[gmx-users] RE : essential dynamics
Hi, After searching though gmxuserlist I found the relevant thread for ED... I followed the following steps :- 1) g_covar - to generate a covariance matrix and diagonalize it (for c-alpha atoms only) 2) g_anaeig - to generate eigen vectors 3)g_rmsf - for calculating RMSD of first 8 eigen vectors , I got an error at this step that - Fatal error: Molecule in topology has atom numbers below and above natoms (230). You are probably trying to use a trajectory which does not match the first 230 a toms of the run input file. You can make a matching run input file with tpbconv. --- California, R.I.P. (Red Hot Chili Peppars) 4) then I used make_ndx - for generating an index file containing only c-alpha atoms..which was done successfully 5) Further I used tpbconv - to generate a .tpr file for calculating the rmsf ... but I am getting the following error at this step .. Fatal error: Molecule in topology has atom numbers below and above natoms (230). You are probably trying to use a trajectory which does not match the first 230 a toms of the run input file. You can make a matching run input file with tpbconv. --- California, R.I.P. (Red Hot Chili Peppars) Pls help what has to be done in order to generate the .tpr file ... -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] General MD question
Dear All, A quick question as I have not really delved into code for gromacs ever, nor know anyone close whom has worked on it. If I set up an MD simulation using a 4 protein complex, and 1 small peptide, plus waters, etc...and run the whole thing the proteins never move, only the amino acids within(constant temp RT and pressure 1 bar). Two domains make one complex, and another two the other. Basically, if I seperate the domains say 5, 10, 15 angstrom, etc...the amino acids will drift (the chains) towards each other, but the two large (global) protein units never move their center (I know I can make it work with Pull vectors, but why not in the simple system with a generated initial randomized velocities), I woundered why they are fixed in a normal run with minimal parameters? Is there a reason (specific to developers), historical reason, or other? As waters move around fine, and anything else added (salt, small molecules of 20-30 atoms, water) except the central molecule(s) of interest. Grüsse Stephan Watkins -- Neu: GMX De-Mail - Einfach wie E-Mail, sicher wie ein Brief! Jetzt De-Mail-Adresse reservieren: http://portal.gmx.net/de/go/demail -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] mdrun with append option
On 1/02/2011 7:50 AM, Sai Pooja wrote: I think I have figured out the reason. It is because I am carrying out replica exchange (manual) after every mdrun. If the exchange occurs, I exchange the checkpoint files, extend the simulation by 500 steps and continue. The new simulation starts from exchanged cptfile. It seems that whenever the exchange occurs, the earlier log,traj files are not appended. They are instead overwritten. the obv solution is to save and index these files with the relevant replicas everytime an exchange occurs. This would have been good to know earlier. If replica-exchange leads to the ensemble of the .tpr not matching the ensemble of the .cpt, then IIRC 4.5.3 mdrun will refuse to start from the .cpt, which means the subsequent mdrun will start from the .tpr only. Certainly a non-appending mdrun prints a warning (or error, I forget which) message to the log file, but perhaps the use of -append (erroneously) doesn't do that. Please have a look and see if that is the issue. There is an environment variable that can be set to tell mdrun that you (think you) know what you are doing mismatching .tpr and .cpt. Mark However, i have a more general question. Since mdrun still runs with the exchanged checkpoint files and starts from the point where the previous run ended, can I be assured that an exchange has been affected - since tpr files correspond to the replica-box and cpi to the most recent exchanged replicas? Pooja On Mon, Jan 31, 2011 at 2:33 PM, Sai Pooja saipo...@gmail.com mailto:saipo...@gmail.com wrote: I manually index checkpoint files after every mdrun. What troubles me is the randomness with which -append fails/works. For eg, I have a simulation which runs from 3ns, 1ps in 1 mdrun. Now oddly enough, the logfile starts from 1184ps(in the end, I do remember the one starting from 0 but that was overwritten it seems) and the rest is appended uptil the 3000ps step. Why would append work from 1184ps to 3000ps but not for the previous ones?Could it have anything to do with the network/cluster? If that is the case is it safer to create a new file everytime and then concatenate them after say every 100ps? Pooja On Sat, Jan 29, 2011 at 6:52 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 30/01/2011 10:39 AM, Sai Pooja wrote: I would be happy to supply more information.. if someone could please look into this.. otherwise I will have to switch to storing every file and then just concatenating them which seems like a rather roundabout way of doing it. As I suggested a few emails ago, are you sure that -cpi file exists? If your numerical suffixes are indexing restarts, then unless you've done some manual copying that you haven't told us about, it won't. Your filename scheme seems a bit contorted - like you're trying to do the work that GROMACS 4.5.x will just do for you if you let it. Otherwise, you'll have to do some detective work with gmxcheck on the -cpi to see what might be the issue. In your case, an initial mdrun -deffnm rex_3 (perhaps save some copies while you're experimenting) and subsequently tpbconv -extend blah -f rex_3 -o rex_3 mdrun -deffnm rex_3 -append will work and be much simpler than whatever you're trying to do with filenames :-) Mark On Fri, Jan 28, 2011 at 4:37 PM, Sai Pooja saipo...@gmail.com mailto:saipo...@gmail.com wrote: This is the command: nbs submit -command (/usr/local/gromacs/4.5.1/bin/mdrun_mpi -s rex_3.tpr -e rex_3 -c after_rex_3 -cpi restart3 -cpo restart3 -ap pend -g rexlog3 -x rextraj3); -nproc 1 -name GENHAM-DIHEDRAL-3 -mail start end Pooja On Fri, Jan 28, 2011 at 4:20 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 29/01/2011 3:56 AM, Sai Pooja wrote: Hi, I am using tpbconv and mdrun to extend a simulation. I use it with the append option but the files still get overwritten or erased. Can someone help me in this regard? Pooja Commands (in python) cmd = '(%s/tpbconv -extend %f -s rex_%d.tpr -o rex_%d.tpr)' %(GROMPATH,dtstep,i,i) os.system(cmd) time.sleep(1) cmd = 'nbs submit -command ' cmd += '(%s/mdrun_mpi -noh -noversion -s rex_%d.tpr -e rex_%d -c after_rex_%d -cpi restart%d -cpo restart%d -append -g rexlog%d -x rextraj%d
Re: [gmx-users] Source Code for Lennard Jones Interaction
On 1/02/2011 9:04 AM, Apoorv Kalyankar wrote: Hello, I was wondering where can I find the source code for the Lennard Jones interaction (both simple cut-off and shifted cut-off) implemented in GROMACS 3.3. There is no single routine in that version or any other. Look at src/gmxlib/nonbonded/nb_generic.c in 4.5.3 for clues on how things work. 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] extending a simulation
Dear gmx-users, In order to extend my simulations, i am using grompp in the following fashion: grompp -np 8 -t amphiphilic_512dppc_50ns -c amphiphilic_512dppc_50ns -e amphiphilic_512dppc_50ns -f 850ns.mdp -p dppc.top -o amphiphilic_512dppc_900ns followed by mdrun mpiexec -np 8 mdrun_mpi.openmpi -np 8 -s amphiphilic_512dppc_900ns -o amphiphilic_512dppc_900ns -e amphiphilic_512dppc_900ns -g amphiphilic_512dppc_900ns I am using gromacs 3.3.3 and the reason for using grompp for extension is because i wanted to change nxtxout, nxtvout, values from the previous file. my question is when using grompp in the above fashion i get this message: Checking consistency between energy and charge groups... getting data from old trajectory ... Reading Coordinates, Velocities and Box size from old trajectory Will read whole trajectory trn version: GMX_trn_file (single precision) Reading frame1700 time 51000.000 Using frame at t = 51000 ps Starting time for run is 51000 ps Opened ampiphilic_512dppc_50ns.edr as single precision energy file Reading frame 1700 time 51000.000 READ 3 PRESSURE COUPLING MU'S FROM ampiphilic_512dppc_50ns.edr writing run input file... here does single precision imply that grompp is not using double precesion data even though the input file .trr is full precision file if so is it possible to use full precision for extension of trajectory. -Thanks and Regards, Adwait. This message was sent using IMP, the Internet Messaging Program. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] General MD question
Hi Stephan, On Jan 31, 2011, at 5:18 PM, lloyd riggs wrote: Dear All, A quick question as I have not really delved into code for gromacs ever, nor know anyone close whom has worked on it. If I set up an MD simulation using a 4 protein complex, and 1 small peptide, plus waters, etc...and run the whole thing the proteins never move, only the amino acids within(constant temp RT and pressure 1 bar). Two domains make one complex, and another two the other. Basically, if I seperate the domains say 5, 10, 15 angstrom, etc...the amino acids will drift (the chains) towards each other, but the two large (global) protein units never move their center (I know I can make it work with Pull vectors, but why not in the simple system with a generated initial randomized velocities), I woundered why they are fixed in a normal run with minimal parameters? Is there a reason (specific to developers), historical reason, or other? As waters move around fine, and anything else added (salt, small molecules of 20-30 atoms, water) except the central molecule(s) of interest. In a 'normal' run they should not be fixed. Could it be that you did accidentally fix them by specifying center of mass removal (comm-grps in .mdp)? Carsten Grüsse Stephan Watkins -- Neu: GMX De-Mail - Einfach wie E-Mail, sicher wie ein Brief! Jetzt De-Mail-Adresse reservieren: http://portal.gmx.net/de/go/demail -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: RE : essential dynamics
Hi Bharat, On Tue, Feb 1, 2011 at 8:33 AM, bharat gupta bharat.85.m...@gmail.com wrote: Hi, After searching though gmxuserlist I found the relevant thread for ED... I followed the following steps :- What thread are you referring to? 1) g_covar - to generate a covariance matrix and diagonalize it (for c-alpha atoms only) 2) g_anaeig - to generate eigen vectors g_covar calculates the eigenvectors. It's what you end up with through diagonalization. 3)g_rmsf - for calculating RMSD of first 8 eigen vectors , I got an error at this step that - g_rmsf is not for calculating RMSD, and hasn't got much to do with eigenvector analysis. That's what g_anaeig is for (like with the option -rmsf). Using g_anaeig will avoid the error you observe. As a side note, 3 ns is rather short for this sort of thing. You have to check the cosine content of the first principal components to see if you've reached equilibrium already. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] 4.5.3 Installation under Cygwin
Thanks for the response. I tried building gromacs using cmake and the procedure from the wiki. Are there custom flags that I have to pass to cmake for it to work under cygwin? The cmake procedure seems to run fine without any errors, but I cannot evoke any gromacs tool following installation. I get the error: $ g_energy -h /usr/local/gromacs/bin/g_energy.exe: error while loading shared libraries: cyggmxana-6.dll: cannot open shared object file: No such file or directory I found info on the mailing list related to the absence of DLLs, but the fix seemed to be applied to version 3.3.3 http://lists.gromacs.org/pipermail/gmx-users/2009-May/042204.html Is there something I am missing? Thanks, Mike On Jan 31 2011, Mark Abraham wrote: On 01/31/11, toma0...@umn.edu wrote: Hello, I am trying to install gromacs 4.5.3 on my desktop under Cygwin. Using the installation procedure from the Wiki: (http://www.gromacs.org/Downloads/Installation_Instructions/Cygwin_HOWTO Install fftw-3.2.2 with ./configure --enable-sse --enable-float make make install Then install gromacs with: ./configure --enable-shared LDFLAGS='-L/usr/local/lib' make The installation fails here with many errors not being able to find libraries associated with fftw tracing back to this error: *** Warning: This system can not link to static lib archive /usr/local/lib/libfftw3f.la. *** I have the capability to make that library automatically link in when *** you link to this library. But I can only do this if you have a *** shared version of the library, which you do not appear to have. The installation procedure from the Wiki works fine with gromacs-4.0.7. This error only occurs with the 4.5 series. Are there different default settings for where gromacs looks for fftw between 4.0.7 and 4.5.3? Any help would be appreciated. I ran into the same issue a while back. I don't know what causes it. I found that using a CMake-based build on Cygwin worked. 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] General MD question
Hi Stephan, It all a matter of time scale. Large molecules == slower movements (compare trucks and motor-bikes). Cheers, Itamar. On 1 February 2011 03:18, lloyd riggs lloyd.ri...@gmx.ch wrote: Dear All, A quick question as I have not really delved into code for gromacs ever, nor know anyone close whom has worked on it. If I set up an MD simulation using a 4 protein complex, and 1 small peptide, plus waters, etc...and run the whole thing the proteins never move, only the amino acids within(constant temp RT and pressure 1 bar). Two domains make one complex, and another two the other. Basically, if I seperate the domains say 5, 10, 15 angstrom, etc...the amino acids will drift (the chains) towards each other, but the two large (global) protein units never move their center (I know I can make it work with Pull vectors, but why not in the simple system with a generated initial randomized velocities), I woundered why they are fixed in a normal run with minimal parameters? Is there a reason (specific to developers), historical reason, or other? As waters move around fine, and anything else added (salt, small molecules of 20-30 atoms, water) except the central molecule(s) of interest. Grüsse Stephan Watkins -- Neu: GMX De-Mail - Einfach wie E-Mail, sicher wie ein Brief! Jetzt De-Mail-Adresse reservieren: http://portal.gmx.net/de/go/demail -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- -- In theory, there is no difference between theory and practice. But, in practice, there is. - Jan L.A. van de Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victoria 3800 | Australia | | Tel: +61 3 9902 9376 | Fax: +61 3 9902 9500 | E-mail: itamar.k...@monash.edu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: RE : essential dynamics
Thanks for the reply ... I am following this thread - http://oldwww.gromacs.org/pipermail/gmx-users/2004-May/010438.html http://oldwww.gromacs.org/pipermail/gmx-users/2004-May/010438.htmlAlso I read the following paper http://pubs.acs.org/doi/abs/10.1021/jp983120q (Internal dynamics of GFP) in which they have carried out such projections of the eigen vector in order to find the regions showing minimum and maximum amplitudes.. What I am thinking is shall I take those c-alpha atoms that are well stable and equilibrated after referring to RMSD graph generated after simulation ... I am stating here what I have done so far and what I have to analyze :- I exchanged the loops regions of GFP with loops of longer length taken from pdb .. I simulated both the crystal str. and modeled strs. to compare how the loop incorporation leads to the change in the structure of GFP Since the RMSD of the GFP crystal str and that of model are in comparable range .. I thought of looking at the motions of loops in the structure that are giving such fluctuations in RMSD of model and for that I decided to generate eigen vectors and project them in 3d (like the one given in paper mentioned above) to see how that particular loop behaves .. I don't know whether what I have hypothesized is correct or not .. since I am not able to find any other insilico method apart from MDS for such a study .. Also if my prediction comes out to be good enough I have to carry out such insertion in the wet lab and has to check for fluorescence ..any help in this regard will be appreciated... On Tue, Feb 1, 2011 at 1:28 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Bharat, On Tue, Feb 1, 2011 at 8:33 AM, bharat gupta bharat.85.m...@gmail.com wrote: Hi, After searching though gmxuserlist I found the relevant thread for ED... I followed the following steps :- What thread are you referring to? 1) g_covar - to generate a covariance matrix and diagonalize it (for c-alpha atoms only) 2) g_anaeig - to generate eigen vectors g_covar calculates the eigenvectors. It's what you end up with through diagonalization. 3)g_rmsf - for calculating RMSD of first 8 eigen vectors , I got an error at this step that - g_rmsf is not for calculating RMSD, and hasn't got much to do with eigenvector analysis. That's what g_anaeig is for (like with the option -rmsf). Using g_anaeig will avoid the error you observe. As a side note, 3 ns is rather short for this sort of thing. You have to check the cosine content of the first principal components to see if you've reached equilibrium already. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Charge groups
Dear All Suppose I determined partial charges on atoms of my molecules. How can I make charge groups of them? For example I have a drug of 50 atom(of course along with it's hidrogenes), and all of my data for charges are as 1.3465728 (suppose they are accurate and different to eachother) Is it possible to make charge groups with zero net charge? How?How can I learn these? Is there any server to do this for me? Thanks in advance for your guide. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] segmentation fault: g_velacc
Dear All, I am using the gromacs 4.0.7 version and I was trying to calculate the momentum autocorrelation function by using the -m flag. However, I get a segmentation fault as follows: trn version: GMX_trn_file (double precision) Reading frame 0 time0.000 Segmentation fault When I don't use the -m option, I have no problem. Upon searching the userslist, I found this thread: http://lists.gromacs.org/pipermail/gmx-users/2010-October/054813.html and a patch, but I don't find any related bugs reported elsewhere. So, I am just wondering if I sould go ahead and use the patch or if there could be something else that is wrong. Will appreciate any kind of pointers. Sincerely, Vignesh -- R.Vigneshwar Graduate Student, Dept. of Chemical Biomolecular Engg, National University of Singapore, Singapore Strive for Excellence, Never be satisfied with the second Best!! I arise in the morning torn between a desire to improve the world and a desire to enjoy the world. This makes it hard to plan the day. (E.B. White) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] hbond constraint
Denny Frost wrote: Since gromacs allows you to use quite a few different force fields with different naming schemes, how does it know (from reading the topology file) which atoms are hydrogens to enforce the hbond constraints? Atom types are present in [atoms], indicating what all of the constituent atoms are based on force field nomenclature. -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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Charge groups
mohsen ramezanpour wrote: Dear All Suppose I determined partial charges on atoms of my molecules. How can I make charge groups of them? Look for similar groups in the force field you're using, and refer to the Gromacs manual, section 4.6.2. For example I have a drug of 50 atom(of course along with it's hidrogenes), and all of my data for charges are as 1.3465728 (suppose they are accurate and different to eachother) Sounds like a wildly inappropriate total charge. Is it possible to make charge groups with zero net charge? How?How can I learn these? Is there any server to do this for me? Thanks in advance for your guide. Refer to the documentation of whatever program you're using to do these calculations. Force field parameterization is hard; don't expect immediate success. Even if you can get sensible charges, they still may not be sufficiently accurate within the guidelines of the chosen force field after you've done whatever validation is required. -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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] segmentation fault: g_velacc
Vigneshwar Ramakrishnan wrote: Dear All, I am using the gromacs 4.0.7 version and I was trying to calculate the momentum autocorrelation function by using the -m flag. However, I get a segmentation fault as follows: trn version: GMX_trn_file (double precision) Reading frame 0 time0.000 Segmentation fault When I don't use the -m option, I have no problem. Upon searching the userslist, I found this thread: http://lists.gromacs.org/pipermail/gmx-users/2010-October/054813.html and a patch, but I don't find any related bugs reported elsewhere. So, I am just wondering if I sould go ahead and use the patch or if there could be something else that is wrong. Will appreciate any kind of pointers. Either apply the patch or upgrade to a newer version of Gromacs that contains this bug fix. -Justin Sincerely, Vignesh -- R.Vigneshwar Graduate Student, Dept. of Chemical Biomolecular Engg, National University of Singapore, Singapore Strive for Excellence, Never be satisfied with the second Best!! I arise in the morning torn between a desire to improve the world and a desire to enjoy the world. This makes it hard to plan the day. (E.B. White) -- 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] segmentation fault: g_velacc
Hi, apparently this bug fix made it to 4.5, but not to 4.0. I will apply the fix also there. Carsten On Feb 1, 2011, at 1:58 PM, Justin A. Lemkul wrote: Vigneshwar Ramakrishnan wrote: Dear All, I am using the gromacs 4.0.7 version and I was trying to calculate the momentum autocorrelation function by using the -m flag. However, I get a segmentation fault as follows: trn version: GMX_trn_file (double precision) Reading frame 0 time0.000 Segmentation fault When I don't use the -m option, I have no problem. Upon searching the userslist, I found this thread: http://lists.gromacs.org/pipermail/gmx-users/2010-October/054813.html and a patch, but I don't find any related bugs reported elsewhere. So, I am just wondering if I sould go ahead and use the patch or if there could be something else that is wrong. Will appreciate any kind of pointers. Either apply the patch or upgrade to a newer version of Gromacs that contains this bug fix. -Justin Sincerely, Vignesh -- R.Vigneshwar Graduate Student, Dept. of Chemical Biomolecular Engg, National University of Singapore, Singapore Strive for Excellence, Never be satisfied with the second Best!! I arise in the morning torn between a desire to improve the world and a desire to enjoy the world. This makes it hard to plan the day. (E.B. White) -- 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] extending a simulation
On 1/02/2011 8:27 PM, Adwait Mevada wrote: Dear gmx-users, In order to extend my simulations, i am using grompp in the following fashion: grompp -np 8 -t amphiphilic_512dppc_50ns -c amphiphilic_512dppc_50ns -e amphiphilic_512dppc_50ns -f 850ns.mdp -p dppc.top -o amphiphilic_512dppc_900ns followed by mdrun mpiexec -np 8 mdrun_mpi.openmpi -np 8 -s amphiphilic_512dppc_900ns -o amphiphilic_512dppc_900ns -e amphiphilic_512dppc_900ns -g amphiphilic_512dppc_900ns I am using gromacs 3.3.3 and the reason for using grompp for extension is because i wanted to change nxtxout, nxtvout, values from the previous file. my question is when using grompp in the above fashion i get this message: Checking consistency between energy and charge groups... getting data from old trajectory ... Reading Coordinates, Velocities and Box size from old trajectory Will read whole trajectory trn version: GMX_trn_file (single precision) Reading frame1700 time 51000.000 Using frame at t = 51000 ps Starting time for run is 51000 ps Opened ampiphilic_512dppc_50ns.edr as single precision energy file Reading frame 1700 time 51000.000 READ 3 PRESSURE COUPLING MU'S FROM ampiphilic_512dppc_50ns.edr writing run input file... here does single precision imply that grompp is not using double precesion Yes. data even though the input file .trr is full precision file Full precision could be single or double. if so is it possible to use full precision for extension of trajectory. You are doing so. 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] segmentation fault: g_velacc
Hi Vigneshwar, the problem is fixed now in the release-4-0-patches branch. Carsten On Feb 1, 2011, at 2:00 PM, Carsten Kutzner wrote: Hi, apparently this bug fix made it to 4.5, but not to 4.0. I will apply the fix also there. Carsten On Feb 1, 2011, at 1:58 PM, Justin A. Lemkul wrote: Vigneshwar Ramakrishnan wrote: Dear All, I am using the gromacs 4.0.7 version and I was trying to calculate the momentum autocorrelation function by using the -m flag. However, I get a segmentation fault as follows: trn version: GMX_trn_file (double precision) Reading frame 0 time0.000 Segmentation fault When I don't use the -m option, I have no problem. Upon searching the userslist, I found this thread: http://lists.gromacs.org/pipermail/gmx-users/2010-October/054813.html and a patch, but I don't find any related bugs reported elsewhere. So, I am just wondering if I sould go ahead and use the patch or if there could be something else that is wrong. Will appreciate any kind of pointers. Either apply the patch or upgrade to a newer version of Gromacs that contains this bug fix. -Justin Sincerely, Vignesh -- R.Vigneshwar Graduate Student, Dept. of Chemical Biomolecular Engg, National University of Singapore, Singapore Strive for Excellence, Never be satisfied with the second Best!! I arise in the morning torn between a desire to improve the world and a desire to enjoy the world. This makes it hard to plan the day. (E.B. White) -- 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] mdrun with append option
Thanks Mark. So if the simulation doesn't start from the checkpoint file, from where are the initial coordinates velocities etc. taken from?... the trajectory files? Also, I could not find the environment variable... and I am not sure how to use one. Pooja On Tue, Feb 1, 2011 at 3:03 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 1/02/2011 7:50 AM, Sai Pooja wrote: I think I have figured out the reason. It is because I am carrying out replica exchange (manual) after every mdrun. If the exchange occurs, I exchange the checkpoint files, extend the simulation by 500 steps and continue. The new simulation starts from exchanged cptfile. It seems that whenever the exchange occurs, the earlier log,traj files are not appended. They are instead overwritten. the obv solution is to save and index these files with the relevant replicas everytime an exchange occurs. This would have been good to know earlier. If replica-exchange leads to the ensemble of the .tpr not matching the ensemble of the .cpt, then IIRC 4.5.3 mdrun will refuse to start from the .cpt, which means the subsequent mdrun will start from the .tpr only. Certainly a non-appending mdrun prints a warning (or error, I forget which) message to the log file, but perhaps the use of -append (erroneously) doesn't do that. Please have a look and see if that is the issue. There is an environment variable that can be set to tell mdrun that you (think you) know what you are doing mismatching .tpr and .cpt. Mark However, i have a more general question. Since mdrun still runs with the exchanged checkpoint files and starts from the point where the previous run ended, can I be assured that an exchange has been affected - since tpr files correspond to the replica-box and cpi to the most recent exchanged replicas? Pooja On Mon, Jan 31, 2011 at 2:33 PM, Sai Pooja saipo...@gmail.com wrote: I manually index checkpoint files after every mdrun. What troubles me is the randomness with which -append fails/works. For eg, I have a simulation which runs from 3ns, 1ps in 1 mdrun. Now oddly enough, the logfile starts from 1184ps(in the end, I do remember the one starting from 0 but that was overwritten it seems) and the rest is appended uptil the 3000ps step. Why would append work from 1184ps to 3000ps but not for the previous ones?Could it have anything to do with the network/cluster? If that is the case is it safer to create a new file everytime and then concatenate them after say every 100ps? Pooja On Sat, Jan 29, 2011 at 6:52 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 30/01/2011 10:39 AM, Sai Pooja wrote: I would be happy to supply more information.. if someone could please look into this.. otherwise I will have to switch to storing every file and then just concatenating them which seems like a rather roundabout way of doing it. As I suggested a few emails ago, are you sure that -cpi file exists? If your numerical suffixes are indexing restarts, then unless you've done some manual copying that you haven't told us about, it won't. Your filename scheme seems a bit contorted - like you're trying to do the work that GROMACS 4.5.x will just do for you if you let it. Otherwise, you'll have to do some detective work with gmxcheck on the -cpi to see what might be the issue. In your case, an initial mdrun -deffnm rex_3 (perhaps save some copies while you're experimenting) and subsequently tpbconv -extend blah -f rex_3 -o rex_3 mdrun -deffnm rex_3 -append will work and be much simpler than whatever you're trying to do with filenames :-) Mark On Fri, Jan 28, 2011 at 4:37 PM, Sai Pooja saipo...@gmail.com wrote: This is the command: nbs submit -command (/usr/local/gromacs/4.5.1/bin/mdrun_mpi -s rex_3.tpr -e rex_3 -c after_rex_3 -cpi restart3 -cpo restart3 -ap pend -g rexlog3 -x rextraj3); -nproc 1 -name GENHAM-DIHEDRAL-3 -mail start end Pooja On Fri, Jan 28, 2011 at 4:20 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 29/01/2011 3:56 AM, Sai Pooja wrote: Hi, I am using tpbconv and mdrun to extend a simulation. I use it with the append option but the files still get overwritten or erased. Can someone help me in this regard? Pooja Commands (in python) cmd = '(%s/tpbconv -extend %f -s rex_%d.tpr -o rex_%d.tpr)' %(GROMPATH,dtstep,i,i) os.system(cmd) time.sleep(1) cmd = 'nbs submit -command ' cmd += '(%s/mdrun_mpi -noh -noversion -s rex_%d.tpr -e rex_%d -c after_rex_%d -cpi restart%d -cpo restart%d -append -g rexlog%d -x rextraj%d /dev/null); ' %(GROMPATH,i,i,i,i,i,i,i) cmd += ' ' cmd += '-nproc 1 ' cmd += '-name GENHAM-DIHEDRAL-%d '%(i) cmd += '-mail start end ' cmd += '-elapsed_limit 16h rexid' os.system(cmd) More useful for diagnostic and record-preservation purposes is to construct the cmd string and print it to stdout (or something). At the moment it is far from clear that your -cpi file
Re: [gmx-users] mdrun with append option
From the website: If you change the integrator or ensemble, you should pass the checkpoint file to tpbconv only, not to mdrun, since the state might change and thus output files can not be appended. So now instead of supplying the checkpoint file to mdrun I supply it to tpbconv... does this assure that the simulations start from the coordinates/velocities specified by the .cpt file? Pooja On Tue, Feb 1, 2011 at 11:20 AM, Sai Pooja saipo...@gmail.com wrote: Thanks Mark. So if the simulation doesn't start from the checkpoint file, from where are the initial coordinates velocities etc. taken from?... the trajectory files? Also, I could not find the environment variable... and I am not sure how to use one. Pooja On Tue, Feb 1, 2011 at 3:03 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 1/02/2011 7:50 AM, Sai Pooja wrote: I think I have figured out the reason. It is because I am carrying out replica exchange (manual) after every mdrun. If the exchange occurs, I exchange the checkpoint files, extend the simulation by 500 steps and continue. The new simulation starts from exchanged cptfile. It seems that whenever the exchange occurs, the earlier log,traj files are not appended. They are instead overwritten. the obv solution is to save and index these files with the relevant replicas everytime an exchange occurs. This would have been good to know earlier. If replica-exchange leads to the ensemble of the .tpr not matching the ensemble of the .cpt, then IIRC 4.5.3 mdrun will refuse to start from the .cpt, which means the subsequent mdrun will start from the .tpr only. Certainly a non-appending mdrun prints a warning (or error, I forget which) message to the log file, but perhaps the use of -append (erroneously) doesn't do that. Please have a look and see if that is the issue. There is an environment variable that can be set to tell mdrun that you (think you) know what you are doing mismatching .tpr and .cpt. Mark However, i have a more general question. Since mdrun still runs with the exchanged checkpoint files and starts from the point where the previous run ended, can I be assured that an exchange has been affected - since tpr files correspond to the replica-box and cpi to the most recent exchanged replicas? Pooja On Mon, Jan 31, 2011 at 2:33 PM, Sai Pooja saipo...@gmail.com wrote: I manually index checkpoint files after every mdrun. What troubles me is the randomness with which -append fails/works. For eg, I have a simulation which runs from 3ns, 1ps in 1 mdrun. Now oddly enough, the logfile starts from 1184ps(in the end, I do remember the one starting from 0 but that was overwritten it seems) and the rest is appended uptil the 3000ps step. Why would append work from 1184ps to 3000ps but not for the previous ones?Could it have anything to do with the network/cluster? If that is the case is it safer to create a new file everytime and then concatenate them after say every 100ps? Pooja On Sat, Jan 29, 2011 at 6:52 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 30/01/2011 10:39 AM, Sai Pooja wrote: I would be happy to supply more information.. if someone could please look into this.. otherwise I will have to switch to storing every file and then just concatenating them which seems like a rather roundabout way of doing it. As I suggested a few emails ago, are you sure that -cpi file exists? If your numerical suffixes are indexing restarts, then unless you've done some manual copying that you haven't told us about, it won't. Your filename scheme seems a bit contorted - like you're trying to do the work that GROMACS 4.5.x will just do for you if you let it. Otherwise, you'll have to do some detective work with gmxcheck on the -cpi to see what might be the issue. In your case, an initial mdrun -deffnm rex_3 (perhaps save some copies while you're experimenting) and subsequently tpbconv -extend blah -f rex_3 -o rex_3 mdrun -deffnm rex_3 -append will work and be much simpler than whatever you're trying to do with filenames :-) Mark On Fri, Jan 28, 2011 at 4:37 PM, Sai Pooja saipo...@gmail.com wrote: This is the command: nbs submit -command (/usr/local/gromacs/4.5.1/bin/mdrun_mpi -s rex_3.tpr -e rex_3 -c after_rex_3 -cpi restart3 -cpo restart3 -ap pend -g rexlog3 -x rextraj3); -nproc 1 -name GENHAM-DIHEDRAL-3 -mail start end Pooja On Fri, Jan 28, 2011 at 4:20 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 29/01/2011 3:56 AM, Sai Pooja wrote: Hi, I am using tpbconv and mdrun to extend a simulation. I use it with the append option but the files still get overwritten or erased. Can someone help me in this regard? Pooja Commands (in python) cmd = '(%s/tpbconv -extend %f -s rex_%d.tpr -o rex_%d.tpr)' %(GROMPATH,dtstep,i,i) os.system(cmd) time.sleep(1) cmd = 'nbs submit -command ' cmd += '(%s/mdrun_mpi -noh -noversion -s rex_%d.tpr -e rex_%d -c after_rex_%d
Re: [gmx-users] mdrun with append option
Sai Pooja wrote: From the website: If you change the integrator or ensemble, you should pass the checkpoint file to tpbconv only, not to mdrun, since the state might change and thus output files can not be appended. Are you changing the integrator, ensemble, and/or other settings? If not, this statement does not apply. For a simple -append after extending via tpbconv, this is not applicable. So now instead of supplying the checkpoint file to mdrun I supply it to tpbconv... does this assure that the simulations start from the coordinates/velocities specified by the .cpt file? For a simple extension, you do not pass the .cpt file to tpbconv. http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Version_4 Thanks Mark. So if the simulation doesn't start from the checkpoint file, from where are the initial coordinates velocities etc. taken from?... the trajectory files? Mark's previous message already answered this. -Justin Also, I could not find the environment variable... and I am not sure how to use one. Pooja On Tue, Feb 1, 2011 at 3:03 AM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 1/02/2011 7:50 AM, Sai Pooja wrote: I think I have figured out the reason. It is because I am carrying out replica exchange (manual) after every mdrun. If the exchange occurs, I exchange the checkpoint files, extend the simulation by 500 steps and continue. The new simulation starts from exchanged cptfile. It seems that whenever the exchange occurs, the earlier log,traj files are not appended. They are instead overwritten. the obv solution is to save and index these files with the relevant replicas everytime an exchange occurs. This would have been good to know earlier. If replica-exchange leads to the ensemble of the .tpr not matching the ensemble of the .cpt, then IIRC 4.5.3 mdrun will refuse to start from the .cpt, which means the subsequent mdrun will start from the .tpr only. Certainly a non-appending mdrun prints a warning (or error, I forget which) message to the log file, but perhaps the use of -append (erroneously) doesn't do that. Please have a look and see if that is the issue. There is an environment variable that can be set to tell mdrun that you (think you) know what you are doing mismatching .tpr and .cpt. Mark However, i have a more general question. Since mdrun still runs with the exchanged checkpoint files and starts from the point where the previous run ended, can I be assured that an exchange has been affected - since tpr files correspond to the replica-box and cpi to the most recent exchanged replicas? Pooja On Mon, Jan 31, 2011 at 2:33 PM, Sai Pooja saipo...@gmail.com mailto:saipo...@gmail.com wrote: I manually index checkpoint files after every mdrun. What troubles me is the randomness with which -append fails/works. For eg, I have a simulation which runs from 3ns, 1ps in 1 mdrun. Now oddly enough, the logfile starts from 1184ps(in the end, I do remember the one starting from 0 but that was overwritten it seems) and the rest is appended uptil the 3000ps step. Why would append work from 1184ps to 3000ps but not for the previous ones?Could it have anything to do with the network/cluster? If that is the case is it safer to create a new file everytime and then concatenate them after say every 100ps? Pooja On Sat, Jan 29, 2011 at 6:52 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 30/01/2011 10:39 AM, Sai Pooja wrote: I would be happy to supply more information.. if someone could please look into this.. otherwise I will have to switch to storing every file and then just concatenating them which seems like a rather roundabout way of doing it. As I suggested a few emails ago, are you sure that -cpi file exists? If your numerical suffixes are indexing restarts, then unless you've done some manual copying that you haven't told us about, it won't. Your filename scheme seems a bit contorted - like you're trying to do the work that GROMACS 4.5.x will just do for you if you let it. Otherwise, you'll have to do some detective work with gmxcheck on the -cpi to see what might be the issue. In your case, an initial mdrun -deffnm rex_3
[gmx-users] g_velacc
Hello, I am trying to calculate the Velocity Autocorrelation Function for my system using g_velacc. I have system of 128 ionic liquids (128 cations and 128 anions). I run the trajectory for 20 ns. I used following command . g_velacc -f 3.trr -n emi-etso4-127-no.ndx -s 3.tpr -o I selected system The output file, vac.xvg, have no data. Can any one tell why its not wirting. Thanks Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] mdrun with append option
I am doing a manual replica exchange(generalized hamiltonian rem) after every mdrun. If the replica exchange is successful, then I exchange checkpoint files. For example, consider the following: Simulation parameters:B1.B2 Replicas(coordinates and velocities):.R1.R2 0. Tpbconv to extend simulation time ( using -s, -o and -nsteps ONLY) 1. Mdrun run - 500 steps = 1ps 2. Attempt exchange - NOT SUCCESSFUL 3. Exchange implementation: SKIP 4.Continue to next step . 0. Tpbconv to extend simulation time ( using -s, -o and -nsteps ONLY) 1. Mdrun run - 500 steps = 1ps 2. Attempt exchange - If successful, exchange 3. Exchange Implemented by - exchanging checkpointing files 4. Continue to next step 0. Tpbconv to extend simulation time ( using -s, -o and -nsteps ONLY) 1. Mdrun with exchanged .cpt files -NOW this is where the problem shows.. i) The log, xtc files are not appended when beginning after a step with a successful exchange attempt:*According to Mark's previous mail, this could be a result of mismatch in ensembles. Which means that the .cpt is ignored - implying that the mdrun in B1 DOES NOT start from R2.* Therefore, to make R1 run in B2 and R2 run in B1, do I need to supply .cpt to tpbconv instead of mdrun after a successful exchange step? To summarize: APPENDING HAS NOW BECOME A SECONDARY CONCERN, WHAT I AM INTERESTED IN IS A SUCCESSFUL MANUAL REPLICA EXCHANGE RUN AS POINTED OUT ABOVE. I hope my dilemma is clear now. Pooja On Tue, Feb 1, 2011 at 11:42 AM, Justin A. Lemkul jalem...@vt.edu wrote: Sai Pooja wrote: From the website: If you change the integrator or ensemble, you should pass the checkpoint file to tpbconv only, not to mdrun, since the state might change and thus output files can not be appended. Are you changing the integrator, ensemble, and/or other settings? If not, this statement does not apply. For a simple -append after extending via tpbconv, this is not applicable. So now instead of supplying the checkpoint file to mdrun I supply it to tpbconv... does this assure that the simulations start from the coordinates/velocities specified by the .cpt file? For a simple extension, you do not pass the .cpt file to tpbconv. http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Version_4 Thanks Mark. So if the simulation doesn't start from the checkpoint file, from where are the initial coordinates velocities etc. taken from?... the trajectory files? Mark's previous message already answered this. -Justin Also, I could not find the environment variable... and I am not sure how to use one. Pooja On Tue, Feb 1, 2011 at 3:03 AM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 1/02/2011 7:50 AM, Sai Pooja wrote: I think I have figured out the reason. It is because I am carrying out replica exchange (manual) after every mdrun. If the exchange occurs, I exchange the checkpoint files, extend the simulation by 500 steps and continue. The new simulation starts from exchanged cptfile. It seems that whenever the exchange occurs, the earlier log,traj files are not appended. They are instead overwritten. the obv solution is to save and index these files with the relevant replicas everytime an exchange occurs. This would have been good to know earlier. If replica-exchange leads to the ensemble of the .tpr not matching the ensemble of the .cpt, then IIRC 4.5.3 mdrun will refuse to start from the .cpt, which means the subsequent mdrun will start from the .tpr only. Certainly a non-appending mdrun prints a warning (or error, I forget which) message to the log file, but perhaps the use of -append (erroneously) doesn't do that. Please have a look and see if that is the issue. There is an environment variable that can be set to tell mdrun that you (think you) know what you are doing mismatching .tpr and .cpt. Mark However, i have a more general question. Since mdrun still runs with the exchanged checkpoint files and starts from the point where the previous run ended, can I be assured that an exchange has been affected - since tpr files correspond to the replica-box and cpi to the most recent exchanged replicas? Pooja On Mon, Jan 31, 2011 at 2:33 PM, Sai Pooja saipo...@gmail.com mailto:saipo...@gmail.com wrote: I manually index checkpoint files after every mdrun. What troubles me is the randomness with which -append fails/works. For eg, I have a simulation which runs from 3ns, 1ps in 1 mdrun. Now oddly enough, the logfile starts from 1184ps(in the end, I do remember the one starting from 0 but that was
[gmx-users] angle constrain, constrained PF6 anion
Dear all, I am setting up a simulation of ionic liquids with the PF6 anion. According to the potential, the anion should be kept rigid, wich obviously means that bond lengths and angles have to be constrained. LINCS doesn't work with angle constraints (i.e. constraing a triangle), so we decided to use SHAKE. However, SHAKE seems to work a bit strangely: I know SHAKE mustn't be used with domain decomposition, but even if I set the corresponding variable to NO in the mdp file, the simulation crashes on 8 procs and gives the following error message: Fatal error: 1 particles communicated to PME node 7 are more than a cell length out of the domain decomposition cell of their charge group. If I try to run mdrun with -pd (to 'really' switch off domain decomposition), the simulation doesn't chrash but gives nonsense (the energy seems to increase constantly). I am not an expert user so maybe I do something wrong but, anyway, does anyone have an idea how to constrain this anion with Gromacs? I checked mailing list archive but couldn't find any answer corresponding to my question. Thanks in advance. Gyorgy -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] angle constrain, constrained PF6 anion
gyorgy.han...@fc.up.pt wrote: Dear all, I am setting up a simulation of ionic liquids with the PF6 anion. According to the potential, the anion should be kept rigid, wich obviously means that bond lengths and angles have to be constrained. LINCS doesn't work with angle constraints (i.e. constraing a triangle), so we decided to use SHAKE. However, SHAKE seems to work a bit strangely: I know SHAKE mustn't be used with domain decomposition, but even if I set the corresponding variable to NO in the mdp file, the simulation crashes on 8 procs and gives the following error message: Fatal error: 1 particles communicated to PME node 7 are more than a cell length out of the domain decomposition cell of their charge group. If I try to run mdrun with -pd (to 'really' switch off domain decomposition), the simulation doesn't chrash but gives nonsense (the energy seems to increase constantly). I am not an expert user so maybe I do something wrong but, anyway, does anyone have an idea how to constrain this anion with Gromacs? I checked mailing list archive but couldn't find any answer corresponding to my question. Without seeing a complete .mdp file, it's not possible to fully diagnose this problem. The combination of SHAKE + particle decomposition should be stable, but there are a whole host of different things that can go wrong. -Justin Thanks in advance. Gyorgy -- 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] mdrun with append option
Sai Pooja wrote: I am doing a manual replica exchange(generalized hamiltonian rem) after every mdrun. If the replica exchange is successful, then I exchange checkpoint files. For example, consider the following: Simulation parameters:B1.B2 Replicas(coordinates and velocities):.R1.R2 0. Tpbconv to extend simulation time ( using -s, -o and -nsteps ONLY) 1. Mdrun run - 500 steps = 1ps 2. Attempt exchange - NOT SUCCESSFUL 3. Exchange implementation: SKIP 4.Continue to next step . 0. Tpbconv to extend simulation time ( using -s, -o and -nsteps ONLY) 1. Mdrun run - 500 steps = 1ps 2. Attempt exchange - If successful, exchange 3. Exchange Implemented by - exchanging checkpointing files 4. Continue to next step 0. Tpbconv to extend simulation time ( using -s, -o and -nsteps ONLY) 1. Mdrun with exchanged .cpt files -NOW this is where the problem shows.. i) The log, xtc files are not appended when beginning after a step with a successful exchange attempt:/According to Mark's previous mail, this could be a result of mismatch in ensembles. Which means that the .cpt is ignored - implying that the mdrun in B1 DOES NOT start from R2./ Sounds like a reasonable conclusion. Therefore, to make R1 run in B2 and R2 run in B1, do I need to supply .cpt to tpbconv instead of mdrun after a successful exchange step? Either tpbconv or grompp can do this. Check the resulting .tpr with gmxdump to make sure it's using the proper coordinates, velocities, etc from the .cpt file and you'll have your answer as to whether or not it's working as you want. -Justin To summarize: APPENDING HAS NOW BECOME A SECONDARY CONCERN, WHAT I AM INTERESTED IN IS A SUCCESSFUL MANUAL REPLICA EXCHANGE RUN AS POINTED OUT ABOVE. I hope my dilemma is clear now. Pooja On Tue, Feb 1, 2011 at 11:42 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Sai Pooja wrote: From the website: If you change the integrator or ensemble, you should pass the checkpoint file to tpbconv only, not to mdrun, since the state might change and thus output files can not be appended. Are you changing the integrator, ensemble, and/or other settings? If not, this statement does not apply. For a simple -append after extending via tpbconv, this is not applicable. So now instead of supplying the checkpoint file to mdrun I supply it to tpbconv... does this assure that the simulations start from the coordinates/velocities specified by the .cpt file? For a simple extension, you do not pass the .cpt file to tpbconv. http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Version_4 Thanks Mark. So if the simulation doesn't start from the checkpoint file, from where are the initial coordinates velocities etc. taken from?... the trajectory files? Mark's previous message already answered this. -Justin Also, I could not find the environment variable... and I am not sure how to use one. Pooja On Tue, Feb 1, 2011 at 3:03 AM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 1/02/2011 7:50 AM, Sai Pooja wrote: I think I have figured out the reason. It is because I am carrying out replica exchange (manual) after every mdrun. If the exchange occurs, I exchange the checkpoint files, extend the simulation by 500 steps and continue. The new simulation starts from exchanged cptfile. It seems that whenever the exchange occurs, the earlier log,traj files are not appended. They are instead overwritten. the obv solution is to save and index these files with the relevant replicas everytime an exchange occurs. This would have been good to know earlier. If replica-exchange leads to the ensemble of the .tpr not matching the ensemble of the .cpt, then IIRC 4.5.3 mdrun will refuse to start from the .cpt, which means the subsequent mdrun will start from the .tpr only. Certainly a non-appending mdrun prints a warning (or error, I forget which) message to the log file, but perhaps the use of -append (erroneously) doesn't do that. Please have a look and see if that is the issue. There is an environment variable that can be set to tell mdrun that you (think you) know what you are doing
Re: [gmx-users] luck
Mr Bernard Ramos wrote: Hi! I am actually following your lysozyme tutorial. I ve been using different pdb files including that of water, methanol, 1AKI, etc. The pdb2gmx does not generate any topology file. No files are generated and I get this error: -- pdb2gmx, VERSION 4.5.3 Source code file: futil.c, line:491 File input/output 1AKI.pdb For more etc -- Then this file doesn't exist in the working directory. What is the command you're issuing (exact copy and paste from the terminal, please)? What are the contents of the working directory? -Justin --- On *Mon, 1/31/11, Mr Bernard Ramos /bgrquan...@yahoo.com/* wrote: From: Mr Bernard Ramos bgrquan...@yahoo.com Subject: Re: [gmx-users] luck To: jalem...@vt.edu, Discussion list for GROMACS users gmx-users@gromacs.org Date: Monday, January 31, 2011, 1:14 PM thanks. Here is the error i mentioned a while back with using pdb2gmx: -- File input/output error: filename.pdb For more information, visit -- thanks for the time --- On *Mon, 1/31/11, Justin A. Lemkul /jalem...@vt.edu/* wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] luck To: Gromacs Users' List gmx-users@gromacs.org Date: Monday, January 31, 2011, 12:33 PM Mr Bernard Ramos wrote: Do I need to type in g_luck instead? Typing an email and waiting for a response takes far more time and effort than simply trying it yourself ;) -Justin --- On *Mon, 1/31/11, Justin A. Lemkul /jalem...@vt.edu http://us.mc527.mail.yahoo.com/mc/compose?to=jalem...@vt.edu/* wrote: From: Justin A. Lemkul jalem...@vt.edu http://us.mc527.mail.yahoo.com/mc/compose?to=jalem...@vt.edu Subject: Re: [gmx-users] luck To: Discussion list for GROMACS users gmx-users@gromacs.org http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org Date: Monday, January 31, 2011, 12:11 PM Mr Bernard Ramos wrote: Hi everyone! I have two questions. 1. after I installed gromacs 4.5.3 and which mdrun was able to give the correct path, I was not able to run luck. Instead, luck gives an error command not found. Is this ok? What went wrong? Do I need to install again gromacs? The program is now called g_luck. 2. I tried doing pdb2gmx. The error points the structure file *.pdb as the error. Does this in dicate that the program was not installed properly or there is an error with the pdb file. If the program has given you a fatal error, then the program is correctly installed and working. It is your input that is somehow wrong. Without the actual error message, it's impossible to say what's wrong. -Justin Thanks -- 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://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT
Re: [gmx-users] luck
Mr Bernard Ramos wrote: this is the command i am using: pbd2gmx -f 1AKI.pdb -o 1AKI_processed.gro -water spce then I choose a force fileld. then I get the error and no new files generated at all. My working directory is: /cygdrive/c/MDProgram/Gromacs453/bin/molecule tests I assume that .../Gromacs453/bin is the location where the Gromacs binaries are installed? It's a bad idea to run commands from the location of the installation or its subdirectories. It's also a possibility that the space in molecule tests is causing problems with filename parsing, but that's a bit of a guess. Move the necessary files to a new location, in a directory named without spaces, and try again. -Justin --- On *Wed, 2/2/11, Justin A. Lemkul /jalem...@vt.edu/* wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] luck To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Wednesday, February 2, 2011, 2:15 AM Mr Bernard Ramos wrote: Hi! I am actually following your lysozyme tutorial. I ve been using different pdb files including that of water, methanol, 1AKI, etc. The pdb2gmx does not generate any topology file. No files are generated and I get this error: -- pdb2gmx, VERSION 4.5.3 Source code file: futil.c, line:491 File input/output 1AKI.pdb For more etc -- Then this file doesn't exist in the working directory. What is the command you're issuing (exact copy and paste from the terminal, please)? What are the contents of the working directory? -Justin --- On *Mon, 1/31/11, Mr Bernard Ramos /bgrquan...@yahoo.com http://us.mc527.mail.yahoo.com/mc/compose?to=bgrquan...@yahoo.com/* wrote: From: Mr Bernard Ramos bgrquan...@yahoo.com http://us.mc527.mail.yahoo.com/mc/compose?to=bgrquan...@yahoo.com Subject: Re: [gmx-users] luck To: jalem...@vt.edu http://us.mc527.mail.yahoo.com/mc/compose?to=jalem...@vt.edu, Discussion list for GROMACS users gmx-users@gromacs.org http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org Date: Monday, January 31, 2011, 1:14 PM thanks. Here is the error i mentioned a while back with using pdb2gmx: -- File input/output error: filename.pdb For more information, visit -- thanks for the time --- On *Mon, 1/31/11, Justin A. Lemkul /jalem...@vt.edu http://us.mc527.mail.yahoo.com/mc/compose?to=jalem...@vt.edu/* wrote: From: Justin A. Lemkul jalem...@vt.edu http://us.mc527.mail.yahoo.com/mc/compose?to=jalem...@vt.edu Subject: Re: [gmx-users] luck To: Gromacs Users' List gmx-users@gromacs.org http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org Date: Monday, January 31, 2011, 12:33 PM Mr Bernard Ramos wrote: Do I need to type in g_luck instead? Typing an email and waiting for a response takes far more time and effort than simply trying it yourself ;) -Justin --- On *Mon, 1/31/11, Justin A. Lemkul /jalem...@vt.edu http://us.mc527.mail.yahoo.com/mc/compose?to=jalem...@vt.edu http://us.mc527.mail.yahoo.com/mc/compose?to=jalem...@vt.edu/* wrote: From: Justin A. Lemkul jalem...@vt.edu http://us.mc527.mail.yahoo.com/mc/compose?to=jalem...@vt.edu http://us.mc527.mail.yahoo.com/mc/compose?to=jalem...@vt.edu Subject: Re: [gmx-users] luck To: Discussion list for GROMACS users gmx-users@gromacs.org http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org Date: Monday, January 31, 2011, 12:11 PM Mr Bernard Ramos wrote: Hi everyone! I have two questions. 1. after I installed gromacs 4.5.3 and which mdrun was able to give the correct path, I was not able to run luck. Instead, luck gives an error command not found. Is this ok? What went wrong? Do I need to install again gromacs? The program is now called g_luck.
Re: [gmx-users] angle constrain, constrained PF6 anion
The mdp file is attached. Best, Gyorgy Quoting Justin A. Lemkul jalem...@vt.edu: gyorgy.han...@fc.up.pt wrote: Dear all, I am setting up a simulation of ionic liquids with the PF6 anion. According to the potential, the anion should be kept rigid, wich obviously means that bond lengths and angles have to be constrained. LINCS doesn't work with angle constraints (i.e. constraing a triangle), so we decided to use SHAKE. However, SHAKE seems to work a bit strangely: I know SHAKE mustn't be used with domain decomposition, but even if I set the corresponding variable to NO in the mdp file, the simulation crashes on 8 procs and gives the following error message: Fatal error: 1 particles communicated to PME node 7 are more than a cell length out of the domain decomposition cell of their charge group. If I try to run mdrun with -pd (to 'really' switch off domain decomposition), the simulation doesn't chrash but gives nonsense (the energy seems to increase constantly). I am not an expert user so maybe I do something wrong but, anyway, does anyone have an idea how to constrain this anion with Gromacs? I checked mailing list archive but couldn't find any answer corresponding to my question. Without seeing a complete .mdp file, it's not possible to fully diagnose this problem. The combination of SHAKE + particle decomposition should be stable, but there are a whole host of different things that can go wrong. -Justin Thanks in advance. Gyorgy -- 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists title= BMIM PF6 bulk simulation cpp = /usr/bin/cpp ; RUN CONTROL PARAMETERS ;l_bfgs integrator = md;steep ; Start time and timestep in ps tinit= 0 dt = 0.0001 ! just to see if it starts nsteps = 25000 ; mode for center of mass motion removal comm-mode= linear ; number of steps for center of mass motion removal nstcomm = 10 ; group(s) for center of mass motion removal ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size ;emtol= 50 ;emstep = 0.5 ;lincs_iter = 3 ;lincs_warnangle = 50 ; Frequency of steepest descents steps when doing CG ;nstcgsteep = 1000 ;nbfgscorr= 10 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 0 nstvout = 0 nstfout = 0 ; Checkpointing helps you continue after crashes nstcheckpoint= 1 ; Output frequency for energies to log file and energy file nstlog = 1 nstenergy= 1 ; Output frequency and precision for xtc file nstxtcout= 1 xtc-precision= 1000 ; This selects the subset of atoms for the xtc file. You can ; select multiple groups. By default all atoms will be written. xtc-grps = ; Selection of energy groups energygrps = ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 25 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = xyz ; nblist cut-off rlist= 1.5 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME ; can RF also be used? rcoulomb-switch = 0 rcoulomb = 1.5 ; Dielectric constant (DC) for cut-off or DC of reaction field epsilon_rf = ; Method for doing Van der Waals vdw-type = Shift ; cut-off lengths rvdw-switch = 1.1 rvdw = 1.2 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM
[gmx-users] lactam bridge problems
I want to create a peptide bond between glu and lys using Gromacs 4.5.3. One option that I have is to modify the topology file (bonds, angles, etc.) but I also want to do a number of these lactam bridges so it is a pain to make the bonds, delete the atoms in glu and lys that are not needed and renumber the .itp and .gro files. The other option is to add the lactam glu (LCE) and lactam lys (LCK) as residues to the force field. So far I have added LCE and LCK to gromos53a6 and opls-aa but i always get the same error: Atom HZ1 not found in rtp database in residue LCK, it looks a bit like HZ - there is no HZ1 in all my files but pdb2gmx seem to be looking for it. The naming is consistent (HZ is specified in the .rtp files, in the pdb file). Here are the modiifcation that I made involving gromos53a6. Following the Adding a residue to a force field section in the gromacs website 1.) In aminoacids.rtp (I'm just showing LCK) [ LCK ] [ atoms ] N N -0.31000 0 H H 0.31000 0 CA CH1 0.0 1 CB CH2 0.0 1 CG CH2 0.0 2 CD CH2 0.0 2 CE CH2 0.0 3 NZ N -0.31000 3 ; same atom type as amide N HZ H 0.31000 3 ; same atom type as amide H C C 0.450 4 O O -0.450 4 [ bonds ] N H gb_2 N CA gb_21 CA CB gb_27 CA C gb_27 CB CG gb_27 CG CD gb_27 CD CE gb_27 CE NZ gb_21 ; same bond as N-CA NZ HZ gb_2 ; same bond as N-H C O gb_5 C +N gb_10 [ angles ] ; ai aj ak gromos type -C N H ga_32 -C N CA ga_31 H N CA ga_18 N CA CB ga_13 N CA C ga_13 CB CA C ga_13 CA CB CG ga_15 CB CG CD ga_15 CG CD CE ga_15 CD CE NJ ga_15 CE NJ HJ ga_31 CA C O ga_30 CA C +N ga_19 O C +N ga_33 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 CA N C CB gi_2 C CA +N O gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_14 -C N CA C gd_39 N CA CB CG gd_34 N CA C +N gd_40 CA CB CG CD gd_34 CB CG CD CE gd_34 CG CD CE NJ gd_34 CD CE NJ HJ gd_29 2.) HBD has been update LCK 2 1 1 H N -C CA 2 4 HZ NZ CE CD 3.) no new atom types introduced atomtypes.atp and ffnonbonded.itp not modified. Note: I did try introducing new atom types in a previous attempt (not on this attempt) but I still get the same error above. 4.) no new bond types introduced (ffbonded.itp is not modified). 5.) In residuetypes.dat (the new residues were declared) LCK Protein LCE Protein 6.) specbond.dat (the peptide bond was introduced) LCE CD 1 LCK NZ 1 0.133 LCTM LCTM It seems like pdb2gmx is still looking at my new residues as if they were lys and glu and that might be the source of the error (In my original pdb file, LCE and LCK were used so the error does not come from there and the atom names are also consistent). Here's a portion of the pdb file that I used: ATOM 1759 N LCK B 20 -3.985 -0.668 6.218 1.00 20.00 N ATOM 1760 CA LCK B 20 -3.534 -1.515 5.127 1.00 20.00 C ATOM 1761 C LCK B 20 -2.096 -1.976 5.372 1.00 20.00 C ATOM 1762 O LCK B 20 -1.823 -3.174 5.413 1.00 20.00 O ATOM 1763 HA LCK B 20 -4.173 -2.398 5.113 1.00 20.00 H ATOM 1764 CB LCK B 20 -3.662 -0.780 3.790 1.00 20.00 C ATOM 1765 1HB LCK B 20 -4.701 -0.500 3.623 1.00 20.00 H ATOM 1766 2HB LCK B 20 -3.084 0.143 3.823 1.00 20.00 H ATOM 1767 CG LCK B 20 -3.171 -1.655 2.635 1.00 20.00 C ATOM 1768 1HG LCK B 20 -2.125 -1.918 2.792 1.00 20.00 H ATOM 1769 2HG LCK B 20 -3.735 -2.588 2.616 1.00 20.00 H ATOM 1770 CD LCK B 20 -3.326 -0.932 1.296 1.00 20.00 C ATOM 1771 1HD LCK B 20 -3.061 0.119 1.413 1.00 20.00 H ATOM 1772 2HD LCK B 20 -2.635 -1.356 0.567 1.00 20.00 H ATOM 1773 CE LCK B 20 -4.760 -1.047 0.774 1.00 20.00 C ATOM 1774 1HE LCK B 20 -4.973 -2.081 0.503 1.00 20.00 H ATOM 1775 2HE LCK B 20 -5.463 -0.771 1.560 1.00 20.00 H ATOM 1776 NZ LCK B 20 -4.955 -0.170 -0.403 1.00 20.00 N ATOM 1777 HZ LCK B 20 -5.909 -0.258 -0.736 1.00 20.00 H ATOM 1778
Re: [gmx-users] luck
thanks. It was able to generate the needed files as indicated in the tutorial. I trnasfered my working directory. many thanks. Bernard --- On Wed, 2/2/11, Justin A. Lemkul jalem...@vt.edu wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] luck To: Gromacs Users' List gmx-users@gromacs.org Date: Wednesday, February 2, 2011, 2:32 AM Mr Bernard Ramos wrote: this is the command i am using: pbd2gmx -f 1AKI.pdb -o 1AKI_processed.gro -water spce then I choose a force fileld. then I get the error and no new files generated at all. My working directory is: /cygdrive/c/MDProgram/Gromacs453/bin/molecule tests I assume that .../Gromacs453/bin is the location where the Gromacs binaries are installed? It's a bad idea to run commands from the location of the installation or its subdirectories. It's also a possibility that the space in molecule tests is causing problems with filename parsing, but that's a bit of a guess. Move the necessary files to a new location, in a directory named without spaces, and try again. -Justin --- On *Wed, 2/2/11, Justin A. Lemkul /jalem...@vt.edu/* wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] luck To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Wednesday, February 2, 2011, 2:15 AM Mr Bernard Ramos wrote: Hi! I am actually following your lysozyme tutorial. I ve been using different pdb files including that of water, methanol, 1AKI, etc. The pdb2gmx does not generate any topology file. No files are generated and I get this error: -- pdb2gmx, VERSION 4.5.3 Source code file: futil.c, line:491 File input/output 1AKI.pdb For more etc -- Then this file doesn't exist in the working directory. What is the command you're issuing (exact copy and paste from the terminal, please)? What are the contents of the working directory? -Justin --- On *Mon, 1/31/11, Mr Bernard Ramos /bgrquan...@yahoo.com http://us.mc527.mail.yahoo.com/mc/compose?to=bgrquan...@yahoo.com/* wrote: From: Mr Bernard Ramos bgrquan...@yahoo.com http://us.mc527.mail.yahoo.com/mc/compose?to=bgrquan...@yahoo.com Subject: Re: [gmx-users] luck To: jalem...@vt.edu http://us.mc527.mail.yahoo.com/mc/compose?to=jalem...@vt.edu, Discussion list for GROMACS users gmx-users@gromacs.org http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org Date: Monday, January 31, 2011, 1:14 PM thanks. Here is the error i mentioned a while back with using pdb2gmx: -- File input/output error: filename.pdb For more information, visit -- thanks for the time --- On *Mon, 1/31/11, Justin A. Lemkul /jalem...@vt.edu http://us.mc527.mail.yahoo.com/mc/compose?to=jalem...@vt.edu/* wrote: From: Justin A. Lemkul jalem...@vt.edu http://us.mc527.mail.yahoo.com/mc/compose?to=jalem...@vt.edu Subject: Re: [gmx-users] luck To: Gromacs Users' List gmx-users@gromacs.org http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org Date: Monday, January 31, 2011, 12:33 PM Mr Bernard Ramos wrote: Do I need to type in g_luck instead? Typing an email and waiting for a response takes far more time and effort than simply trying it yourself ;) -Justin --- On *Mon, 1/31/11, Justin A. Lemkul /jalem...@vt.edu http://us.mc527.mail.yahoo.com/mc/compose?to=jalem...@vt.edu http://us.mc527.mail.yahoo.com/mc/compose?to=jalem...@vt.edu/* wrote: From: Justin A. Lemkul jalem...@vt.edu http://us.mc527.mail.yahoo.com/mc/compose?to=jalem...@vt.edu http://us.mc527.mail.yahoo.com/mc/compose?to=jalem...@vt.edu Subject: Re: [gmx-users] luck To: Discussion list for GROMACS users gmx-users@gromacs.org http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org Date: Monday, January 31, 2011, 12:11 PM Mr Bernard Ramos wrote: Hi everyone! I have two
Re: [gmx-users] angle constrain, constrained PF6 anion
There's at least one problem that I see: dt = 0.0001 ! just to see if it starts This line won't be parsed properly. Check your mdout.mdp to see what grompp is assigning as a value for dt. You shouldn't need to set a value this small to see if it's going to work or not, anyway. It would also be useful to know what sort of minimization and equilibration you've done prior to this step, since most cases of the system collapsing are generally attributed to one of three problems: 1. Poor starting geometry/insufficient minimization and/or equilibration 2. Bad parameters 3. Incorrect .mdp settings -Justin gyorgy.han...@fc.up.pt wrote: The mdp file is attached. Best, Gyorgy Quoting Justin A. Lemkul jalem...@vt.edu: gyorgy.han...@fc.up.pt wrote: Dear all, I am setting up a simulation of ionic liquids with the PF6 anion. According to the potential, the anion should be kept rigid, wich obviously means that bond lengths and angles have to be constrained. LINCS doesn't work with angle constraints (i.e. constraing a triangle), so we decided to use SHAKE. However, SHAKE seems to work a bit strangely: I know SHAKE mustn't be used with domain decomposition, but even if I set the corresponding variable to NO in the mdp file, the simulation crashes on 8 procs and gives the following error message: Fatal error: 1 particles communicated to PME node 7 are more than a cell length out of the domain decomposition cell of their charge group. If I try to run mdrun with -pd (to 'really' switch off domain decomposition), the simulation doesn't chrash but gives nonsense (the energy seems to increase constantly). I am not an expert user so maybe I do something wrong but, anyway, does anyone have an idea how to constrain this anion with Gromacs? I checked mailing list archive but couldn't find any answer corresponding to my question. Without seeing a complete .mdp file, it's not possible to fully diagnose this problem. The combination of SHAKE + particle decomposition should be stable, but there are a whole host of different things that can go wrong. -Justin Thanks in advance. Gyorgy -- 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_velacc
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 02/01/2011 05:49 PM, Nilesh Dhumal wrote: Hello, I am trying to calculate the Velocity Autocorrelation Function for my system using g_velacc. I have system of 128 ionic liquids (128 cations and 128 anions). I run the trajectory for 20 ns. I used following command . g_velacc -f 3.trr -n emi-etso4-127-no.ndx -s 3.tpr -o I selected system The output file, vac.xvg, have no data. Can any one tell why its not wirting. Perhaps you have not velocities stored in your trr file or the index file is empty. /Flo Thanks Nilesh - -- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Phone: +49(0)711/685-6-3613 Fax: +49-(0)711/685-6-3658 EMail: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAk1IXaQACgkQLpNNBb9GiPknNQCgyPiuIJCNofRU+wot5+E/b8be 910AoN64tjsWFhG1adFSGOYF4RBcYr2D =g8ci -END PGP SIGNATURE- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Inaccurate pressure readings
Sorry to revisit this subject, but this output does not make sense. In the log file from my NPT simulation, the pressure readings fluctuate between about 300 bar and -300 bar, which I gather is pretty normal. However, at the end of the log file, it reports the average pressure being almost 1000 bar. g_energy also reports this value. In my mdp file, nstenergy is equal to nstlog, so the frequency of data is the same in the .edr file. How is is possible that the final average would be greater than any value obtained during the simulation? On Thu, Jan 20, 2011 at 4:33 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 21/01/2011 10:12 AM, Denny Frost wrote: Sorry, I'm referring to a lot of runs here - some fluctuate more than others and some have greater average values than others. The average value is never greater than the maximum fluctuation in each run, so that is not a problem. The average given by g_energy, however, is not close to 1.0 bar in any of my runs. Some runs give an average pressure of 10 bar, some give an average value of -1000 bar. In addition to all the points Justin mentioned, I'd observe that you're generating velocities at the start of the run, so the system will not be equilibrated for some time after that. See the advice here www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation. Anyway, you don't want to collect data for averages until after equilibration. Secondly, tau-t of 0.1 is useful for equilibration, but a bit too stringent for actual simulations. Using v-rescale T-coupling is probably a good idea too. Until you address all these issues about the numerical quality of your model of reality, hoping for observables to correlate with reality is not justified. Mark On Thu, Jan 20, 2011 at 3:51 PM, Dallas Warren dallas.war...@monash.eduwrote: Then something you have said isn’t right. In first email you said that the pressure varies between -400 and +400 bar. Now you say that the average can vary from -1000 to +1000 bar. If the instantaneous pressure is varying from -1000 to +1000 bar, then that is not a real issue. However, if the average can be from -1000 to +1000 bar, then that definitely is. Which one is it? Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. *From:* gmx-users-boun...@gromacs.org [mailto: gmx-users-boun...@gromacs.org] *On Behalf Of *Denny Frost *Sent:* Friday, 21 January 2011 9:23 AM *To:* Discussion list for GROMACS users *Subject:* Re: [gmx-users] Inaccurate pressure readings The average I calculate is not within -10 to 10, it is on the order of -1000 to 1000 On Thu, Jan 20, 2011 at 3:11 PM, Dallas Warren dallas.war...@monash.edu wrote: You have a variable that is fluctuating over a range of 800+ units (three orders of magnitude) and want the average to be 1.0? It is not a problem as such. If you can get a large enough data set of pressure data, and it will have to be very large, then you might get it close to one. But as long the average you calculate is within may be an order of magnitude (-10 to 10) then there is nothing to get too worried about. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. *From:* gmx-users-boun...@gromacs.org [mailto: gmx-users-boun...@gromacs.org] *On Behalf Of *Denny Frost *Sent:* Friday, 21 January 2011 9:07 AM *To:* gmx-users@gromacs.org *Subject:* [gmx-users] Inaccurate pressure readings I am running a variety of NPT simulations with polar, non-polar, and ionic compounds. Although my results for density agree well with experimental values, the pressures I get from g_energy are off by 1 to 3 orders of magnitude. In the log file, the pressure fluctuates around a lot from -400 to 400 bar, which seems to be normal according to other posts on this list, but the average (which is what g_energy gives me) is not 1.0 bar, as I specified. Does anyone know how to correct this problem? Pressure coupling parameters: Pcoupl = berendsen pcoupltype = isotropic tau_p = 1.0 ref_p = 1.0 compressibility = 4.5e-5 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www
Re: [gmx-users] lactam bridge problems
Justin, thanks a lot. I got the pdb2gmx to work now by changing the .hdb. I hope the simulation will be smooth sailing as well. Thanks, Jerez --- On Tue, 2/1/11, Justin A. Lemkul jalem...@vt.edu wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] lactam bridge problems To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Tuesday, February 1, 2011, 11:57 AM Jerez Te wrote: I want to create a peptide bond between glu and lys using Gromacs 4.5.3. One option that I have is to modify the topology file (bonds, angles, etc.) but I also want to do a number of these lactam bridges so it is a pain to make the bonds, delete the atoms in glu and lys that are not needed and renumber the .itp and .gro files. The other option is to add the lactam glu (LCE) and lactam lys (LCK) as residues to the force field. So far I have added LCE and LCK to gromos53a6 and opls-aa but i always get the same error: Atom HZ1 not found in rtp database in residue LCK, it looks a bit like HZ - there is no HZ1 in all my files but pdb2gmx seem to be looking for it. The naming is consistent (HZ is specified in the .rtp files, in the pdb file). Here are the modiifcation that I made involving gromos53a6. Following the Adding a residue to a force field section in the gromacs website 1.) In aminoacids.rtp (I'm just showing LCK) [ LCK ] [ atoms ] N N -0.31000 0 H H 0.31000 0 CA CH1 0.0 1 CB CH2 0.0 1 CG CH2 0.0 2 CD CH2 0.0 2 CE CH2 0.0 3 NZ N -0.31000 3 ; same atom type as amide N HZ H 0.31000 3 ; same atom type as amide H C C 0.450 4 O O -0.450 4 [ bonds ] N H gb_2 N CA gb_21 CA CB gb_27 CA C gb_27 CB CG gb_27 CG CD gb_27 CD CE gb_27 CE NZ gb_21 ; same bond as N-CA NZ HZ gb_2 ; same bond as N-H C O gb_5 C +N gb_10 [ angles ] ; ai aj ak gromos type -C N H ga_32 -C N CA ga_31 H N CA ga_18 N CA CB ga_13 N CA C ga_13 CB CA C ga_13 CA CB CG ga_15 CB CG CD ga_15 CG CD CE ga_15 CD CE NJ ga_15 CE NJ HJ ga_31 CA C O ga_30 CA C +N ga_19 O C +N ga_33 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 CA N C CB gi_2 C CA +N O gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_14 -C N CA C gd_39 N CA CB CG gd_34 N CA C +N gd_40 CA CB CG CD gd_34 CB CG CD CE gd_34 CG CD CE NJ gd_34 CD CE NJ HJ gd_29 2.) HBD has been update LCK 2 1 1 H N -C CA 2 4 HZ NZ CE CD 3.) no new atom types introduced atomtypes.atp and ffnonbonded.itp not modified. Note: I did try introducing new atom types in a previous attempt (not on this attempt) but I still get the same error above. 4.) no new bond types introduced (ffbonded.itp is not modified). 5.) In residuetypes.dat (the new residues were declared) LCK Protein LCE Protein 6.) specbond.dat (the peptide bond was introduced) LCE CD 1 LCK NZ 1 0.133 LCTM LCTM It seems like pdb2gmx is still looking at my new residues as if they were lys and glu and that might be the source of the error (In my original pdb file, LCE and LCK were used so the error does not come from there and the atom names are also consistent). Here's a portion of the pdb file that I used: ATOM 1759 N LCK B 20 -3.985 -0.668 6.218 1.00 20.00 N ATOM 1760 CA LCK B 20 -3.534 -1.515 5.127 1.00 20.00 C ATOM 1761 C LCK B 20 -2.096 -1.976 5.372 1.00 20.00 C ATOM 1762 O LCK B 20 -1.823 -3.174 5.413 1.00 20.00 O ATOM 1763 HA LCK B 20 -4.173 -2.398 5.113 1.00 20.00 H ATOM 1764 CB LCK B 20 -3.662 -0.780 3.790 1.00 20.00 C ATOM 1765 1HB LCK B 20 -4.701 -0.500 3.623 1.00 20.00 H ATOM 1766 2HB LCK B 20 -3.084
Re: [gmx-users] Inaccurate pressure readings
Denny Frost wrote: Sorry to revisit this subject, but this output does not make sense. In the log file from my NPT simulation, the pressure readings fluctuate between about 300 bar and -300 bar, which I gather is pretty normal. However, at the end of the log file, it reports the average pressure being almost 1000 bar. g_energy also reports this value. In my mdp file, nstenergy is equal to nstlog, so the frequency of data is the same in the .edr file. How is is possible that the final average would be greater than any value obtained during the simulation? As I recall from the previous discussion, there were lots of things wrong with your .mdp file and many things to troubleshoot. Can you please post: 1. The .mdp file you're using 2. The contents of the AVERAGES and RMS FLUCTUATIONS sections of your .log file 3. The g_energy output (not the header stuff, just the actual meaningful result) -Justin On Thu, Jan 20, 2011 at 4:33 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 21/01/2011 10:12 AM, Denny Frost wrote: Sorry, I'm referring to a lot of runs here - some fluctuate more than others and some have greater average values than others. The average value is never greater than the maximum fluctuation in each run, so that is not a problem. The average given by g_energy, however, is not close to 1.0 bar in any of my runs. Some runs give an average pressure of 10 bar, some give an average value of -1000 bar. In addition to all the points Justin mentioned, I'd observe that you're generating velocities at the start of the run, so the system will not be equilibrated for some time after that. See the advice here www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation. Anyway, you don't want to collect data for averages until after equilibration. Secondly, tau-t of 0.1 is useful for equilibration, but a bit too stringent for actual simulations. Using v-rescale T-coupling is probably a good idea too. Until you address all these issues about the numerical quality of your model of reality, hoping for observables to correlate with reality is not justified. Mark On Thu, Jan 20, 2011 at 3:51 PM, Dallas Warren dallas.war...@monash.edu mailto:dallas.war...@monash.edu wrote: Then something you have said isn’t right. In first email you said that the pressure varies between -400 and +400 bar. Now you say that the average can vary from -1000 to +1000 bar. If the instantaneous pressure is varying from -1000 to +1000 bar, then that is not a real issue. However, if the average can be from -1000 to +1000 bar, then that definitely is. Which one is it? Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu mailto:dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. *From:* gmx-users-boun...@gromacs.org mailto:gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org mailto:gmx-users-boun...@gromacs.org] *On Behalf Of *Denny Frost *Sent:* Friday, 21 January 2011 9:23 AM *To:* Discussion list for GROMACS users *Subject:* Re: [gmx-users] Inaccurate pressure readings The average I calculate is not within -10 to 10, it is on the order of -1000 to 1000 On Thu, Jan 20, 2011 at 3:11 PM, Dallas Warren dallas.war...@monash.edu mailto:dallas.war...@monash.edu wrote: You have a variable that is fluctuating over a range of 800+ units (three orders of magnitude) and want the average to be 1.0? It is not a problem as such. If you can get a large enough data set of pressure data, and it will have to be very large, then you might get it close to one. But as long the average you calculate is within may be an order of magnitude (-10 to 10) then there is nothing to get too worried about. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu mailto:dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. *From:* gmx-users-boun...@gromacs.org
Re: [gmx-users] Inaccurate pressure readings
Here is the mdp file title = HEX cpp = /lib/cpp constraints = hbonds integrator = md dt = 0.002 ; ps ! nsteps = 250 ; total 5ns. nstcomm = 10 nstxout = 5 nstvout = 5 nstfout = 0 nstlog = 5000 nstenergy = 5000 nstxtcout = 25000 nstlist = 10 ns_type = grid pbc = xyz coulombtype = Cut-off vdwtype = Cut-off rlist = 1.2 rcoulomb= 1.2 rvdw= 1.2 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 ; Berendsen temperature coupling is on in two groups Tcoupl = v-rescale tc_grps = HEX tau_t = 0.1 ref_t = 300 nsttcouple = 1 ; Energy monitoring energygrps = HEX ; Isotropic pressure coupling is now on Pcoupl = berendsen pcoupltype = isotropic ;pc-grps = BMI PFF tau_p = 1.0 ref_p = 1.0 compressibility = 4.5e-5 ; Generate velocites is off at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 10 This is the 'averages' section = = ### == = === A V E R A G E S = = ### == St atistics over 1 001 steps u sing 1001 f rames Energies (kJ/mo l) Bond Angle Ry ckaert-Bell. LJ (SR) Coulomb (SR) 4.57E+03 3.62E+03 3.34E+03 -2.08E+04 0.00E+00 Potential Kinetic En. Total Energy Temperature Pressure (bar) -9.28E+03 1.63E+04 7.05E+03 3.00E+02 9.96E+02 Box-X Box-Y Box-Z 5.47E+00 5.47E+00 5.47E+00 Total Virial (k J/mol) 5.44E+02 -1.30E-01 8.27E-02 -1.30E-01 5.44E+02 3.46E-02 8.27E-02 3.46E-02 5.44E+02 Pressure (bar) 9.96E+02 2.34E-02 -1.51E-02 2.34E-02 9.96E+02 -2.77E-02 -1.51E-02 -2.77E-02 9.96E+02 Total Dipole (D ) 0.00E+00 0.00E+00 0.00E+00 I don't have an RMS section on my log file. The final xvg file that comes from g_energy is much too long to post here, but contains exactly what is in the log file. The interactive output from g_energy is, however, thus: Pressure = 995.9 bar (error = 0.65 bar) On Tue, Feb 1, 2011 at 1:49 PM, Justin A. Lemkul jalem...@vt.edu wrote: Denny Frost wrote: Sorry to revisit this subject, but this output does not make sense. In the log file from my NPT simulation, the pressure readings fluctuate between about 300 bar and -300 bar, which I gather is pretty normal. However, at the end of the log file, it reports the average pressure being almost 1000 bar. g_energy also reports this value. In my mdp file, nstenergy is equal to nstlog, so the frequency of data is the same in the .edr file. How is is possible that the final average would be greater than any value obtained during the simulation? As I recall from the previous discussion, there were lots of things wrong with your .mdp file and many things to troubleshoot. Can you please post: 1. The .mdp file you're using 2. The contents of the AVERAGES and RMS FLUCTUATIONS sections of your .log file 3. The g_energy output (not the header stuff, just the actual meaningful result) -Justin On Thu, Jan 20, 2011 at 4:33 PM, Mark Abraham mark.abra...@anu.edu.aumailto: mark.abra...@anu.edu.au wrote: On 21/01/2011 10:12 AM, Denny Frost wrote: Sorry, I'm referring to a lot of runs here - some fluctuate more than others and some have greater average values than others. The average value is never greater than the maximum fluctuation in each run, so that is not a problem. The average given by g_energy, however, is not close to 1.0 bar in any of my runs. Some runs give an average pressure of 10 bar, some give an average value of -1000 bar. In addition to all the points Justin mentioned, I'd observe that you're generating velocities at the start of the run, so the system will not be equilibrated for some time after that. See the advice here www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation . Anyway, you don't want to collect data for averages until after equilibration. Secondly, tau-t of 0.1 is useful for equilibration, but a bit too stringent for actual simulations. Using v-rescale T-coupling is probably a good idea too. Until you address all these issues about the numerical quality of your model of reality, hoping for observables to correlate with reality is not justified. Mark On Thu, Jan 20, 2011 at 3:51 PM, Dallas Warren dallas.war...@monash.edu mailto:dallas.war...@monash.edu wrote: Then something you have said isn’t right. In first email you said that the pressure varies between -400 and +400 bar. Now you say that the average
[gmx-users] Dynamics of non-protein molecules.
Dear All, I'm trying to use gromacs for molecular dynamics of surfactant micelles formation and dissolution. While reading User's manual and some beginners tutorials some questions and problems occur. 1. Is there some software for creating .pdb or .top file for non proteins molecules like surfactants (SDS,LAS,AOT, Tween's) or I have to make them by hand? 2. Do I have to do something special to allow surfactant molecules to move freely towards each other or to take apart? 3. Does any body see any other potential pitfalls in such type of simulation? Thanks. Yasen Atanasov post doc Department of Chemical Engendering Sofia University. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Inaccurate pressure readings
Denny Frost wrote: snip This is the 'averages' section = = ### == = === A V E R A G E S = = ### == St atistics over 1 001 steps u sing 1001 f rames Energies (kJ/mo l) Bond Angle Ry ckaert-Bell. LJ (SR) Coulomb (SR) 4.57E+03 3.62E+03 3.34E+03 -2.08E+04 0.00E+00 Potential Kinetic En. Total Energy Temperature Pressure (bar) -9.28E+03 1.63E+04 7.05E+03 3.00E+02 9.96E+02 Box-X Box-Y Box-Z 5.47E+00 5.47E+00 5.47E+00 Total Virial (k J/mol) 5.44E+02 -1.30E-01 8.27E-02 -1.30E-01 5.44E+02 3.46E-02 8.27E-02 3.46E-02 5.44E+02 Pressure (bar) 9.96E+02 2.34E-02 -1.51E-02 2.34E-02 9.96E+02 -2.77E-02 -1.51E-02 -2.77E-02 9.96E+02 Total Dipole (D ) 0.00E+00 0.00E+00 0.00E+00 OK, that all looks as expected, except of course the pressure. I don't have an RMS section on my log file. Is this 4.5.3? It looks like a whole lot of interesting diagnostic and other information is now not printed to the .log file that used to be. Too bad. The final output of the g_energy command is this (for pressure): OK, so I'm guessing this isn't complete, but what is really weird is that (1) your .mdp file calls for a 5-ns run, but these data are for (at least) 10 ns or so and (2) there are multiple data sets, such that you're looping back over zero at least twice. Strangely, if you analyze just the 0-9990 chunks independently, they all give sensible pressures (not quite 1, but +/-7). To address point #1: Have you done a continuation with a checkpoint file, or are you posting the wrong .mdp file? If you did a continuation, are the data in the original 5-ns run sensible? I'm wondering if something broke down along the way. For #2, what exactly are you passing to g_energy? As in, what groups are displayed and what exactly are you choosing? -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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Dynamics of non-protein molecules.
Yasen Atanasov wrote: Dear All, I'm trying to use gromacs for molecular dynamics of surfactant micelles formation and dissolution. While reading User's manual and some beginners tutorials some questions and problems occur. 1. Is there some software for creating .pdb or .top file for non proteins molecules like surfactants (SDS,LAS,AOT, Tween's) or I have to make them by hand? There are numerous tools for generating coordinate files, and is rather easy: http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources Coming up with sensible topologies, on the other hand, is substantially more difficult: http://www.gromacs.org/Documentation/How-tos/Parameterization 2. Do I have to do something special to allow surfactant molecules to move freely towards each other or to take apart? You can do normal (unrestrained) MD to see if this accomplishes your goal, otherwise if you want to examine directed processes, you can use the pull code to bias your system in some way. 3. Does any body see any other potential pitfalls in such type of simulation? Too broad of a question to get any useful advice, sorry :) -Justin Thanks. Yasen Atanasov post doc Department of Chemical Engendering Sofia University. -- 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Inaccurate pressure readings
Sorry about that, I tried to delete that post because it was too long. The mdp file used to generate that data in the xvg file was the same except for the nsteps parameter. Also, I copied that file from excel where I was analyzing it and didn't realize until afterward that it had cut off the first digit starting with step 10,000. The run really went from 0-20 ns. Sorry about that, again, I tried to delete the post. Anyway, I agree with you that the data from the xvg file is sensible and makes me feel better about my simulation. I analyzed the xvg file and found that it gives nearly identical values for temperature, Box vectors, and density as given by the g_energy summary, but pressure and surface tension are off by many orders of magnitude and sometimes sign. If you calculate the surface tension using the pressure tensor values given by the g_energy summary and the xvg output file, both are internally consistent, but do not agree with each other. I understand where the data in the xvg file came from because I watched it develop as my run progressed. I don't know where the g_energy summary is getting those numbers from (or the log file averaging for that matter). Here is my g_energy command: g_energy -f md.edr -s md.tpr -o energy.xvg -b 19000 -e 2 I think I might just write a script file to parse the xvg file from g_energy to get me the correct values. On Tue, Feb 1, 2011 at 3:31 PM, Justin A. Lemkul jalem...@vt.edu wrote: Denny Frost wrote: snip This is the 'averages' section = = ### == = === A V E R A G E S = = ### == St atistics over 1 001 steps u sing 1001 f rames Energies (kJ/mo l) Bond Angle Ry ckaert-Bell. LJ (SR) Coulomb (SR) 4.57E+03 3.62E+03 3.34E+03 -2.08E+04 0.00E+00 Potential Kinetic En. Total Energy Temperature Pressure (bar) -9.28E+03 1.63E+04 7.05E+03 3.00E+02 9.96E+02 Box-X Box-Y Box-Z 5.47E+00 5.47E+00 5.47E+00 Total Virial (k J/mol) 5.44E+02 -1.30E-01 8.27E-02 -1.30E-01 5.44E+02 3.46E-02 8.27E-02 3.46E-02 5.44E+02 Pressure (bar) 9.96E+02 2.34E-02 -1.51E-02 2.34E-02 9.96E+02 -2.77E-02 -1.51E-02 -2.77E-02 9.96E+02 Total Dipole (D ) 0.00E+00 0.00E+00 0.00E+00 OK, that all looks as expected, except of course the pressure. I don't have an RMS section on my log file. Is this 4.5.3? It looks like a whole lot of interesting diagnostic and other information is now not printed to the .log file that used to be. Too bad. The final output of the g_energy command is this (for pressure): OK, so I'm guessing this isn't complete, but what is really weird is that (1) your .mdp file calls for a 5-ns run, but these data are for (at least) 10 ns or so and (2) there are multiple data sets, such that you're looping back over zero at least twice. Strangely, if you analyze just the 0-9990 chunks independently, they all give sensible pressures (not quite 1, but +/-7). To address point #1: Have you done a continuation with a checkpoint file, or are you posting the wrong .mdp file? If you did a continuation, are the data in the original 5-ns run sensible? I'm wondering if something broke down along the way. For #2, what exactly are you passing to g_energy? As in, what groups are displayed and what exactly are you choosing? -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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Inaccurate pressure readings
Denny Frost wrote: Sorry about that, I tried to delete that post because it was too long. The mdp file used to generate that data in the xvg file was the same except for the nsteps parameter. Also, I copied that file from excel where I was analyzing it and didn't realize until afterward that it had cut off the first digit starting with step 10,000. The run really went from 0-20 ns. Sorry about that, again, I tried to delete the post. Anyway, I agree with you that the data from the xvg file is sensible and makes me feel better about my simulation. I analyzed the xvg file and found that it gives nearly identical values for temperature, Box vectors, and density as given by the g_energy summary, but pressure and surface tension are off by many orders of magnitude and sometimes sign. If you calculate the surface tension using the pressure tensor values given by the g_energy summary and the xvg output file, both are internally consistent, but do not agree with each other. I understand where the data in the xvg file came from because I watched it develop as my run progressed. I don't know where the g_energy summary is getting those numbers from (or the log file averaging for that matter). Here is my g_energy command: g_energy -f md.edr -s md.tpr -o energy.xvg -b 19000 -e 2 I think I might just write a script file to parse the xvg file from g_energy to get me the correct values. This smells strongly of a bug. The output is all sensible, but the calculated averages are junk. Please upload a test case to redmine as a new issue so this can be fixed. -Justin On Tue, Feb 1, 2011 at 3:31 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Denny Frost wrote: snip This is the 'averages' section = = ### == = === A V E R A G E S = = ### == St atistics over 1 001 steps u sing 1001 f rames Energies (kJ/mo l) Bond Angle Ry ckaert-Bell. LJ (SR) Coulomb (SR) 4.57E+03 3.62E+03 3.34E+03 -2.08E+04 0.00E+00 Potential Kinetic En. Total Energy Temperature Pressure (bar) -9.28E+03 1.63E+04 7.05E+03 3.00E+02 9.96E+02 Box-X Box-Y Box-Z 5.47E+00 5.47E+00 5.47E+00 Total Virial (k J/mol) 5.44E+02 -1.30E-01 8.27E-02 -1.30E-01 5.44E+02 3.46E-02 8.27E-02 3.46E-02 5.44E+02 Pressure (bar) 9.96E+02 2.34E-02 -1.51E-02 2.34E-02 9.96E+02 -2.77E-02 -1.51E-02 -2.77E-02 9.96E+02 Total Dipole (D ) 0.00E+00 0.00E+00 0.00E+00 OK, that all looks as expected, except of course the pressure. I don't have an RMS section on my log file. Is this 4.5.3? It looks like a whole lot of interesting diagnostic and other information is now not printed to the .log file that used to be. Too bad. The final output of the g_energy command is this (for pressure): OK, so I'm guessing this isn't complete, but what is really weird is that (1) your .mdp file calls for a 5-ns run, but these data are for (at least) 10 ns or so and (2) there are multiple data sets, such that you're looping back over zero at least twice. Strangely, if you analyze just the 0-9990 chunks independently, they all give sensible pressures (not quite 1, but +/-7). To address point #1: Have you done a continuation with a checkpoint file, or are you posting the wrong .mdp file? If you did a continuation, are the data in the original 5-ns run sensible? I'm wondering if something broke down along the way. For #2, what exactly are you passing to g_energy? As in, what groups are displayed and what exactly are you choosing? -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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] Protein in a solvated box
Hi, I have protein in a solvated box. When I used VMD to look at the system, I've found that the protein is not located at the center, but rather at the corner section. I would like to know why. Thanks for your insight in advance. Simon -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Protein in a solvated box
simon sham wrote: Hi, I have protein in a solvated box. When I used VMD to look at the system, I've found that the protein is not located at the center, but rather at the corner section. I would like to know why. FAQ #11: http://www.gromacs.org/Documentation/FAQs This should really be #1; it gets asked almost every week... -Justin Thanks for your insight in advance. Simon -- 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] mdrun with append option
When I use .cpt file with tpbconv, I get the error pasted below. I checked the cpt file with gmxdump and it is not empty and has the same number of atoms. Reading toplogy and stuff from rex_1.tpr Reading file rex_1.tpr, VERSION 4.5.1 (single precision) NOTE: Reading the state from trajectory is an obsolete feaure of tpbconv. Continuation should be done by loading a checkpoint file with mdrun -cpi This guarantees that all state variables are transferred. tpbconv is now only useful for increasing nsteps, but even that can often be avoided by using mdrun -maxh Modifying ir-bContinuation to TRUE READING COORDS, VELS AND BOX FROM TRAJECTORY restart1.cpt... --- Program tpbconv, VERSION 4.5.1 Source code file: tpbconv.c, line: 451 Fatal error: Number of atoms in Topology (8962) is not the same as in Trajectory (0) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors On Tue, Feb 1, 2011 at 1:04 PM, Justin A. Lemkul jalem...@vt.edu wrote: Sai Pooja wrote: I am doing a manual replica exchange(generalized hamiltonian rem) after every mdrun. If the replica exchange is successful, then I exchange checkpoint files. For example, consider the following: Simulation parameters:B1.B2 Replicas(coordinates and velocities):.R1.R2 0. Tpbconv to extend simulation time ( using -s, -o and -nsteps ONLY) 1. Mdrun run - 500 steps = 1ps 2. Attempt exchange - NOT SUCCESSFUL 3. Exchange implementation: SKIP 4.Continue to next step . 0. Tpbconv to extend simulation time ( using -s, -o and -nsteps ONLY) 1. Mdrun run - 500 steps = 1ps 2. Attempt exchange - If successful, exchange 3. Exchange Implemented by - exchanging checkpointing files 4. Continue to next step 0. Tpbconv to extend simulation time ( using -s, -o and -nsteps ONLY) 1. Mdrun with exchanged .cpt files -NOW this is where the problem shows.. i) The log, xtc files are not appended when beginning after a step with a successful exchange attempt:/According to Mark's previous mail, this could be a result of mismatch in ensembles. Which means that the .cpt is ignored - implying that the mdrun in B1 DOES NOT start from R2./ Sounds like a reasonable conclusion. Therefore, to make R1 run in B2 and R2 run in B1, do I need to supply .cpt to tpbconv instead of mdrun after a successful exchange step? Either tpbconv or grompp can do this. Check the resulting .tpr with gmxdump to make sure it's using the proper coordinates, velocities, etc from the .cpt file and you'll have your answer as to whether or not it's working as you want. -Justin To summarize: APPENDING HAS NOW BECOME A SECONDARY CONCERN, WHAT I AM INTERESTED IN IS A SUCCESSFUL MANUAL REPLICA EXCHANGE RUN AS POINTED OUT ABOVE. I hope my dilemma is clear now. Pooja On Tue, Feb 1, 2011 at 11:42 AM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] mdrun with append option
Sai Pooja wrote: When I use .cpt file with tpbconv, I get the error pasted below. I checked the cpt file with gmxdump and it is not empty and has the same number of atoms. So use grompp, as I suggested before. Using gmxdump to verify the number of atoms is also not what I suggested; it can be used as a means to verify that the proper coordinates and velocities were assembled in the new .tpr file. -Justin Reading toplogy and stuff from rex_1.tpr Reading file rex_1.tpr, VERSION 4.5.1 (single precision) NOTE: Reading the state from trajectory is an obsolete feaure of tpbconv. Continuation should be done by loading a checkpoint file with mdrun -cpi This guarantees that all state variables are transferred. tpbconv is now only useful for increasing nsteps, but even that can often be avoided by using mdrun -maxh Modifying ir-bContinuation to TRUE READING COORDS, VELS AND BOX FROM TRAJECTORY restart1.cpt... --- Program tpbconv, VERSION 4.5.1 Source code file: tpbconv.c, line: 451 Fatal error: Number of atoms in Topology (8962) is not the same as in Trajectory (0) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors On Tue, Feb 1, 2011 at 1:04 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Sai Pooja wrote: I am doing a manual replica exchange(generalized hamiltonian rem) after every mdrun. If the replica exchange is successful, then I exchange checkpoint files. For example, consider the following: Simulation parameters:B1.B2 Replicas(coordinates and velocities):.R1.R2 0. Tpbconv to extend simulation time ( using -s, -o and -nsteps ONLY) 1. Mdrun run - 500 steps = 1ps 2. Attempt exchange - NOT SUCCESSFUL 3. Exchange implementation: SKIP 4.Continue to next step . 0. Tpbconv to extend simulation time ( using -s, -o and -nsteps ONLY) 1. Mdrun run - 500 steps = 1ps 2. Attempt exchange - If successful, exchange 3. Exchange Implemented by - exchanging checkpointing files 4. Continue to next step 0. Tpbconv to extend simulation time ( using -s, -o and -nsteps ONLY) 1. Mdrun with exchanged .cpt files -NOW this is where the problem shows.. i) The log, xtc files are not appended when beginning after a step with a successful exchange attempt:/According to Mark's previous mail, this could be a result of mismatch in ensembles. Which means that the .cpt is ignored - implying that the mdrun in B1 DOES NOT start from R2./ Sounds like a reasonable conclusion. Therefore, to make R1 run in B2 and R2 run in B1, do I need to supply .cpt to tpbconv instead of mdrun after a successful exchange step? Either tpbconv or grompp can do this. Check the resulting .tpr with gmxdump to make sure it's using the proper coordinates, velocities, etc from the .cpt file and you'll have your answer as to whether or not it's working as you want. -Justin To summarize: APPENDING HAS NOW BECOME A SECONDARY CONCERN, WHAT I AM INTERESTED IN IS A SUCCESSFUL MANUAL REPLICA EXCHANGE RUN AS POINTED OUT ABOVE. I hope my dilemma is clear now. Pooja On Tue, Feb 1, 2011 at 11:42 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: -- 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] mdrun with append option
On 2/02/2011 3:38 AM, Sai Pooja wrote: From the website: If you change the integrator or ensemble, you should pass the checkpoint file to tpbconv only, not to mdrun, since the state might change and thus output files can not be appended. Where was that? It could use clarification. Mark So now instead of supplying the checkpoint file to mdrun I supply it to tpbconv... does this assure that the simulations start from the coordinates/velocities specified by the .cpt file? Pooja On Tue, Feb 1, 2011 at 11:20 AM, Sai Pooja saipo...@gmail.com mailto:saipo...@gmail.com wrote: Thanks Mark. So if the simulation doesn't start from the checkpoint file, from where are the initial coordinates velocities etc. taken from?... the trajectory files? Also, I could not find the environment variable... and I am not sure how to use one. Pooja On Tue, Feb 1, 2011 at 3:03 AM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 1/02/2011 7:50 AM, Sai Pooja wrote: I think I have figured out the reason. It is because I am carrying out replica exchange (manual) after every mdrun. If the exchange occurs, I exchange the checkpoint files, extend the simulation by 500 steps and continue. The new simulation starts from exchanged cptfile. It seems that whenever the exchange occurs, the earlier log,traj files are not appended. They are instead overwritten. the obv solution is to save and index these files with the relevant replicas everytime an exchange occurs. This would have been good to know earlier. If replica-exchange leads to the ensemble of the .tpr not matching the ensemble of the .cpt, then IIRC 4.5.3 mdrun will refuse to start from the .cpt, which means the subsequent mdrun will start from the .tpr only. Certainly a non-appending mdrun prints a warning (or error, I forget which) message to the log file, but perhaps the use of -append (erroneously) doesn't do that. Please have a look and see if that is the issue. There is an environment variable that can be set to tell mdrun that you (think you) know what you are doing mismatching .tpr and .cpt. Mark However, i have a more general question. Since mdrun still runs with the exchanged checkpoint files and starts from the point where the previous run ended, can I be assured that an exchange has been affected - since tpr files correspond to the replica-box and cpi to the most recent exchanged replicas? Pooja On Mon, Jan 31, 2011 at 2:33 PM, Sai Pooja saipo...@gmail.com mailto:saipo...@gmail.com wrote: I manually index checkpoint files after every mdrun. What troubles me is the randomness with which -append fails/works. For eg, I have a simulation which runs from 3ns, 1ps in 1 mdrun. Now oddly enough, the logfile starts from 1184ps(in the end, I do remember the one starting from 0 but that was overwritten it seems) and the rest is appended uptil the 3000ps step. Why would append work from 1184ps to 3000ps but not for the previous ones?Could it have anything to do with the network/cluster? If that is the case is it safer to create a new file everytime and then concatenate them after say every 100ps? Pooja On Sat, Jan 29, 2011 at 6:52 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 30/01/2011 10:39 AM, Sai Pooja wrote: I would be happy to supply more information.. if someone could please look into this.. otherwise I will have to switch to storing every file and then just concatenating them which seems like a rather roundabout way of doing it. As I suggested a few emails ago, are you sure that -cpi file exists? If your numerical suffixes are indexing restarts, then unless you've done some manual copying that you haven't told us about, it won't. Your filename scheme seems a bit contorted - like you're trying to do the work that GROMACS 4.5.x will just do for you if you let it. Otherwise, you'll have to do some detective work with gmxcheck on the -cpi to see what might be the issue. In your case, an initial mdrun -deffnm rex_3 (perhaps save some copies while you're experimenting) and subsequently tpbconv -extend blah -f rex_3 -o rex_3 mdrun -deffnm rex_3 -append will work and be much simpler than whatever you're
Re: [gmx-users] mdrun with append option
Mark Abraham wrote: On 2/02/2011 3:38 AM, Sai Pooja wrote: From the website: If you change the integrator or ensemble, you should pass the checkpoint file to tpbconv only, not to mdrun, since the state might change and thus output files can not be appended. Where was that? It could use clarification. Last sentence here: http://www.gromacs.org/Documentation/How-tos/Doing_Restarts#Version_4.x Looks like maybe this is some kind of obsolete statement? Introduced May 27, 2010. -Justin Mark So now instead of supplying the checkpoint file to mdrun I supply it to tpbconv... does this assure that the simulations start from the coordinates/velocities specified by the .cpt file? Pooja On Tue, Feb 1, 2011 at 11:20 AM, Sai Pooja saipo...@gmail.com mailto:saipo...@gmail.com wrote: Thanks Mark. So if the simulation doesn't start from the checkpoint file, from where are the initial coordinates velocities etc. taken from?... the trajectory files? Also, I could not find the environment variable... and I am not sure how to use one. Pooja On Tue, Feb 1, 2011 at 3:03 AM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 1/02/2011 7:50 AM, Sai Pooja wrote: I think I have figured out the reason. It is because I am carrying out replica exchange (manual) after every mdrun. If the exchange occurs, I exchange the checkpoint files, extend the simulation by 500 steps and continue. The new simulation starts from exchanged cptfile. It seems that whenever the exchange occurs, the earlier log,traj files are not appended. They are instead overwritten. the obv solution is to save and index these files with the relevant replicas everytime an exchange occurs. This would have been good to know earlier. If replica-exchange leads to the ensemble of the .tpr not matching the ensemble of the .cpt, then IIRC 4.5.3 mdrun will refuse to start from the .cpt, which means the subsequent mdrun will start from the .tpr only. Certainly a non-appending mdrun prints a warning (or error, I forget which) message to the log file, but perhaps the use of -append (erroneously) doesn't do that. Please have a look and see if that is the issue. There is an environment variable that can be set to tell mdrun that you (think you) know what you are doing mismatching .tpr and .cpt. Mark However, i have a more general question. Since mdrun still runs with the exchanged checkpoint files and starts from the point where the previous run ended, can I be assured that an exchange has been affected - since tpr files correspond to the replica-box and cpi to the most recent exchanged replicas? Pooja On Mon, Jan 31, 2011 at 2:33 PM, Sai Pooja saipo...@gmail.com mailto:saipo...@gmail.com wrote: I manually index checkpoint files after every mdrun. What troubles me is the randomness with which -append fails/works. For eg, I have a simulation which runs from 3ns, 1ps in 1 mdrun. Now oddly enough, the logfile starts from 1184ps(in the end, I do remember the one starting from 0 but that was overwritten it seems) and the rest is appended uptil the 3000ps step. Why would append work from 1184ps to 3000ps but not for the previous ones?Could it have anything to do with the network/cluster? If that is the case is it safer to create a new file everytime and then concatenate them after say every 100ps? Pooja On Sat, Jan 29, 2011 at 6:52 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 30/01/2011 10:39 AM, Sai Pooja wrote: I would be happy to supply more information.. if someone could please look into this.. otherwise I will have to switch to storing every file and then just concatenating them which seems like a rather roundabout way of doing it. As I suggested a few emails ago, are you sure that -cpi file exists? If your numerical suffixes are indexing restarts, then unless you've done some manual copying that you haven't told us about, it won't. Your filename scheme seems a bit contorted - like you're trying to do the work that GROMACS 4.5.x will just do for you if you let it. Otherwise, you'll have to do some detective work with gmxcheck on the -cpi to see what might be the issue. In your case, an initial mdrun -deffnm rex_3
Re: [gmx-users] Re: RE : essential dynamics
I searched the user list in order to get some idea about calculating cosine content of first PCA .. but I am not able to do so ?? Can u direct me to a good thread or discussion.. On Tue, Feb 1, 2011 at 2:04 AM, bharat gupta bharat.85.m...@gmail.comwrote: Thanks for the reply ... I am following this thread - http://oldwww.gromacs.org/pipermail/gmx-users/2004-May/010438.html http://oldwww.gromacs.org/pipermail/gmx-users/2004-May/010438.htmlAlso I read the following paper http://pubs.acs.org/doi/abs/10.1021/jp983120q (Internal dynamics of GFP) in which they have carried out such projections of the eigen vector in order to find the regions showing minimum and maximum amplitudes.. What I am thinking is shall I take those c-alpha atoms that are well stable and equilibrated after referring to RMSD graph generated after simulation ... I am stating here what I have done so far and what I have to analyze :- I exchanged the loops regions of GFP with loops of longer length taken from pdb .. I simulated both the crystal str. and modeled strs. to compare how the loop incorporation leads to the change in the structure of GFP Since the RMSD of the GFP crystal str and that of model are in comparable range .. I thought of looking at the motions of loops in the structure that are giving such fluctuations in RMSD of model and for that I decided to generate eigen vectors and project them in 3d (like the one given in paper mentioned above) to see how that particular loop behaves .. I don't know whether what I have hypothesized is correct or not .. since I am not able to find any other insilico method apart from MDS for such a study .. Also if my prediction comes out to be good enough I have to carry out such insertion in the wet lab and has to check for fluorescence ..any help in this regard will be appreciated... On Tue, Feb 1, 2011 at 1:28 AM, Tsjerk Wassenaar tsje...@gmail.comwrote: Hi Bharat, On Tue, Feb 1, 2011 at 8:33 AM, bharat gupta bharat.85.m...@gmail.com wrote: Hi, After searching though gmxuserlist I found the relevant thread for ED... I followed the following steps :- What thread are you referring to? 1) g_covar - to generate a covariance matrix and diagonalize it (for c-alpha atoms only) 2) g_anaeig - to generate eigen vectors g_covar calculates the eigenvectors. It's what you end up with through diagonalization. 3)g_rmsf - for calculating RMSD of first 8 eigen vectors , I got an error at this step that - g_rmsf is not for calculating RMSD, and hasn't got much to do with eigenvector analysis. That's what g_anaeig is for (like with the option -rmsf). Using g_anaeig will avoid the error you observe. As a side note, 3 ns is rather short for this sort of thing. You have to check the cosine content of the first principal components to see if you've reached equilibrium already. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] segmentation fault: g_velacc
Thanks very much, Dr. Kutzner! On Tue, Feb 1, 2011 at 9:14 PM, Carsten Kutzner ckut...@gwdg.de wrote: Hi Vigneshwar, the problem is fixed now in the release-4-0-patches branch. Carsten On Feb 1, 2011, at 2:00 PM, Carsten Kutzner wrote: Hi, apparently this bug fix made it to 4.5, but not to 4.0. I will apply the fix also there. Carsten On Feb 1, 2011, at 1:58 PM, Justin A. Lemkul wrote: Vigneshwar Ramakrishnan wrote: Dear All, I am using the gromacs 4.0.7 version and I was trying to calculate the momentum autocorrelation function by using the -m flag. However, I get a segmentation fault as follows: trn version: GMX_trn_file (double precision) Reading frame 0 time0.000 Segmentation fault When I don't use the -m option, I have no problem. Upon searching the userslist, I found this thread: http://lists.gromacs.org/pipermail/gmx-users/2010-October/054813.html and a patch, but I don't find any related bugs reported elsewhere. So, I am just wondering if I sould go ahead and use the patch or if there could be something else that is wrong. Will appreciate any kind of pointers. Either apply the patch or upgrade to a newer version of Gromacs that contains this bug fix. -Justin Sincerely, Vignesh -- R.Vigneshwar Graduate Student, Dept. of Chemical Biomolecular Engg, National University of Singapore, Singapore Strive for Excellence, Never be satisfied with the second Best!! I arise in the morning torn between a desire to improve the world and a desire to enjoy the world. This makes it hard to plan the day. (E.B. White) -- 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- R.Vigneshwar Graduate Student, Dept. of Chemical Biomolecular Engg, National University of Singapore, Singapore Strive for Excellence, Never be satisfied with the second Best!! I arise in the morning torn between a desire to improve the world and a desire to enjoy the world. This makes it hard to plan the day. (E.B. White) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
