Re: [gmx-users] How many ps needs a simulation?
On Wed, 10 May 2006 19:29:26 -0700 (PDT) jahanshah ashkani [EMAIL PROTECTED] wrote: Thanks, In fact I have a sequence with 1277 residue. It is stable even in 50ps. But when I continue to simulation my pc is restarted in 4 steps, automaticly. I should say that this step needs about 100 h time. 50 ps for a protein of 1277 residue is probably equivalent to the first minute of a marathon. The system size you chose can be considered enormous ! Anyway as M and W already said, the simulation length that would give you a reasonable answer depends entirely on what question you want to answer and the quality of the answer you want. From a 50ps simulation you have absolutely no answer at all !! Good luck XAvier ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How many ps needs a simulation?
Dallas B. Warren wrote: How many ps needs a simulation? How long is a piece of string? rofl... didn't see until now we both had the same response to this question! Cheers, Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] How many ps needs a simulation?
Mark, rofl... didn't see until now we both had the same response to this question! Yeah, spun me out a bit too when your repsonse arrived after I had sent mine ;-) Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacology Victorian College of Pharmacy, Monash University 381 Royal Parade, Parkville VIC 3010 [EMAIL PROTECTED] +61 3 9903 9524 - When the only tool you own is a hammer, every problem begins to resemble a nail. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] question on pulling 2 groups in afm run
Dear gromacs users, I met a problem on pulling 2 groups in a afm pulling run. When mdrun processes input file, error messages such as unknown left-hand : group_2 appear for group_2, afm_rate2, afm_k2, afm_dir2 and afm_init2. However, pulling one group is OK. My pull.ppa is verbose = yes runtype = afm group_1 = a_TER1 group_2 = a_TER2 pulldim = N N Y afm_rate1 = 0.01 afm_rate2 = 0.01 afm_k1= 1000 afm_k2= 1000 afm_dir1 = 0 0 1 afm_dir2 = 0 0 1 afm_init1 = 13.639 3.264 4.486 afm_init2 = 14.221 3.873 2.790 The group definition in pull.ndx is [ a_TER1 ] 1136 [ a_TER2 ] 2425 Could anyone tell me what's wrong here? Thanks a lot Best regards Linchen Gong ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How many ps needs a simulation?
Hi Jahan,You mention your computer restarted. Now that sounds serious. Can you give more details about that? What happens in the log-file before the crash. Was it gromacs or something else that caused it? Are you running windows or *nix? Furthermore, as mentioned before, how long the simulation should be, depends on what you want to get from it. If you try to fold your sequence, I'd guess you need at least 5-10 seconds.., and a few lifetimes of simulation if we don't get much faster computers soon. Still, if you're interested in functional processes, you're facing very long relaxation times, which I estimate could well be about 20-25 ns or more (as I've seen for a quite globular protein of my own, about half the size of yours). That means that before you get some real information you need simulation times of 40-50 ns at least. You can check the relaxation or convergence of your simulation by looking at the cosine content of the principal components (g_anaeig -h). If you're interested in local phenomena, you may be able to get away with shorter time scales. By the way, if your protein is more or less rigid, you can cut down the computational cost by choosing a proper definition of your simulation box. If your interested you can contact me off the list for that (but keep other questions regarded to the simulations directed to the list please). TsjerkOn 5/11/06, Dallas B. Warren [EMAIL PROTECTED] wrote: Mark, rofl... didn't see until now we both had the same response to this question!Yeah, spun me out a bit too when your repsonse arrived after I had sentmine ;-)Catch ya,Dr. Dallas Warren LecturerDepartment of Pharmaceutical Biology and PharmacologyVictorian College of Pharmacy, Monash University381 Royal Parade, Parkville VIC 3010[EMAIL PROTECTED] +61 3 9903 9524-When the only tool you own is a hammer, every problem begins to resemblea nail.___gmx-users mailing list gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, M.Sc.Groningen Biomolecular Sciences and Biotechnology Institute (GBB)Dept. of Biophysical ChemistryUniversity of Groningen Nijenborgh 49747AG Groningen, The Netherlands+31 50 363 4336 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Value for bonded force constant (Kb)
Hi Gmxions, The value Kb = 1673.6 KJ/mol nm2 working good for restraining distance (type6, Harmonic potential) between Fe(II) and corresponding ligating atoms N and O (of amino acids) at the end of 5000 steps of energy minimization. That is newly introduced Kb value is able to restraint at around 2-3 A (Which is the average value found from crystal structure) when comparing to more than 5A in the absence of Kb value. I am going to start MD with a hope that this success will also be there at the end of 2ns simulation Is there any second thought? With thanks! B.Nataraj On Wed, 10 May 2006 05:16:26 -0700, raja [EMAIL PROTECTED] said: Hi Mr Tsjerkw, Thanks for your mail. Infact I intented to attach the reference link but I missed it. Anyway here is the link where I taken the value of Kb. Infact the reference only talk between Fe and O atoms. I belive this value will be more reasonably for my purpose. I will update the outcome of the result of MD using this restraints after my work completes. In mean time here is the reference link http://www.jbc.org/cgi/content/full/280/51/42188 For quick find out on the page , use this key work force constant of 4.0 kcal/mol/Å2 and please let me know the validity of my judgement. With Thanks ! B.Nataraj On Wed, 10 May 2006 13:50:17 +0200, Tsjerk Wassenaar [EMAIL PROTECTED] said: Hi Raja, No objections from my side. But if you could also include the references resulting from your literature study, that would be nice to have in the archive (may save somebody searching the literature to find some iron - ligand parameters). Cheers, Tsjerk On 5/10/06, raja [EMAIL PROTECTED] wrote: Hi gmxions, Based on the litterature search , I am going to use Kb value of 4 Kcal/mol A2 (1673.6 KJ/mol nm2)as harmonic bonded force field constant(type 6) for restraining distance of Fe(II) ligated with atoms of 2 Nitrogen and 1 Oxygen. If any one having objection please correct me ): . With thanks ! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Send your email first class ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, M.Sc. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands +31 50 363 4336 -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - A no graphics, no pop-ups email service ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - And now for something completely different ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] angle restraints
Dear users, I have a small system with a number of small peptides. I want to constraint the angle between the N-term to C-term vectors of different peptides. This works well, but if I do a FEP calculation the dG/dl becomes smaller than zero at some point. I expected it to be at least allways greater than zero (zero in the limit that the restraint does not have to do anything), since a force has to be aplied to restraint the angles. Can anybody explain where I am going wrong? Thanks Maarten Send instant messages to your online friends http://uk.messenger.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: question on pulling 2 groups in afm run
Hi Linchen, You may want to try adding the line ngroups=2 to the pull.ppa, right under runtype = afm. It's in the new manual (version 3.3, section 6.2.3). Otherwise, I believe the number of groups defaults to 1, and that's why mdrun gets confused about finding a group_2, afm_rate2, etc. - it's only looking for one of each. I don't promise that will fix your problem, since I don't do much with pulling on multiple groups, but it's a good bet on a place to start. If that doesn't fix it, post the actual error messages. -Emily Walton Dear gromacs users, I met a problem on pulling 2 groups in a afm pulling run. When mdrun processes input file, error messages such as unknown left- hand : group_2 appear for group_2, afm_rate2, afm_k2, afm_dir2 and afm_init2. However, pulling one group is OK. My pull.ppa is verbose = yes runtype = afm group_1 = a_TER1 group_2 = a_TER2 pulldim = N N Y afm_rate1 = 0.01 afm_rate2 = 0.01 afm_k1= 1000 afm_k2= 1000 afm_dir1 = 0 0 1 afm_dir2 = 0 0 1 afm_init1 = 13.639 3.264 4.486 afm_init2 = 14.221 3.873 2.790 The group definition in pull.ndx is [ a_TER1 ] 1136 [ a_TER2 ] 2425 Could anyone tell me what's wrong here? Thanks a lot Best regards Linchen Gong -- ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users End of gmx-users Digest, Vol 25, Issue 40 * ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Topology question
Anthony Cruz wrote: Hi users: I made a small molecule topology using the PRODRG topology generation server but I want to use it with the G43a1 GROMOS96 43a1 Forcefield. How I could change the parameters from GROMACS to GROMOS??? thanks Anthony ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Hi Anthony, search for a mail by christian burisch on this topic, posted on the list yesterday... -- Dipl.-Chem. Steffen Wolf Department of Biophysics University of Bochum ND 04/67 44780 Bochum Germany Tel: +49 (0)234 32 28363 Fax: +49 (0)234 32 14626 E-Mail: [EMAIL PROTECTED] Web: http://www.bph.rub.de ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Ngmx
karamyog singh wrote: Respected gentlemen, I have written another code for simulating atomic oxygen. the code is running fine. however when i view my run using ngmx, the entire box doesn't get filled up.It just shows one plane of atoms. I have a box of 27 atoms but ngmx shows only 9. Can any1 tell me why and the solution to this problem. 27MY OX 27 0.00 0.25 0.50 ; 0.000 0.000 0.000 0.5 0.5 0.5 Your box is of size 0.5x0.5x0.5, so atom 27 overlays exactly with some other atom at 0,0.25,0... evidently you are doing this with all of your atoms! Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Ngmx
Karam,If you think you know why, please share your thoughts.. that can help us provide an answer.Still, gromacs supports all periodic boundary conditions, except for real exotic stuff like spherical (and I can think of a few others). But any crystal packing can be handled. Maybe the easiest for you is to build a single bcc unit cell, with the correct lattice vectors as the box definition. Then run genbox to copy that a certain number of times. Also read the gromacs manual to understand the definition of the box (last line of the .gro file) if you haven't done so. TsjerkOn 5/11/06, karamyog singh [EMAIL PROTECTED] wrote: hmm.. i know about the no. of atoms in bcc. please tell me what to do if i want more than 1 unit cell?gromacs is not supporting periodic boundary conditions for my cell and i think i know y. On 5/11/06, Mark Abraham [EMAIL PROTECTED] wrote: karamyog singh wrote: Thnx Mark. I stil have a doubt. If want to simulate a crystal structure,then how should i go about it? wht changes should be made in the above file? even if i replace the 27th atom with 0.5 0.25 0.5, then too it will overlay some other atom.0.5 == 0 if the size is 0.5. If you've got the atom spacing right for 27atoms in this configuration, then increase your box size to make theperiodic images go in the right spots. At the moment you are overlaying atoms. I understand wht the fault with my conf.gro file is, but if I have to simulate a bcc lattice then wht should the .gro file look like?IIRC, a bcc lattice has two atoms per unit cell e.g . the central one andeight eighths of an atom at each of the cube vertices. Thus I have noidea what you're trying to do with 27 atoms.Mark___gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, M.Sc.Groningen Biomolecular Sciences and Biotechnology Institute (GBB)Dept. of Biophysical ChemistryUniversity of Groningen Nijenborgh 49747AG Groningen, The Netherlands+31 50 363 4336 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Ngmx
the problem continues even if i rescale my box to 1.0 1.0 1.0 :(On 5/11/06, karamyog singh [EMAIL PROTECTED] wrote:hmm.. i know about the no. of atoms in bcc. please tell me what to do if i want more than 1 unit cell? gromacs is not supporting periodic boundary conditions for my cell and i think i know y. On 5/11/06, Mark Abraham [EMAIL PROTECTED] wrote: karamyog singh wrote: Thnx Mark. I stil have a doubt. If want to simulate a crystal structure,then how should i go about it? wht changes should be made in the above file? even if i replace the 27th atom with 0.5 0.25 0.5, then too it will overlay some other atom.0.5 == 0 if the size is 0.5. If you've got the atom spacing right for 27atoms in this configuration, then increase your box size to make theperiodic images go in the right spots. At the moment you are overlaying atoms. I understand wht the fault with my conf.gro file is, but if I have to simulate a bcc lattice then wht should the .gro file look like?IIRC, a bcc lattice has two atoms per unit cell e.g . the central one andeight eighths of an atom at each of the cube vertices. Thus I have noidea what you're trying to do with 27 atoms.Mark___gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] afm pulling and comm_mode
Hi again, I pretty much went about the setting up of afm pulling calculations. Still I am a little bit concern about the results. When using gmx3.2.1 and applying a Linear removal of the center of mass (i.e. translation) I see the cell unit still moving during the simulation in a direction that, looks to me, is opposite to the force I am applying. In fact, when the pulling rate is smaller, the move is not as dramatic. What am I doing wrong? I have no note that with 3.3 this doesn't happen. Did anyone experience something like that? Any tip/suggestion will be greatly appreciated Best M Marta Murcia wrote: Thanks Emily and Maik for your feed-back You both are right regarding the init vector. I happened to be the sign of it as Emily guessed. Changing the direction by doing xpull-xref, ypull -yref, zpull-zref and not xref-xpull.works fine. Thanks for the offer on the script though. Thanks Emily for claryfing my confusion on the directional vector All the best M Maik Goette wrote: Hi There seems to be something wrong with your init-vector. Ich have written a small python script, which simply calculates the vector for convenience purposes. You still need the pull- and COM-group coordinates, though. But that shouldn't be a problem. If you want it, I'll send it via mail. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Marta Murcia wrote: Emily, I just saw your answer Thanks a lot I just have another question about the unit vector describing the direction of pulling. Should it be always a unit vector (1 1 1 for example)? Should I asumme then that the direction of the pulling is the one specified by the init vector or could I used that same vector for example as afm_dir? Also, I don't know if I am doing something wrong but using afm_ini 1 1 1 and afm_dir as the vector that connects the two atoms I've chosen (the pulled and the ref) I am not able to get the spring and the pulled atom at the same coordinates at the beginning of pull.pdo file. # AFM 3.0 # Component selection: 1 1 1 # nSkip 1 # Ref. Group 'm' # Nr. of pull groups 1 # Group 1 'a_13586' afmVec 1.00 1.00 1.00 AfmRate 0.02 AfmK 3000.00 # 0.003.7130005.6270005.181000 3.6940003.7320005.7120005.542000 4.895.472001 I was able to get it, though, using absolute coordinates leaving the reference group blanck (using gromac 3.3 since in 3.2.1 there is a bug on absolute coordinates) #AFM 3.0 # Component selection: 1 1 1 # nSkip 1 # Ref. Group '' # Nr. of pull groups 1 # Group 1 'a_13586' afmVec 1.00 1.00 1.00 AfmRate 0.02 AfmK 3000.00 # 0.00 0.000.000.00 3.6940003.6940005.7120005.712000 4.894.89 what is wrong? am i choosing the wrong starting vector when using a reference group? (Note that I am using xref-xpull, yref-ypull, zref-zpull as afm-ini, 0.019 -0.085 0.291) Again, thanks a lot M Emily Walton wrote: Hi, Dear all, I am simulating an unbinding process with the pull code (afm option). I've been reading previous posts about this option and I just wanted to clarify some ideas and ask some questions. There are: 1-The pulling can be done choosing two different molecules. Why a particular group within a molecule can not be used? Not even as a reference group? Any group that is defined in your index file (specified with mdrun - pn pull.ndx) can be used. Look at made_ndx in the manual to learn how to add new groups. 2-Should I need to fixed the center of mass of the protein to avoid shifts? How can I do that? Would it be OK to use posre for the backbone of the protein with carrying out the pulling? It depends on what you want to do. Typically, something would need to be fixed. In ligand-protein systems, the center of mass of the protein is a reasonable choice. It was used by Grubmuller et al. in their 1996 Science paper on the unbinding of biotin-streptavidin. (Science, 271:954–5, 1996) For unraveling of proteins, one terminal atom may be fixed while the other is pulled. Fixing the center of mass of a group in the index file can be done in the .mdp file you feed to grompp. See the manual, chapter 7. 3-Should I removed all the constraints for the bonds (SHAKE, lincs)? I think this is a matter of preference. Some people do, some people don't. Again, it will depend on your system- is it stable without the constraints? The bonds that are broken with afm pulling are bonds described by non- bonded interaction terms in gromacs. These bonds
[gmx-users] do_dssp : ssdump data
Where can I find the exhaustive list of one letter codes used from secondary structures? (H for helix, T for turn...) I looked at do_dssp.c to figure it out . the array map[]... semes to hold the relevant information, but I got very confused. Any help would be appreciated... Senthil ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] position restraints
Dear all, I'm trying to figure out if there is currently a way to calculate the position restraint energy (for example, if I'm using a posre.itp file to harmonically restrain some atoms) on the fly. Can anyone give me some pointers? I haven't turned up anything useful on this since 2001 on the mailing list. In particular, I would *very much* like to be able to somehow get the position restraint energy without having to save trajectory snapshots and reprocess the trajectory somehow, as I need to get the position restraint energy every 0.2 ps or so over fairly long trajectories, and I would rather not have to save trajectory snapshots this often to disk. Will I have to modify the code to get this, or is there something more straightforward I can do? Thanks, David ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] position restraints
David Mobley wrote: Dear all, I'm trying to figure out if there is currently a way to calculate the position restraint energy (for example, if I'm using a posre.itp file to harmonically restrain some atoms) on the fly. Can anyone give me some pointers? I haven't turned up anything useful on this since 2001 on the mailing list. In particular, I would *very much* like to be able to somehow get the position restraint energy without having to save trajectory snapshots and reprocess the trajectory somehow, as I need to get the position restraint energy every 0.2 ps or so over fairly long trajectories, and I would rather not have to save trajectory snapshots this often to disk. Will I have to modify the code to get this, or is there something more straightforward I can do? It's not entirely clear to me what you want. If you apply position restraints you get the energy. Where's the problem? Thanks, David ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] position restraints
David, OK, I am running MD using position restraints, and I don't get a separate energy output for restraint energy or some such; as far as I can tell the energy of the restraints is grouped in with the total potential energy and never reported separately. I would like it to be reported separately, as well (perhaps in the .ene file). Is there a way I can get this? Thanks, David On 5/11/06, David van der Spoel [EMAIL PROTECTED] wrote: David Mobley wrote: Dear all, I'm trying to figure out if there is currently a way to calculate the position restraint energy (for example, if I'm using a posre.itp file to harmonically restrain some atoms) on the fly. Can anyone give me some pointers? I haven't turned up anything useful on this since 2001 on the mailing list. In particular, I would *very much* like to be able to somehow get the position restraint energy without having to save trajectory snapshots and reprocess the trajectory somehow, as I need to get the position restraint energy every 0.2 ps or so over fairly long trajectories, and I would rather not have to save trajectory snapshots this often to disk. Will I have to modify the code to get this, or is there something more straightforward I can do? It's not entirely clear to me what you want. If you apply position restraints you get the energy. Where's the problem? Thanks, David ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] mdrun_mpi stops at random
Hi all, I have an issue doing parallel runs where the simulation would just hang at seemingly random intervals anywhere from an hour to a day. There are no error messages reported in the logs and nothing funny from dmesg. My set up is two dual-core Pentium D. I run with -np 4 to take advantage of all cores. When I issue a top command when the run is frozen, I notice that mdrun_mpi is at 0% CPU usage and sometimes sleeping on the slave node. On the master node, CPU usage is close to max. There is no network activity according to the blinking lights on my switch as well. When I do a run with -np 2 where one process is run on each computer, the run seems to carry on stably. I am using: Gromacs 3.3.1 Lam 7.1.2 Parallel Knoppix Kernel version 2.6.12 Gromacs was compiled from source. I understand from searching the archives that a few people have had a problem similar to mine, but I could not fine a straight answer. Thanks! Jason ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Re: angle restraints
David, Thanks for your reply. I am currently using 3.3.1 code. I am increase the force, to be able to calculate the free energy required of introducing the angle restraints in the system. I use small force increments each run, using a delta_lambda of 0. Decreasing or increasing in my view only changes the sign of the overall graph, but it should not allow dG/dl to cross zero. Thanks, Maarten From: David Mobley [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Thu, 11 May 2006 09:34:28 -0700 Subject: Re: [gmx-users] angle restraints Maarten, What version of the code are you using? There was a bug in the angle restraints code until 3.3.1 (or 3.3 cvs) which caused angle restraints to turn off gradually as a function of lambda in free energy calculations, if I remember correctly. (See bugzilla for details: http://bugzilla.gromacs.org/show_bug.cgi?id=43). However, I'm not sure that relates to the problem you're describing, but it probably does, depending on the version you are using. What exactly are you changing in the free energy calculation? Are you changing the angle restraint as a function of lambda? If so, which way are you changing it? Decreasing or increasing restraints? David On 5/11/06, Maarten Wolf [EMAIL PROTECTED] wrote: Dear users, I have a small system with a number of small peptides. I want to constraint the angle between the N-term to C-term vectors of different peptides. This works well, but if I do a FEP calculation the dG/dl becomes smaller than zero at some point. I expected it to be at least allways greater than zero (zero in the limit that the restraint does not have to do anything), since a force has to be aplied to restraint the angles. Can anybody explain where I am going wrong? Thanks Maarten Send instant messages to your online friends http://uk.messenger.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users MvG Maarten ** ** Work Adress Julianalaan 136 ** ** 2628 BL Delft ** ** Netherlands ** ** +31(0)15-2789382** ** ___ Switch an email account to Yahoo! Mail, you could win FIFA World Cup tickets. http://uk.mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
