utility of CPU. I found there is only one core which is used by GROMACS. And the utility of this core is separated to 52% and 48% for two mdrun_mpi jobs. How can I do for that? Any and all assistance is greatly appreciated. Hsin-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] Problems with g_energy
Gavin Melaugh wrote: Cheers Justin Just to make sure then to run the simulation with -maxh to avoid the 24hr cut off I use the command: mdrun -pd -s topol.tpr -maxh 23 (using 23 hrs to be overcautious) then to restart: mdrun -pd -cpi state.cpt Do I have to use the -append option in the above command to continue writing to the existing files ? Yep. -Justin Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi justin Basically the gmxdump produces the same as below as does gmxcheck. gmxcheck also produces the following: Checking energy file ener.edr Opened ener.edr as single precision energy file frame: 0 (index 0), t: 0.000Reading energy frame 4000 time 4.000 WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though Timesteps at t=43010 don't match (10, -43010) WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though Timesteps at t=0 don't match (-43010, 0) WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though It is at the point 43010 ps where the simulation had more than likely exceeeded the queue limit. Do you think it would be safer to use the -maxh option of mdrun ? as my jobs several days in duration. That's not a bad idea, if you know there's a limit. It looks like the file somehow got corrupted. You might be able to parse out meaningful data from frames before the corruption using eneconv for the .edr file and trjconv for your trajectories. Then, if you have a .cpt file from an earlier time point, you can restart. If you've been continually over-writing the .cpt files, though, you won't be able to get an exact restart. -Justin Cheers Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi folks I have recently encountered some problems with g_energy which I have not encountered before. I am running simulations for 32 molecular cages on 16 cpus in our local cluster. The maximum time for any one job is 24 hrs. Therfore after 24 hrs the jobs are killed so I countinue the job using the following script: #!/bin/bash #PBS -N mdsubhexcge #PBS -q long_eth #PBS -l nodes=2:ppn=8 #PBS -e test.e #PBS -o test.o #PBS -l walltime=23:59:59 . /etc/profile.d/modules.sh . ~/.bashrc cd /home/gmelaugh/phd/subhexyl/long600to200 cat $PBS_NODEFILE machinefile module load maui torque mpirun -machinefile machinefile -np 16 /home/gmelaugh/gromacs-4.0.7-parallel/bin/mdrun -pd -s topol.tpr -cpi state.cpt -append The bottom command as I gather continues to write the relevant information to the relevant files starting from the last checkpoint. This seems to be the case as the new data is written to both the traj and log files. I am however encountering the following errors when trying to run g_energy: Reading energy frame 4000 time 4.000 WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file ener.edr Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying to skip frame expect a crash though WARNING:
RE: [gmx-users] genbox
Thanks :) but I couldn't manage with that, it makes the same error with editconf as well, the problem was related to having more than one residue inside insert.gro I did it at the end with genconf genconf -nbox 2 2 2 (as u want) -f file.gro -o file_replicate.pdb it will simply replicate the unit. Fahimeh Date: Tue, 20 Apr 2010 09:12:44 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] genbox fahimeh bafti wrote: Thank you Justin but I end up with a new error. now in the insert.pdp file I have a molecule which I need to add 4 copy of that inside the solute.pdb genbox_d -ci insert.pdb -nmol 4 -cp solute.pdb but it gave me: Fatal error: more then one residue in insert molecules program terminated Then you have two options: 1. Use the development (git) version of the code, which I believe can now deal with multi-residue molecules. 2. Use editconf to position all the components of your system. You could, I suppose, hack your insert.pdb to contain one residue (i.e., through renaming and renumbering) and then convert it back, but that sounds like a mess. Probably #2 is the easiest. -Justin Fahimeh Date: Tue, 20 Apr 2010 07:10:59 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] genbox fahimeh bafti Hello, I want to use a file.pdb which has 8 chain of polypeptide, each chain contains 6 residues. I need to expand it to 12 chains of 6 rsidues so I need to add 4 chains or in the other word 24 residues. I think I have to use genbox, so I make another copy of file.pdb and rename it to insert.pdb and i used this command, but it doesn't work. genbox -cp file.pdb -ci insert.pdb -nmole 24 -o out.gro can anybody help me? The implication with genbox -ci -nmol is that the coordinate file passed to -ci contains one molecule, and an additional -nmol molecules are inserted. So if you already have 8, you need a coordinate file with one polypeptide and then: genbox -ci insert.pdb -nmol 4 Note in the documentation that -nmol refers to the number of molecules, not a number of residues, which I think is the root of your problem. -Justin Fahimeh Hotmail: Trusted email with powerful SPAM protection. Sign up now. https://signup.live.com/signup.aspx?id=60969 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@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 Hotmail: Trusted email with Microsoft’s powerful SPAM protection. Sign up now. https://signup.live.com/signup.aspx?id=60969 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing 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 _ Hotmail: Powerful Free email with security by Microsoft. https://signup.live.com/signup.aspx?id=60969-- 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] Size of generating data
hi all I'm running simulation for a protein of about 150 amino acids for 100 steps i.e 2 ns in a system of about 35 GB disk space. is there any way to know the approximate size of generating data. -- Bharath.K.Chakravarthi Ph:9535629260 -- 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] Finishing time donot showing
Sorry MDS means MD simulation the commands are as follows tpbconv -s md.tpr -f md_traj.chk.trr -o md_01.tpr -until 1000 this shows last step before crashing and starts from there until 1000 then mdrun -s md_01.tpr -o md_traj_01.trr -c minim_water.gro -g md.log -e minim_ener_01.edr On Tue, Apr 20, 2010 at 7:50 PM, XAvier Periole x.peri...@rug.nl wrote: On Apr 20, 2010, at 9:14 AM, Bharath.K wrote: Hello all i got a system crash at some steps.. after creating the new .trr file using command tpbconv trr file with tpbconv? you mean tpr? and running MDS what is MDS? by mdrun command the approximate finishing time is not showing. and also a warning is showing as WARNING: this run may generate approximately 4583292 Mb of data That is a bit enormous is there any changes that i should do while giving the command and can i continue with this warning. Which exact command did you use? -- Bharath.K Ph-9535629260 -- 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 -- 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 -- Bharath.K.Chakravarthi Ph:9535629260 -- 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] Size of generating data
On Tuesday 20 April 2010 18:02:50 Bharath.K. Chakravarthi wrote: hi all I'm running simulation for a protein of about 150 amino acids for 100 steps i.e 2 ns in a system of about 35 GB disk space. is there any way to know the approximate size of generating data. The grompp command give you that estimation (at least in the 4.x version) Milan -- 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] interaction parameter, polyolefin solution, ternary system
Hello, My research is concerned with computational thermodynamics of compressible polyolefin solution (polyethylene in n-Hexane as solvent). I am interested in calculation of interaction parameter of ternary system of polyethylene/n-Hexane/ ethylene. Ethylene is unreacted monomer in the solution. I wanted to know if GROMACS can be used to build up the ternary system and if the interaction parameters for this ternary system can be calculated. Many thanks, Moeed -- 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] Finishing time donot showing
tpbconv -s md.tpr -f md_traj.chk.trr -o md_01.tpr -until 1000 this shows last step before crashing and starts from there until 1000 then mdrun -s md_01.tpr -o md_traj_01.trr -c minim_water.gro -g md.log - e minim_ener_01.edr Nothing seem particularly wrong! May be you write your trajectory file too often! Did the original the indicated the same amount of data to be written? which version of gmx you are using? actually using the check point file is relatively easy (-cpi fie.cpt to add to mdrun) and does all the work for you! On Tue, Apr 20, 2010 at 7:50 PM, XAvier Periole x.peri...@rug.nl wrote: On Apr 20, 2010, at 9:14 AM, Bharath.K wrote: Hello all i got a system crash at some steps.. after creating the new .trr file using command tpbconv trr file with tpbconv? you mean tpr? and running MDS what is MDS? by mdrun command the approximate finishing time is not showing. and also a warning is showing as WARNING: this run may generate approximately 4583292 Mb of data That is a bit enormous is there any changes that i should do while giving the command and can i continue with this warning. Which exact command did you use? -- Bharath.K Ph-9535629260 -- 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 -- 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 -- Bharath.K.Chakravarthi Ph:9535629260 -- 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! 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] genbox
fahimeh bafti wrote: Thanks :) but I couldn't manage with that, it makes the same error with editconf as well, the problem was related to having more than one residue inside insert.gro editconf should not have a problem placing multi-residue molecules within a box. That is its main function, so I can only assume you did something wrong. I did it at the end with genconf genconf -nbox 2 2 2 (as u want) -f file.gro -o file_replicate.pdb it will simply replicate the unit. That works. Glad you found a solution. -Justin Fahimeh Date: Tue, 20 Apr 2010 09:12:44 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] genbox fahimeh bafti wrote: Thank you Justin but I end up with a new error. now in the insert.pdp file I have a molecule which I need to add 4 copy of that inside the solute.pdb genbox_d -ci insert.pdb -nmol 4 -cp solute.pdb but it gave me: Fatal error: more then one residue in insert molecules program terminated Then you have two options: 1. Use the development (git) version of the code, which I believe can now deal with multi-residue molecules. 2. Use editconf to position all the components of your system. You could, I suppose, hack your insert.pdb to contain one residue (i.e., through renaming and renumbering) and then convert it back, but that sounds like a mess. Probably #2 is the easiest. -Justin Fahimeh Date: Tue, 20 Apr 2010 07:10:59 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] genbox fahimeh bafti Hello, I want to use a file.pdb which has 8 chain of polypeptide, each chain contains 6 residues. I need to expand it to 12 chains of 6 rsidues so I need to add 4 chains or in the other word 24 residues. I think I have to use genbox, so I make another copy of file.pdb and rename it to insert.pdb and i used this command, but it doesn't work. genbox -cp file.pdb -ci insert.pdb -nmole 24 -o out.gro can anybody help me? The implication with genbox -ci -nmol is that the coordinate file passed to -ci contains one molecule, and an additional -nmol molecules are inserted. So if you already have 8, you need a coordinate file with one polypeptide and then: genbox -ci insert.pdb -nmol 4 Note in the documentation that -nmol refers to the number of molecules, not a number of residues, which I think is the root of your problem. -Justin Fahimeh Hotmail: Trusted email with powerful SPAM protection. Sign up now. https://signup.live.com/signup.aspx?id=60969 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@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 Hotmail: Trusted email with Microsoft’s powerful SPAM protection. Sign up now. https://signup.live.com/signup.aspx?id=60969 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@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 Hotmail: Powerful Free email with security by Microsoft. Get it now. https://signup.live.com/signup.aspx?id=60969 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
Re: [gmx-users] Finishing time donot showing
XAvier Periole wrote: tpbconv -s md.tpr -f md_traj.chk.trr -o md_01.tpr -until 1000 this shows last step before crashing and starts from there until 1000 then mdrun -s md_01.tpr -o md_traj_01.trr -c minim_water.gro -g md.log -e minim_ener_01.edr Nothing seem particularly wrong! May be you write your trajectory file too often! Did the original the indicated the same amount of data to be written? which version of gmx you are using? actually using the check point file is relatively easy (-cpi fie.cpt to add to mdrun) and does all the work for you! Indeed. There's even a step-by-step how-to on the Gromacs site! http://www.gromacs.org/Documentation/How-tos/Extending_Simulations -Justin On Tue, Apr 20, 2010 at 7:50 PM, XAvier Periole x.peri...@rug.nl mailto:x.peri...@rug.nl wrote: On Apr 20, 2010, at 9:14 AM, Bharath.K wrote: Hello all i got a system crash at some steps.. after creating the new .trr file using command tpbconv trr file with tpbconv? you mean tpr? and running MDS what is MDS? by mdrun command the approximate finishing time is not showing. and also a warning is showing as WARNING: this run may generate approximately 4583292 Mb of data That is a bit enormous is there any changes that i should do while giving the command and can i continue with this warning. Which exact command did you use? -- Bharath.K Ph-9535629260 -- 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 thewww 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 -- 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 thewww 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 -- Bharath.K.Chakravarthi Ph:9535629260 -- 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. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing 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] Finishing time donot showing
I'm using gromacs-3.3.3 and here is the parameter .. .. nstxout = 500 nstvout = 1000 nstfout = 0 nstlist = 100 nstlog = 100 nstenergy = 10 nstxtcout = 500 .. .. for writing trajectories in .mdp file and what is check point file and -cpi file.cpt ... i did not get u :( On Tue, 20 Apr 2010 22:20:35 +0530, XAvier Periole x.peri...@rug.nl wrote: tpbconv -s md.tpr -f md_traj.chk.trr -o md_01.tpr -until 1000 this shows last step before crashing and starts from there until 1000 then mdrun -s md_01.tpr -o md_traj_01.trr -c minim_water.gro -g md.log - e minim_ener_01.edr Nothing seem particularly wrong! May be you write your trajectory file too often! Did the original the indicated the same amount of data to be written? which version of gmx you are using? actually using the check point file is relatively easy (-cpi fie.cpt to add to mdrun) and does all the work for you! On Tue, Apr 20, 2010 at 7:50 PM, XAvier Periole x.peri...@rug.nl wrote: On Apr 20, 2010, at 9:14 AM, Bharath.K wrote: Hello all i got a system crash at some steps.. after creating the new .trr file using command tpbconv trr file with tpbconv? you mean tpr? and running MDS what is MDS? by mdrun command the approximate finishing time is not showing. and also a warning is showing as WARNING: this run may generate approximately 4583292 Mb of data That is a bit enormous is there any changes that i should do while giving the command and can i continue with this warning. Which exact command did you use? -- Bharath.K Ph-9535629260 -- 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 -- 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 -- Bharath.K.Chakravarthi Ph:9535629260 -- 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 -- Using Opera's revolutionary e-mail client: http://www.opera.com/mail/ -- 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] Finishing time donot showing
Bharath.K wrote: I'm using gromacs-3.3.3 and here is the parameter .. .. nstxout = 500 nstvout = 1000 nstfout = 0 nstlist = 100 nstlog = 100 nstenergy = 10 nstxtcout = 500 .. .. for writing trajectories in .mdp file and what is check point file and -cpi file.cpt ... i did not get u :( This is why stating your Gromacs version at the outset is useful. Checkpointing was introduced in Gromacs 4.0, so you won't be able to use it. You also have not answered my first question. What is your mdrun command line? Did you use the -v flag? If not, you will not get any information about completion time. There is nothing that the .mdp options or tpbconv will do for you as far as completion time is concerned. -Justin On Tue, 20 Apr 2010 22:20:35 +0530, XAvier Periole x.peri...@rug.nl wrote: tpbconv -s md.tpr -f md_traj.chk.trr -o md_01.tpr -until 1000 this shows last step before crashing and starts from there until 1000 then mdrun -s md_01.tpr -o md_traj_01.trr -c minim_water.gro -g md.log - e minim_ener_01.edr Nothing seem particularly wrong! May be you write your trajectory file too often! Did the original the indicated the same amount of data to be written? which version of gmx you are using? actually using the check point file is relatively easy (-cpi fie.cpt to add to mdrun) and does all the work for you! On Tue, Apr 20, 2010 at 7:50 PM, XAvier Periole x.peri...@rug.nl wrote: On Apr 20, 2010, at 9:14 AM, Bharath.K wrote: Hello all i got a system crash at some steps.. after creating the new .trr file using command tpbconv trr file with tpbconv? you mean tpr? and running MDS what is MDS? by mdrun command the approximate finishing time is not showing. and also a warning is showing as WARNING: this run may generate approximately 4583292 Mb of data That is a bit enormous is there any changes that i should do while giving the command and can i continue with this warning. Which exact command did you use? -- Bharath.K Ph-9535629260 -- 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 -- 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 -- Bharath.K.Chakravarthi Ph:9535629260 -- 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 MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing 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] Finishing time donot showing
no i did not used -v flag at that command may be thats the mistake thank u Justin On Tue, Apr 20, 2010 at 10:54 PM, Justin A. Lemkul jalem...@vt.edu wrote: Bharath.K wrote: I'm using gromacs-3.3.3 and here is the parameter .. .. nstxout = 500 nstvout = 1000 nstfout = 0 nstlist = 100 nstlog = 100 nstenergy = 10 nstxtcout = 500 .. .. for writing trajectories in .mdp file and what is check point file and -cpi file.cpt ... i did not get u :( This is why stating your Gromacs version at the outset is useful. Checkpointing was introduced in Gromacs 4.0, so you won't be able to use it. You also have not answered my first question. What is your mdrun command line? Did you use the -v flag? If not, you will not get any information about completion time. There is nothing that the .mdp options or tpbconv will do for you as far as completion time is concerned. -Justin On Tue, 20 Apr 2010 22:20:35 +0530, XAvier Periole x.peri...@rug.nl wrote: tpbconv -s md.tpr -f md_traj.chk.trr -o md_01.tpr -until 1000 this shows last step before crashing and starts from there until 1000 then mdrun -s md_01.tpr -o md_traj_01.trr -c minim_water.gro -g md.log - e minim_ener_01.edr Nothing seem particularly wrong! May be you write your trajectory file too often! Did the original the indicated the same amount of data to be written? which version of gmx you are using? actually using the check point file is relatively easy (-cpi fie.cpt to add to mdrun) and does all the work for you! On Tue, Apr 20, 2010 at 7:50 PM, XAvier Periole x.peri...@rug.nl wrote: On Apr 20, 2010, at 9:14 AM, Bharath.K wrote: Hello all i got a system crash at some steps.. after creating the new .trr file using command tpbconv trr file with tpbconv? you mean tpr? and running MDS what is MDS? by mdrun command the approximate finishing time is not showing. and also a warning is showing as WARNING: this run may generate approximately 4583292 Mb of data That is a bit enormous is there any changes that i should do while giving the command and can i continue with this warning. Which exact command did you use? -- Bharath.K Ph-9535629260 -- 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 -- 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 -- Bharath.K.Chakravarthi Ph:9535629260 -- 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 MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing 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 -- Bharath.K.Chakravarthi Ph:9535629260 -- 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] Tabulated potentials
Hi Gromacs users, previously I've posted my situation with a simulation and I'm still confused: I have 3 groups of different atoms: A, B and C, and tabulated bonding and non-bonding potentials. The tabulated bonded potentials are specified in the files: table_b1.xvg table_a1.xvg table_a2.xvg table_a3.xvg Because the systems is simply this molecule: A--(B)n--C, the *.mdp file contains the following: coulombtype = user vdw-type= user energygrps = A B C energygrp_table = A B A C B B B C From the manual and tutorials I understand that, for the non bonding part of U, I can suply a file called table.xvg that contains the 7 non-zero columns for r, f, f', g, g', h and h'. The file table.xvg must contain the functions for AB interactions and the remaining interactions must be in the files table_A_C.xvg, table_B_B.xvg and table_B_C.xvg. So, in the command line I can write: mdrun -table table.xvg -tableb table I'm right? As a test I have also included the file table_A_B.xvg (the same potential functions that table.xvg) in the same directory, and when I look at the log file it shows that this file is readed too. I'm still unclear... how must I specify the files in an univocal way for the non bonding interactions that I want? Gromacs version: 4.0.7 Any help will be appreciated. Martin. PD: I've received some private e-mails explaining to me some issues about spam, mailing lists, private mails, etc. Thanks to all and I apologize if I've bother someone, it wasn't my intention. And for those who spontaneously shows me their support, I don't want it and I don't need it! -- 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] Finishing time donot showing
On Apr 20, 2010, at 7:39 PM, Bharath.K. Chakravarthi wrote: no i did not used -v flag at that command may be thats the mistake thank u Justin On Tue, Apr 20, 2010 at 10:54 PM, Justin A. Lemkul jalem...@vt.edu wrote: Bharath.K wrote: I'm using gromacs-3.3.3 and here is the parameter .. .. nstxout = 500 nstvout = 1000 nstfout = 0 nstlist = 100 This might not be the best choice! it is generally kept under 10! It depends on your system/force field though nstlog = 100 nstenergy = 10 nstxtcout = 500 .. .. for writing trajectories in .mdp file and what is check point file and -cpi file.cpt ... i did not get u :( This is why stating your Gromacs version at the outset is useful. Checkpointing was introduced in Gromacs 4.0, so you won't be able to use it. You also have not answered my first question. What is your mdrun command line? Did you use the -v flag? If not, you will not get any information about completion time. There is nothing that the .mdp options or tpbconv will do for you as far as completion time is concerned. -Justin On Tue, 20 Apr 2010 22:20:35 +0530, XAvier Periole x.peri...@rug.nl wrote: tpbconv -s md.tpr -f md_traj.chk.trr -o md_01.tpr -until 1000 this shows last step before crashing and starts from there until 1000 then mdrun -s md_01.tpr -o md_traj_01.trr -c minim_water.gro -g md.log - e minim_ener_01.edr Nothing seem particularly wrong! May be you write your trajectory file too often! Did the original the indicated the same amount of data to be written? which version of gmx you are using? actually using the check point file is relatively easy (-cpi fie.cpt to add to mdrun) and does all the work for you! On Tue, Apr 20, 2010 at 7:50 PM, XAvier Periole x.peri...@rug.nl wrote: On Apr 20, 2010, at 9:14 AM, Bharath.K wrote: Hello all i got a system crash at some steps.. after creating the new .trr file using command tpbconv trr file with tpbconv? you mean tpr? and running MDS what is MDS? by mdrun command the approximate finishing time is not showing. and also a warning is showing as WARNING: this run may generate approximately 4583292 Mb of data That is a bit enormous is there any changes that i should do while giving the command and can i continue with this warning. Which exact command did you use? -- Bharath.K Ph-9535629260 -- 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 -- 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 -- Bharath.K.Chakravarthi Ph:9535629260 -- 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 MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing 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 -- Bharath.K.Chakravarthi Ph:9535629260 -- 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! 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?
Re: [gmx-users] Finishing time donot showing
and XAvier [?] On Tue, Apr 20, 2010 at 11:09 PM, Bharath.K. Chakravarthi bharath.chakravar...@gmail.com wrote: no i did not used -v flag at that command may be thats the mistake thank u Justin On Tue, Apr 20, 2010 at 10:54 PM, Justin A. Lemkul jalem...@vt.eduwrote: Bharath.K wrote: I'm using gromacs-3.3.3 and here is the parameter .. .. nstxout = 500 nstvout = 1000 nstfout = 0 nstlist = 100 nstlog = 100 nstenergy = 10 nstxtcout = 500 .. .. for writing trajectories in .mdp file and what is check point file and -cpi file.cpt ... i did not get u :( This is why stating your Gromacs version at the outset is useful. Checkpointing was introduced in Gromacs 4.0, so you won't be able to use it. You also have not answered my first question. What is your mdrun command line? Did you use the -v flag? If not, you will not get any information about completion time. There is nothing that the .mdp options or tpbconv will do for you as far as completion time is concerned. -Justin On Tue, 20 Apr 2010 22:20:35 +0530, XAvier Periole x.peri...@rug.nl wrote: tpbconv -s md.tpr -f md_traj.chk.trr -o md_01.tpr -until 1000 this shows last step before crashing and starts from there until 1000 then mdrun -s md_01.tpr -o md_traj_01.trr -c minim_water.gro -g md.log - e minim_ener_01.edr Nothing seem particularly wrong! May be you write your trajectory file too often! Did the original the indicated the same amount of data to be written? which version of gmx you are using? actually using the check point file is relatively easy (-cpi fie.cpt to add to mdrun) and does all the work for you! On Tue, Apr 20, 2010 at 7:50 PM, XAvier Periole x.peri...@rug.nl wrote: On Apr 20, 2010, at 9:14 AM, Bharath.K wrote: Hello all i got a system crash at some steps.. after creating the new .trr file using command tpbconv trr file with tpbconv? you mean tpr? and running MDS what is MDS? by mdrun command the approximate finishing time is not showing. and also a warning is showing as WARNING: this run may generate approximately 4583292 Mb of data That is a bit enormous is there any changes that i should do while giving the command and can i continue with this warning. Which exact command did you use? -- Bharath.K Ph-9535629260 -- 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 -- 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 -- Bharath.K.Chakravarthi Ph:9535629260 -- 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 MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing 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 -- Bharath.K.Chakravarthi Ph:9535629260 -- Bharath.K.Chakravarthi Ph:9535629260 330.gif-- 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] Finishing time donot showing
that means generating a trajectory file for every 10 steps rite then i may need more disk space On Tue, Apr 20, 2010 at 11:41 PM, XAvier Periole x.peri...@rug.nl wrote: On Apr 20, 2010, at 7:39 PM, Bharath.K. Chakravarthi wrote: no i did not used -v flag at that command may be thats the mistake thank u Justin On Tue, Apr 20, 2010 at 10:54 PM, Justin A. Lemkul jalem...@vt.eduwrote: Bharath.K wrote: I'm using gromacs-3.3.3 and here is the parameter .. .. nstxout = 500 nstvout = 1000 nstfout = 0 nstlist = 100 This might not be the best choice! it is generally kept under 10! It depends on your system/force field though nstlog = 100 nstenergy = 10 nstxtcout = 500 .. .. for writing trajectories in .mdp file and what is check point file and -cpi file.cpt ... i did not get u :( This is why stating your Gromacs version at the outset is useful. Checkpointing was introduced in Gromacs 4.0, so you won't be able to use it. You also have not answered my first question. What is your mdrun command line? Did you use the -v flag? If not, you will not get any information about completion time. There is nothing that the .mdp options or tpbconv will do for you as far as completion time is concerned. -Justin On Tue, 20 Apr 2010 22:20:35 +0530, XAvier Periole x.peri...@rug.nl wrote: tpbconv -s md.tpr -f md_traj.chk.trr -o md_01.tpr -until 1000 this shows last step before crashing and starts from there until 1000 then mdrun -s md_01.tpr -o md_traj_01.trr -c minim_water.gro -g md.log - e minim_ener_01.edr Nothing seem particularly wrong! May be you write your trajectory file too often! Did the original the indicated the same amount of data to be written? which version of gmx you are using? actually using the check point file is relatively easy (-cpi fie.cpt to add to mdrun) and does all the work for you! On Tue, Apr 20, 2010 at 7:50 PM, XAvier Periole x.peri...@rug.nl wrote: On Apr 20, 2010, at 9:14 AM, Bharath.K wrote: Hello all i got a system crash at some steps.. after creating the new .trr file using command tpbconv trr file with tpbconv? you mean tpr? and running MDS what is MDS? by mdrun command the approximate finishing time is not showing. and also a warning is showing as WARNING: this run may generate approximately 4583292 Mb of data That is a bit enormous is there any changes that i should do while giving the command and can i continue with this warning. Which exact command did you use? -- Bharath.K Ph-9535629260 -- 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 -- 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 -- Bharath.K.Chakravarthi Ph:9535629260 -- 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 MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing 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 -- Bharath.K.Chakravarthi Ph:9535629260 -- 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 list
Re: [gmx-users] Tabulated potentials
Hi I think this is what you need to do: (1) Ensure that the topol.top and index.ndx files are set up in the manner described on the wikki. (2) Put in the mdp file the following: energygrps = A B C energygrp_table = A C B B B C (3) Now create a set of files as follows table.xvg - containing the A B interactions table_A_C.xvg - containing the A C interactions table_B_B.xvg - containing the B B interactions table_B_C.xvg - containing the B C interactions You now run with mdrun -table table.xvg gromacs will read in all these files as energygrp_table tells it that it must read table_A_C.xvg, table_B_B.xvg and table_B_C.xvg as well as table.xvg. To put this all another way, when you use the command vdw-type = user (incidentally I think you said that there are no electrostatics so you can use coulombtype = cut-off as it will make no difference) Then you have to provide a table file with definitions of f(r), g(r) and h(r). Then gromacs it will use this table for all the non-bonded interactions (so in your case AA, AB, AC, BB, BC and CC interactions). However, when you add: energygrp_table = A C Then you are saying, oh but please do something different for A C interactions, do what is in the table_A_C.xvg file instead. As a side note, correct me if I am wrong, but there are no AA or CC interactions in your molecule? With the set up I describe above they would have a functional form equivalent to the A B interaction. This is obviously not important if their parameters are equal to zero. Finally, if your still not sure that stuff has been read in you can look in the log file, which should say what tables have been read in. It will also give you warnings (although these maybe in standard error I can't remember) if your tables are not set up properly. ciao Gareth On Tue, Apr 20, 2010 at 7:38 PM, Martin Vartorelli mrvartore...@gmail.comwrote: Hi Gromacs users, previously I've posted my situation with a simulation and I'm still confused: I have 3 groups of different atoms: A, B and C, and tabulated bonding and non-bonding potentials. The tabulated bonded potentials are specified in the files: table_b1.xvg table_a1.xvg table_a2.xvg table_a3.xvg Because the systems is simply this molecule: A--(B)n--C, the *.mdp file contains the following: coulombtype = user vdw-type= user energygrps = A B C energygrp_table = A B A C B B B C From the manual and tutorials I understand that, for the non bonding part of U, I can suply a file called table.xvg that contains the 7 non-zero columns for r, f, f', g, g', h and h'. The file table.xvg must contain the functions for AB interactions and the remaining interactions must be in the files table_A_C.xvg, table_B_B.xvg and table_B_C.xvg. So, in the command line I can write: mdrun -table table.xvg -tableb table I'm right? As a test I have also included the file table_A_B.xvg (the same potential functions that table.xvg) in the same directory, and when I look at the log file it shows that this file is readed too. I'm still unclear... how must I specify the files in an univocal way for the non bonding interactions that I want? Gromacs version: 4.0.7 Any help will be appreciated. Martin. PD: I've received some private e-mails explaining to me some issues about spam, mailing lists, private mails, etc. Thanks to all and I apologize if I've bother someone, it wasn't my intention. And for those who spontaneously shows me their support, I don't want it and I don't need it! -- 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! 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] Finishing time donot showing
Bharath.K. Chakravarthi wrote: that means generating a trajectory file for every 10 steps rite then i may need more disk space The nstlist parameter has nothing to do with trajectory output. It is the frequency with which the neighborlist is updated. Setting this value too high can (and will!) result in missed short-range interactions and artefacts in the results. Consult the primary literature for whatever force field you're using for an appropriate setting (generally 5-10 in conjunction with a 2-fs timestep, such that the neighborlist is re-generated every 10-20 fs). -Justin On Tue, Apr 20, 2010 at 11:41 PM, XAvier Periole x.peri...@rug.nl mailto:x.peri...@rug.nl wrote: On Apr 20, 2010, at 7:39 PM, Bharath.K. Chakravarthi wrote: no i did not used -v flag at that command may be thats the mistake thank u Justin On Tue, Apr 20, 2010 at 10:54 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Bharath.K wrote: I'm using gromacs-3.3.3 and here is the parameter .. .. nstxout = 500 nstvout = 1000 nstfout = 0 nstlist = 100 This might not be the best choice! it is generally kept under 10! It depends on your system/force field though nstlog = 100 nstenergy = 10 nstxtcout = 500 .. .. for writing trajectories in .mdp file and what is check point file and -cpi file.cpt ... i did not get u :( This is why stating your Gromacs version at the outset is useful. Checkpointing was introduced in Gromacs 4.0, so you won't be able to use it. You also have not answered my first question. What is your mdrun command line? Did you use the -v flag? If not, you will not get any information about completion time. There is nothing that the .mdp options or tpbconv will do for you as far as completion time is concerned. -Justin On Tue, 20 Apr 2010 22:20:35 +0530, XAvier Periole x.peri...@rug.nl mailto:x.peri...@rug.nl wrote: tpbconv -s md.tpr -f md_traj.chk.trr -o md_01.tpr -until 1000 this shows last step before crashing and starts from there until 1000 then mdrun -s md_01.tpr -o md_traj_01.trr -c minim_water.gro -g md.log - e minim_ener_01.edr Nothing seem particularly wrong! May be you write your trajectory file too often! Did the original the indicated the same amount of data to be written? which version of gmx you are using? actually using the check point file is relatively easy (-cpi fie.cpt to add to mdrun) and does all the work for you! On Tue, Apr 20, 2010 at 7:50 PM, XAvier Periole x.peri...@rug.nl mailto:x.peri...@rug.nl wrote: On Apr 20, 2010, at 9:14 AM, Bharath.K wrote: Hello all i got a system crash at some steps.. after creating the new .trr file using command tpbconv trr file with tpbconv? you mean tpr? and running MDS what is MDS? by mdrun command the approximate finishing time is not showing. and also a warning is showing as WARNING: this run may generate approximately 4583292 Mb of data That is a bit enormous is there any changes that i should do while giving the command and can i continue with this warning. Which exact command did you use? -- Bharath.K Ph-9535629260 -- 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 thewww interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read
Re: [gmx-users] Finishing time donot showing
Hi Bharath, It means updating the neighbor lists every 10 steps. You might want to check the manual on those options. Also, you're writing full precision coordinates and velocities very often, and you're writing coordinates to the .xtc file as often as to the .trr file, which is redundant anyhow. You might want to spend a few moments of thought on your intention with the results, and use that to choose those settings optimally. There aren't too many purposes for having such a high resolution for all of the system for a long time. It might well be sufficient to have nstxout and nstvout set to something corresponding to every ns, and have the nstxtcout set to something that will yield a few thousand frames. But it depends on the purpose of course. That's one of the critical moments in setting up your simulations. Cheers, Tsjerk On Tue, Apr 20, 2010 at 8:22 PM, Bharath.K. Chakravarthi bharath.chakravar...@gmail.com wrote: that means generating a trajectory file for every 10 steps rite then i may need more disk space On Tue, Apr 20, 2010 at 11:41 PM, XAvier Periole x.peri...@rug.nl wrote: On Apr 20, 2010, at 7:39 PM, Bharath.K. Chakravarthi wrote: no i did not used -v flag at that command may be thats the mistake thank u Justin On Tue, Apr 20, 2010 at 10:54 PM, Justin A. Lemkul jalem...@vt.edu wrote: Bharath.K wrote: I'm using gromacs-3.3.3 and here is the parameter .. .. nstxout = 500 nstvout = 1000 nstfout = 0 nstlist = 100 This might not be the best choice! it is generally kept under 10! It depends on your system/force field though nstlog = 100 nstenergy = 10 nstxtcout = 500 .. .. for writing trajectories in .mdp file and what is check point file and -cpi file.cpt ... i did not get u :( This is why stating your Gromacs version at the outset is useful. Checkpointing was introduced in Gromacs 4.0, so you won't be able to use it. You also have not answered my first question. What is your mdrun command line? Did you use the -v flag? If not, you will not get any information about completion time. There is nothing that the .mdp options or tpbconv will do for you as far as completion time is concerned. -Justin On Tue, 20 Apr 2010 22:20:35 +0530, XAvier Periole x.peri...@rug.nl wrote: tpbconv -s md.tpr -f md_traj.chk.trr -o md_01.tpr -until 1000 this shows last step before crashing and starts from there until 1000 then mdrun -s md_01.tpr -o md_traj_01.trr -c minim_water.gro -g md.log - e minim_ener_01.edr Nothing seem particularly wrong! May be you write your trajectory file too often! Did the original the indicated the same amount of data to be written? which version of gmx you are using? actually using the check point file is relatively easy (-cpi fie.cpt to add to mdrun) and does all the work for you! On Tue, Apr 20, 2010 at 7:50 PM, XAvier Periole x.peri...@rug.nl wrote: On Apr 20, 2010, at 9:14 AM, Bharath.K wrote: Hello all i got a system crash at some steps.. after creating the new .trr file using command tpbconv trr file with tpbconv? you mean tpr? and running MDS what is MDS? by mdrun command the approximate finishing time is not showing. and also a warning is showing as WARNING: this run may generate approximately 4583292 Mb of data That is a bit enormous is there any changes that i should do while giving the command and can i continue with this warning. Which exact command did you use? -- Bharath.K Ph-9535629260 -- gmx-users mailing list gmx-us...@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 -- gmx-users mailing list gmx-us...@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 -- Bharath.K.Chakravarthi Ph:9535629260 -- gmx-users mailing list gmx-us...@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 MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080
[gmx-users] High quality movies, bmp frames and videomach=poor quality
Hi, I am using tachyon to get high quality still pictures by generating a .dat file, changing the render numbers and then typing this command in the window N:/myhome/VMD1.8.7/tachyon_WIN32.exe -aasamples 12 plot01.dat -format -o plot01.tga This gives great images but now I am stuck on generating movies as I don?t seem to have much choice when using the movie-maker and am clueless at scripting. I need a movie file in .mpg or .avi for submission to a journal (and not bigger than 10MB). Whenever I choose tachyon as the renderer within the movie maker I get frames generated in .dat which I can?t do anything with and when I use tachyon internal the files are automatically written in .bmp. I can?t seem to get my frames in targa or any format other than .bmp. Is there a script command which could give me high quality snapshots in .tga? If I continue with my frames in .bmp and generate a movie in videomach the image quality is very poor (I do this via preview movie and select the highest quality (fast 400x400). TO avoid this I have been using convert in unix to stick frames together but this won't give me a mpg or avi file! Can anyone give me some advice or a script line similar to the one above which would work on a whole trajectory rather than a single frame?. Thanks Jenny -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- 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] High quality movies, bmp frames and videomach=poor quality
mencoder is pretty good but I do not guaranty the size! mencoder mf://file-.tga -mf fps=16:type=tga -ovc lavc -lavcopts vcodec=mjpeg -oac copy -o movie.avi On Apr 20, 2010, at 8:36 PM, Jennifer Williams wrote: Hi, I am using tachyon to get high quality still pictures by generating a .dat file, changing the render numbers and then typing this command in the window N:/myhome/VMD1.8.7/tachyon_WIN32.exe -aasamples 12 plot01.dat - format -o plot01.tga This gives great images but now I am stuck on generating movies as I don?t seem to have much choice when using the movie-maker and am clueless at scripting. I need a movie file in .mpg or .avi for submission to a journal (and not bigger than 10MB). Whenever I choose tachyon as the renderer within the movie maker I get frames generated in .dat which I can?t do anything with and when I use tachyon internal the files are automatically written in .bmp. I can?t seem to get my frames in targa or any format other than .bmp. Is there a script command which could give me high quality snapshots in .tga? If I continue with my frames in .bmp and generate a movie in videomach the image quality is very poor (I do this via preview movie and select the highest quality (fast 400x400). TO avoid this I have been using convert in unix to stick frames together but this won't give me a mpg or avi file! Can anyone give me some advice or a script line similar to the one above which would work on a whole trajectory rather than a single frame?. Thanks Jenny -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- 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! 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] 'SHAKE' : gromacs 4.0.7
Hello gromacs users: I installed the new version of gromacs and tried to run 'mdrun_mpi' in parrallel but it gives the error pasted below. When i switched the constrain from 'shake' to 'lincs' it runs. I know 'shake' algorithm compilation was done but i don't why i am getting this error. The error does not arise when i run it in serial. Any help will be highly appreciated. -- Program mdrun_mpi_d, VERSION 4.0.7 Source code file: constr.c, line: 830 Fatal error: SHAKE is not supported with domain decomposition and constraint that cross charge group boundaries, use LINCS -- best, Rama -- 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] 'SHAKE' : gromacs 4.0.7
Ramachandran G wrote: Hello gromacs users: I installed the new version of gromacs and tried to run 'mdrun_mpi' in parrallel but it gives the error pasted below. When i switched the constrain from 'shake' to 'lincs' it runs. I know 'shake' algorithm compilation was done but i don't why i am getting this error. The error does not arise when i run it in serial. Any help will be highly appreciated. -- Program mdrun_mpi_d, VERSION 4.0.7 Source code file: constr.c, line: 830 Fatal error: SHAKE is not supported with domain decomposition and constraint that cross charge group boundaries, use LINCS -- The error message is really quite explicit. SHAKE + constraints between charge groups = failure. You won't see any error in serial, because you can't run domain decomposition on a single processor. If you want to use SHAKE, either run in serial, or perhaps you can try the old particle decomposition (mdrun -pd), but the results in both cases will certainly be slower than if you use LINCS and domain decomposition. -Justin best, Rama -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing 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] 'SHAKE' : gromacs 4.0.7
When you run GROMACS in parallel, by default it does domain descomposition, so if your constraints run across the charge groups, SHAKE can not run. El mar, 20-04-2010 a las 14:49 -0700, Ramachandran G escribió: Hello gromacs users: I installed the new version of gromacs and tried to run 'mdrun_mpi' in parrallel but it gives the error pasted below. When i switched the constrain from 'shake' to 'lincs' it runs. I know 'shake' algorithm compilation was done but i don't why i am getting this error. The error does not arise when i run it in serial. Any help will be highly appreciated. -- Program mdrun_mpi_d, VERSION 4.0.7 Source code file: constr.c, line: 830 Fatal error: SHAKE is not supported with domain decomposition and constraint that cross charge group boundaries, use LINCS -- best, Rama -- 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! 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 simulation in dual core PC
On 21/04/2010 12:55 AM, Hsin-Lin wrote: Hi, I want to use my dual core PC to do the simulation. The version of GROMACS installed is version 4.0.5. According the message post by others on mailing list before. I type lamboot first, and type the commend: mpirun -np 2 mdrun_mpi -s 200ns.tpr -e 200ns.edr -o 200ns.trr -g 200ns.log -c 200ns.gro. When the simulation starts, I use the commend, top, to check the utility of CPU. I found there is only one core which is used by GROMACS. And the utility of this core is separated to 52% and 48% for two mdrun_mpi jobs. Depending what is being measured by what, this could be a correct result. We can't really tell because we don't know how you've set up LAM, or how your top works. Do a short test calculation with one and two processors and compare the run times. 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] interaction parameter, polyolefin solution, ternary system
On 21/04/2010 2:43 AM, Moeed wrote: Hello, My research is concerned with computational thermodynamics of compressible polyolefin solution (polyethylene in n-Hexane as solvent). I am interested in calculation of interaction parameter of ternary system of polyethylene/n-Hexane/ ethylene. Ethylene is unreacted monomer in the solution. I wanted to know if GROMACS can be used to build up the ternary system and if the Yes, but not easily. interaction parameters for this ternary system can be calculated. Probably, depends what observables they're based on. 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] query on constraint-force pull code
Hi, I would like to use constraint force pull code to calculate the free energy of association of two peptide using the distance between center of mass of two peptides as reaction coordinate. I am planning to use gromacs 4. Here I have some queries: 1. Since I will constraint method, I guess, I do not have to use any force-constant ( unlike umbrella sampling) . If that is correct, do I need to specify a pulling rate ? If so, what will be a typically appropriate range of value to start with ? 2. In umbrella sampling technique, we check the overlap of position histogram of two consecutive windows to check the convergence . Here , using constraint force technique, what should I check for convergence. Is that the force ? 3. Once I get time series of force for all windows, how should I unbias the effect of constraint and what formula I should use to integrate the force? Is that integration implemented in gromacs ? Thanks Sanku -- 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
