[gmx-users] Problem with continuation of files using checkpoint files
Dear All, I am doing protein simulations using Gromacs4.0.2. For continuation or extension of runs, i am using tpbconv command. In the manual its given that for exact binary identical run, one needs to use checkpoint file with mdrun. So, for the tpbconv generated file when I am using checkpoint. I am getting warnings as below. Gromacs is parallelly installed, but I am using on single node. tpbconv_4 -s md_1.tpr -f md_1.trr -e md_1 .edr -o md_2.tpr -extend 2000.0 mdrun_4 -s md_2.tpr -cpi md_1.cpt -deffnm md_2.tpr I am getting the message as: Reading checkpoint file md_1.cpt generated: Thu Feb 12 08:42:50 2009 Gromacs binary or parallel settings not identical to previous run. Continuation still works, but is not guaranteed to be binary identical, see the log file for details. Gromacs binary or parallel settings not identical to previous run. Continuation still works, but is not guaranteed to be binary identical. Looking at the log file: Reading checkpoint file md_1.cpt file generated by: mdrun_4 file generated at: Thu Feb 12 08:42:50 2009 GROMACS build time:Wed Dec 24 23:09:37 EST 2008 GROMACS build user:comp...@localhost.localdomain GROMACS build machine: Linux 2.6.9-67.ELsmp x86_64 simulation part #: 1 step: 50 time: 2000.00 #PP-nodes mismatch, current program: 2 checkpoint file: 1 If anyone can please suggest, what might be the problem. What is meant by PP nodes mismatch? Thanks in advance. Regards Monika ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] eigenvalues
Hi. As far as I know, PCA analysis breaks your total motion in system, or rather decouples it into respective motions. And by the eigenvectors and the corresponding eigenvalues it means that this 1st vector or the 2nd vector contributes this percent of the total motion. It is system-dependent. Is this really related to the difference in the degrees of freedom of two different systems (that I am a bit skeptic about) with which you are confusing it now. If I am missing something here, then anyone please correct me. Regards, Monika On Thu, Jan 8, 2009 at 4:31 PM, sanja...@iitb.ac.in wrote: dear gromacs users, i did PCA analysis for my trajectory using g_covar and g_anaeig, i have taken trajectory of 25ns from both protein alone and protein_withligands(i did two simulation one with ligands and other by removing the ligands from pdb file)and extracted eigenvalues along first 10 eigenvector, when i compared eigenvalues i find that protein_withligands has high values in compare to protein alone, but from literature protein alone is more flexible structure and after ligand binding it changes in to more rigid structure. primary analysis like RMSD, RMSF calculation showing high values for protein alone in compare to protien_withligands. i think i should also get higher eigenvalue for protein alone.. is any thing wrong with my trajectory. i had used same mdp file for both simulation. i am sending values of Ist 10 eigenvector for make my question more clear. any suggestion is appreciable protein-withligands 1 1.48497 2 0.674994 3 0.410547 4 0.279636 5 0.237182 6 0.213209 7 0.158359 8 0.140052 9 0.126227 10 0.113618 protein alone 1 0.526848 2 0.351471 3 0.267247 4 0.248945 5 0.222829 6 0.204475 7 0.158441 8 0.12583 9 0.0970591 10 0.0923962 thanks sanjay ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] eigenvalues
Hi Tsjerk, Thank you very much for correcting me. And yes that is variance, not the literal motion. Regards, Monika On Fri, Jan 9, 2009 at 6:50 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Monika, As far as I know, PCA analysis breaks your total motion in system, or rather decouples it into respective motions. Well, formally, PCA tries to provide an explanation of the total variance in the system, in terms of a set of new, linearly unrelated variables. And by the eigenvectors and the corresponding eigenvalues it means that this 1st vector or the 2nd vector contributes this percent of the total motion. Variance is not motion. I can be running small circles, being very motile, but having a small variance. I can also steadily go from one place to another. Though I don't need to be very active, there'll be a large variance in my position. So the variance is more linked to the range of conformations and the extent of the conformational space accessible than of the motility. Only if you can be sure that there's no trend - no going from one place to the other - but periodic motions (running circles), you can say the variance is a measure of motility. It is system-dependent. Is this really related to the difference in the degrees of freedom of two different systems (that I am a bit skeptic about) with which you are confusing it now. No, not of different systems, but of the same (very similar) system(s) under different conditions, each in equilibrium, yes. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] RMSD calculations by g_rms
Dear All, I have two queries regarding the rmsd calculations of gromacs run. 1. I was trying to calculate rmsd for 3ns run of my protein system. I did it in two ways: VMD (RMSD Traj tool) and g_rms. I found great differences in pattern. I know that VMD gives values in angstrom, instead g_rms gives values in pm. The thing is that in case of VMD traj calculation, I get the rmsd values in decreasing order from around 5.5 to 0.5 angstroms. But in g_rms I get in ascending order from 0.0 to 0.5nm. And this should be the right thing (ascending order). This thing really confuses me that why is it happening? Has anyone also encountered such problem?? I am using xtc for VMD. 2. I have given two consecutive 3ns runs in continuation. first for 3ns, then next again for 3ns. In latter, I used unconstrained-start=yes. When I am concatenating these xtc files, to get total of 6ns, and then doing g_rms, I am getting a dip at 3000 and there it seems to follow earlier pattern of VMD. that 1 to 3000ps- values of rmsd decreases from 0.5 to 0.005 nm, then 3001 to 6000ps - values of rmsd increases from 0.0698 to 0.248 nm. In case of alone rmsd calculations, 3ns rmsd showed increasing deviations from 0.0005 to 0.509 nm. 6ns run rmsd too showed increasing deviations from 0.00 to 0.248nm But when I am concatenating them, then the 3ns run showed deviations down (different from its original) and 6ns showed up (similar to its original). I really dont know what is happening and why?? Where the things are going hay-ward?? For g_rms, I am using backbone for least square fit and protein for rmsd calculation. Similar pattern in all. Any kind of suggestions are welcome.. Regards, Monika ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Dimer simulations using Gromacs
Dear All, I wish to do some simulations using dimer of protein. I have generated .gro file for that. I am able to minimize structure, but when I am trying to give it for equilibration run. I am getting error as: Warning: 1-4 interaction between 5786 and 5791 at distance 5.468 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file On looking the gro file it seems that these atom numbers corresponds to two different chains of the dimer. But it is trying to map it as one protein molecule instead of two as can be seen from the topol.top file. [ molecules ] ; Compound#mols Protein 1 FAD 1 NAD 1 FAD 1 NAD 1 SOL 123000 My question is that is it normal for gromacs to read dimer as single unit in .gro file. Or do I need to make some modifications in .gro and .top file to make it read as two entities. Suggestions are required for this. Thanking you, Regards, Monika ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] karthik
Hii.. Well they are there on the gromacs website only. Go to documentation page and you can get the requisites and installation tips all there. form there u can download and compile and install. And regarding that zipped file, u unzip it as tar -xzf *.tar.gz look for installation notes there and do accordingly. Gromacs installation is quite straightforward. Happy Installing!!! Monika On Wed, 2007-12-19 at 12:02 +0530, Anupam Nath Jha wrote: hii i am karthik while installing gromacs in linux redhat entriprise version i encountered problems like fftw3 3.0.1,and libfftw3f.so.3 dependencies are you can find all this on net. just by giving the search fftw. required for installation are missing.how do i get those and from where one more thing is to how to install using tar.gz - 5, 50, 500, 5000 - Store N number of mails in your inbox. Click here. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Replica Exchange MD using Gromacs
Thank you very much all for your consideration and fruitful advices. Regards, Monika On Wed, 2007-12-05 at 18:15 +1100, Mark Abraham wrote: Xavier Periole wrote: Dear Monika, the setup of a REMD simulation is actually quite straightforward. In the following I describe steps that would lead you to have a REMD simulation running on a given system. The success of the simulation will depend entirely on the problem you are addressing and the criterion you judge it. Although REMD simulation are helping in increasing sampling they do not provide the ultimate answer. This should be kept in mind. I've added a section on replica-exchange to http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation which people may wish to review. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Replica Exchange MD using Gromacs
Hi!! Thanks for suggestion. But still the problem is that whatever literature i have, I could just get the way that they just did replica exchange at these or that intervals. But still couldn't get clear the protocol of doing replica exchange using Gromacs. That's why i wished for some pieces of advice from the experts who have successfully implemented REMD using Gromacs. Thanks a lot.. Regards, Monika On Fri, 2007-11-30 at 14:27 +0200, OZGE ENGIN wrote: Hi Monica, I had not found a detailed tutorial about it; however, you can search for papers in which the simulations are performed via REMD.This will be helpful. Ozge. -Original Message- From: Monika Sharma [EMAIL PROTECTED] To: gmx-users@gromacs.org Date: Fri, 30 Nov 2007 17:04:07 +0530 (IST) Subject: [gmx-users] Replica Exchange MD using Gromacs Dear All, I am trying REMD for the first time using Gromacs. But I am not finding any much helpful material regarding the replica exchange using Gromacs. Can anyone who has done REMD please let me know about any good tutorial where I can understand the way this replica exchange work in gromacs and the right protocol to do so.. Thanks a lot in advance.. Regards, Monika CCNSB, IIIT, Hyderabad. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Replica Exchange MD using Gromacs
Dear All, I am trying REMD for the first time using Gromacs. But I am not finding any much helpful material regarding the replica exchange using Gromacs. Can anyone who has done REMD please let me know about any good tutorial where I can understand the way this replica exchange work in gromacs and the right protocol to do so.. Thanks a lot in advance.. Regards, Monika CCNSB, IIIT, Hyderabad. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Nucleic Acid Simulations with Gromacs
Dear All, I want to start nucleic acid simulations. I am using gromacs3.3.1. But I could not find any mention of Nucleic Acids in any of the force-field provided by gromacs distro. So does it mean that one _can not_ simulate nucleic acids with gromacs. Has anyone tried? And if someone can guide me through?? Thanks in advance Regards, Monika ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Nucleic Acid Simulations with Gromacs
Thank you all for helping me. I will surely try the ffamber ports available. Regards, monika Yang Ye wrote: Please don't use the OPLS NA forcefield. It is largely based on AMBER (OPLS takes different approach in parameterization, so you know that direct migration is so correct) and not verified. I had some communications with that group on this issue. It has some teaching value on making topology of small molecules in OPLS format but except this, don't use for serious business. Regards, Yang Ye On 10/2/2007 6:58 PM, [EMAIL PROTECTED] wrote: Hi, On the gromacs webpage in user contributions-topologies you have (at least) 2 forcefields do download that allow you to simulate NA. The first is OPLS NA records from rnp-group (http://rnp-group.genebee.msu.su/3d/oplsa_ff.html). It is for gromacs 3.2.1, so minor manual adjustments for 3.3.1 are required. The second is AMBER ff variants from Stanford (http://folding.stanford.edu/ffamber/). Good Luck Grzegorz Wieczorek Department of Bioinformatics Institute of Biochemistry and Biophysics Polish Academy of Sciences ul. Pawinskiego 5a 02-106 Warszawa, Poland On Tue, 2 Oct 2007, Monika Sharma wrote: Dear All, I want to start nucleic acid simulations. I am using gromacs3.3.1. But I could not find any mention of Nucleic Acids in any of the force-field provided by gromacs distro. So does it mean that one _can not_ simulate nucleic acids with gromacs. Has anyone tried? And if someone can guide me through?? Thanks in advance Regards, Monika ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Storage of large output files
Thanks Mark for your reply. Thats a sound advice. I will really take care of. Actually, through my previous mail, I wanted to know that what other groups are using as storage devices for the backup of their large files, that must have figured out that which way is best- economical and efficient way to store their data. Regards, Monika Mark Abraham wrote: Monika Sharma wrote: Dear All, We have started our venture into MD recently, for which we are using our in-house resources. Now that MD runs are giving very large output files like for trr files. The files keep piling up and using spaces on the work machines. This is creating problems with the depletion of space with every run. Can anyone please suggest an economical and efficient way how to take backup of such a large files of the order of Gb or so, so that we dont end up piling up our work machines with such files. And the data need to be saved for future references.. First, consider whether you are producing more output than you need. Look at the options for output frequency of positions and velocities in .trr files, whether you should be using .xtc files, and whether you should only be outputting subsets of your data. Normally you only want a full frame of positions and velocities in your .trr file with frequency with which you might ever want to do an exact restart (and make sure your energy output frequency is a suitable multiple so you also have energies at this time). This frequency is invariably much smaller than the frequency with which you want output data. If you only want position data for your solute for your later analysis, then outputting only that group to an .xtc file with frequency as low as you'd ever need will be a tiny fraction of the cost of a .trr file of the whole system with positions and velocities at every step. Be aware that analysis types that require autocorrelation functions need data sampled much more frequently than the characteristic times of the system. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Another problem with Stimulated Annealing
Thanks for your reply. So what you meant by it, that the steep option will always be at 0K. and what this gen_temp will corresponds to?? and SA wont have meaning for steep. Can you please help me in understanding some things? 1. md integrator wont be a good option for minimization? since it can take different temperature. 2. steep integrator will work on temp 0K only, whatsoever the temperature couple or velocity generation value we provide?? These seems to be baffling.. what to use first and how to proceed?? I have gone through manual and tutorials, but still seems confused. Please do suggest... regards, Monika David van der Spoel wrote: Monika Sharma wrote: Dear All, While doing SA, I am observing that when i am using steep as option for minimization, then the md log file generated takes ref_t as 0K temp only, but when i am using md as integratore, the temp for ref_t is taken as 375K( temp i gave).. See below... Its quite strange there is no temperature in a minimization. + log file with steep as integrator: - grpopts: nrdf: 27419.8 451854 ref_t: 0 0 tau_t: 0 0 anneal: Single Single ann_npoints: 4 4 ann. times [0]: 0.0 2.0 4.0 6.0 ann. temps [0]:375.0 350.0 325.0 300.0 ann. times [1]: 0.0 2.0 4.0 6.0 ann. temps [1]:375.0 350.0 325.0 300.0 acc:0 0 0 nfreeze: N N N - -++ log file with md as integrator: - grpopts: nrdf: 27419.8 301239 ref_t:375 375 tau_t:0.1 0.1 anneal: Single Single ann_npoints: 4 4 ann. times [0]: 0.0 2.0 4.0 6.0 ann. temps [0]:375.0 350.0 325.0 300.0 ann. times [1]: 0.0 2.0 4.0 6.0 ann. temps [1]:375.0 350.0 325.0 300.0 acc:0 0 0 nfreeze: N N N _--- The mdp file is same for both but only diff is the integrator.. Here is mdp file: title = cpp = /lib/cpp define = -DFLEXIBLE constraints = none integrator = steep (here the only diff as md) nsteps = 5000 dt = 0.02 init_step = 0 ;langevin dynamics bd_fric = 0 ld_seed = 1993 ;minimization emtol = 100 emstep = 1.0 ;output control nstxout = 10 nstvout = 10 nstfout = 10 nstlog = 10 nstenergy = 10 nstxtcout = 10 xtc_precision = 100 xtc_grps= energygrps = ; Neighbor searching nstlist = 10 ns_type = grid pbc = xyz rlist = 1.5 ; electrostatics coulombtype = PME rcoulomb= 1.5 epsilon_r = 1.0 ; van der waals params vdwtype = cutoff rvdw= 2.0 ; table params table-extension = 3 ;PME params for ewald calc. fourierspacing = 0.15 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; temperature coupling tcoupl = berendsen tc-grps = protein non-protein tau_t = 0.1 0.1 ref_t = 375 375 ; pressure coupling pcoupl = berendsen pcoupltype = isotropic tau_p = 1.2 compressibility = 4.5e-5 ref_p = 1.01325 ; simulated annealing params annealing = single single annealing_npoints = 4 4 annealing_time = 0 246 02 4 6 annealing_temp = 375 350 325 300 375 350 325 300 ;velocity generation gen_vel = no gen_temp= 375 gen_seed= 1732529 --- So my ques is that does that really means that SA works with md only, not steep. Is it a bug or some reason behind it?? I have not come across any... but with md run I am not getting any value. the run is crashing, only the steep is showing some output, but that at 0K?? Can someone suggest anything for a succesful SA-MD? Thanks in advance Regards, Monika ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED
Re: [gmx-users] grompp or parameter file problem?
Hello Anna, Did you checked your .gro file for the representation of atoms for water molecules and the itp files? I mean the atoms may be represented differently, that sometimes cause problem, even in my case that seemed to be problem. And one thing more does your system have its structure water molecules also? Do check their representation also... Cheers.. Monika Yang Ye wrote: On 6/21/2007 6:20 PM, Anna Reymer wrote: On 6/20/07, Mark Abraham [EMAIL PROTECTED] wrote: Anna Reymer wrote: Hello all! I am trying to simulate DNA dodecamer in TIP3P water with Amber 99 port. I was ablle to produce dna+solvent.top (attached file) and dna+solvent.gro. When running grompp: grompp -f em.mdp -c dna+solvent.gro -p dna+solvent.top -o out.tpr with the following em.mdp: - ; DNA energy minimization in water ; cpp = /lib/cpp -traditional define = include = -I/***/share/gromacs/top/ffamber99.itp This is not the right approach, but might not be the cause of the problem. Your .top should #include this file itself (see http://wiki.gromacs.org/index.php/include_file_mechanism). This -I flag provides an alternate path search in looking for this file. The three asterixes are weird... use the correct path, and make it a path, not a file. Mark Hi Mark! The tree asterixes is just the path to my folder. The path is quite long and I substituted it in the mail by three asterixes in the file it is a normal 100 letters path. My top file included the file itself and I tried to provide a path to top directory not only to a special file, but neither path to the top directory no path to file did not provide any good changes. Thank you very much for your help! then you shall only put a path after -I, instead of the file name. regards /anna ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] grompp or parameter file problem?
Hello Anna, One thing. It is that the topology file includes in solvent topology section is tip3p.itp, but you are using amber99. Is it same as ffamber_tip3p.itp. If not, then i think you can try changing it to ffamber_tip3p.itp.. Hope it helps.. Monika Yang Ye wrote: On 6/21/2007 6:20 PM, Anna Reymer wrote: On 6/20/07, Mark Abraham [EMAIL PROTECTED] wrote: Anna Reymer wrote: Hello all! I am trying to simulate DNA dodecamer in TIP3P water with Amber 99 port. I was ablle to produce dna+solvent.top (attached file) and dna+solvent.gro. When running grompp: grompp -f em.mdp -c dna+solvent.gro -p dna+solvent.top -o out.tpr with the following em.mdp: - ; DNA energy minimization in water ; cpp = /lib/cpp -traditional define = include = -I/***/share/gromacs/top/ffamber99.itp This is not the right approach, but might not be the cause of the problem. Your .top should #include this file itself (see http://wiki.gromacs.org/index.php/include_file_mechanism). This -I flag provides an alternate path search in looking for this file. The three asterixes are weird... use the correct path, and make it a path, not a file. Mark Hi Mark! The tree asterixes is just the path to my folder. The path is quite long and I substituted it in the mail by three asterixes in the file it is a normal 100 letters path. My top file included the file itself and I tried to provide a path to top directory not only to a special file, but neither path to the top directory no path to file did not provide any good changes. Thank you very much for your help! then you shall only put a path after -I, instead of the file name. regards /anna ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] gromacs on IBM Power 5 Linux Machine: Preprocessor problem
Dear All, We have this IBM POWER5 machine with Linux SLES. The FFTW and GROMACS are compiling without any errors (compiler is gcc), but when we are trying to run a job on the machine, its exiting saying illegal instruction. Looking at the things, it seemed that the cpp it generated is just a dummy, and cannot execute. I even tried using as make CFLAGS='-mcpu=power5 -mtune=power5' for fftw and gromacs also, but it doesnt seems to work. If anyone can please help me out to osrt this problem.. Thanks in advance Monika ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] gromacs on IBM Power 5 Linux Machine: Preprocessor problem
I am using Gromacs3.3 version, and I was trying grompp for energy minimization, which is not working. Even the mdrun didnt work. The same file seems to work properly on simple Fedora linux PC, but not on IBM Power linux. Dont know then what the problem is?? Mark Abraham wrote: Monika Sharma wrote: Dear All, We have this IBM POWER5 machine with Linux SLES. The FFTW and GROMACS are compiling without any errors (compiler is gcc), but when we are trying to run a job on the machine, its exiting saying illegal instruction. Looking at the things, it seemed that the cpp it generated is just a dummy, and cannot execute. cpp is not generated by the above process. It needs to be already present on your machine. You'd also be well advised to tell us *which* gromacs program you're trying to run when you get your illegal instruction, because we can't read minds. I even tried using as make CFLAGS='-mcpu=power5 -mtune=power5' for fftw and gromacs also, but it doesnt seems to work. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
