[gmx-users] Exclusions and pairs
Dear Gromacs users: Am I right assuming that [exclusions] do not affect the interactions defined by [pairs]? This seems to be implied from the note in section 5.3.4 in the manual: Note that one should add exclusions for all atom pairs participating in pair interactions type 3, otherwise such pairs will also end up in the normal neighbor lists. I think, however, that it can be confusing given the overall concept: [exclusions] removes non-bonded interactions, and [pairs] defines non-bonded interactions. One could think that pairs would be excluded too. May I suggest a more explicit statement to be added to the 5.4 sections (that [exclusions] do not affect [pairs]? Ignacio -- 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] Free energy calculations with BAR and TI
--- On Fri, 2/11/12, Tom Kirchner tom.kirch...@strath.ac.uk wrote: Actually, this is a known problem. You should find the description and solution in the archive. I had the same problem, so this may make your search more easy :) Thank you, it's good to know I'm not doing something wrong. Indeed, changing 298.15 to 298 in the .xvg files fixed it, and the effect on the result is smaller than the statistical error, I bet. Could anyone comment on my other question (whether the BAR simulations can be used for standard TI)? Ignacio -- 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] Can't center box with trjconv
I must be doing something wrong, but I can't get trjconv to center the simulation on a residue. The simulation box is cubic, the system is formed by an 8-atom frozen molecule and 800 water molecules. I try to center the box with: $ trjconv -f system.cpt -s system.tpr -o conf.gro -center (system.cpt and system.tpr are the result of a simulation) I select group 2 (the frozen molecule) as a center group, and I get this in the output conf.gro: 1ACR C11 0.074 0.042 1.443 0. 0. 0. 1ACR H12 0.130 0.139 1.443 0. 0. 0. 1ACR O3 0.133 2.822 1.443 0. 0. 0. 1ACR C24 2.811 0.056 1.443 0. 0. 0. 1ACR H25 2.771 0.158 1.443 0. 0. 0. 1ACR C36 2.731 2.834 1.443 0. 0. 0. 1ACRH3a7 2.622 2.843 1.443 0. 0. 0. 1ACRH3b8 2.775 2.734 1.443 0. 0. 0. as you see, the molecule is clearly broken (a difference of more than 2 nm in coordinates), and when visualized, it's indeed in the box's edge. I've tried with different combinations of -pdb res/mol, -boxcenter zero/tric/rect, -ur compact, but I always get the molecule broken, sometimes in a corner, sometimes in an edge. In case it matters, the initial configuration for the simulation has: 1ACR C11 0.138870 0.039109 0.00 1ACR H12 0.195321 0.135855 0.00 1ACR O3 0.197788 -0.067044 0.00 1ACR C24 -0.009210 0.052984 0.00 1ACR H25 -0.049761 0.154673 0.00 1ACR C36 -0.089322 -0.054436 0.00 1ACRH3a7 -0.198186 -0.045502 0.00 1ACRH3b8 -0.045500 -0.154639 0.00 and, as I said, this residue (and molecule) is set as frozen, and it is actually frozen during the simulation. Is there some bug/limitation in trjconv? Am I doing something wrong? Thanks, Ignacio -- 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] Free energy calculation on a frozen fragment
Hi all, I'm interested in calculating the free-energy change when a frozen part of the system changes. The change, in general, implies a change in coordinates and in non-bonded parameters. As far as I know, there's no efficient way to calculate this currently in gromacs. The only way I see is adding the two endpoints of the frozen fragment, and progressively turn on and off the electrostatic and vdw interactions (that is, use a dual-topology approach). This can be calculated either with TI or with BAR. But this is quite cumbersome, and it would be more efficient if one could change the frozen coordinates with lambda. Something similar can be done with position restraints, but these don't give a frozen enough geometry, and I'm not sure the results would be quite reliable. When calculating dH/dlambda with a frozen fragment, the contributions from the changing charges and non-bonded parameters are correctly included, what is missing is the contribution from the changing coordinates, and I believe this can be obtained if I can get an output of the average force (in vector form) on each affected atom. Is there some way to get this information (without storing the forces for the whole system)? Assuming that forces on frozen atoms are calculated at all. With the average force I can get the contribution to dH/dlambda, but this would only work with TI, for BAR I would need to be able to calculate the energy with different coordinates, and I'm afraid that's harder. Any other ideas on how to calculate the free energy when the coordinates of a frozen fragment change? Thanks. Ignacio -- 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] Exclusions in TIP4P
Hi all, In the OPLS-AA tip4p.itp file I see: [ moleculetype ] ; molname nrexcl SOL 2 and [ exclusions ] 1 2 3 4 2 1 3 4 3 1 2 4 4 1 2 3 If bonded interactions are included (FLEXIBLE defined), interactions between atoms 1, 2, 3 are already excluded, right? And is it needed to have both the n-m and m-n exclusions listed? Wouldn't it be the same with this?: [ exclusions ] 1 2 3 4 2 3 4 3 4 Thanks, Ignacio -- 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] Impropers in OPLS-AA
Hi all, I'm trying to build a topology file for a new molecule (benzimidazole) with the OPLS-AA force field, and I'm confused about which dihedrals and impropers I should include. I'm assuming that the molecule is similar enough to indole and adenine/guanine to use their parameters (except maybe their atomic charges, but I'll disregard this for the moment). I've decided to build an .rtp file and use pdb2gmx to create the topology. All is fine with bonds, angles and dihedrals, I think. In the .rtp I include the atomtypes and bonds, and all connected angles and dihedrals are automatically generated, and I guess that's the right thing here. But which impropers should I include? (I mean, what is the default in OPLS-AA, or what is it designed for). I've tried to find it in the OPLS literature, but couldn't find a clear indication of which exact terms to include in a (arbitrary) molecule. I tried to look at the TRP residue in the aminoacids.rtp file, but it only raised some doubts: 1. There are no defined impropers around the bridge atoms CD2 and CE2. 2. Each improper has the central atom as the 3rd atom, and not the 2nd, as the macro names suggest (improper_Z_CA_X_Y). Maybe this does not matter? So, can anyone tell me (or point me to somewhere where I can read it) whether I should include *all* impropers around aromatic atoms and which is the right order for OPLS-AA? Thanks, Ignacio -- 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] OPLS specific problem in gromacs 4.5.4
--- On Wed, 30/5/12, patrick wintrode pat_w...@yahoo.com wrote: After creating a box using editconf and then solvating using genbox, I try to add ions and get the infamous number of coordinates in .gro does not match number of coordinates in topology error. I've had this problem after solvating a PDB that already contained waters. The genbox command reported that N waters should be added, but since there were already n waters in the PDB, it added only N-n waters to the topology, while it should have added the whole lot of N molecules. Changing the number in the .top file solved this. -- 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] PME nodes
Hi all, There must be something I don't fully understand, by running grompp on a system, I get this: Estimate for the relative computational load of the PME mesh part: 0.32 Good, that's approximately 1/3, or a 2:1 PP:PME ratio, which is the recommended value for a dodecahedral box. But then I run the dynamics with mdrun_mpi -np 8 (different cores in a single physical machine) and I get: Initializing Domain Decomposition on 8 nodes [...] Using 0 separate PME nodes I would have expected at least 2 nodes (3:1, 0.25) to be used for PME, so there's obviously something wrong in my assumption. Should I be looking somewhere in the output to find out why? Would it be better to try to get some dedicated PME node(s) (even in a single machine)? Thanks, Ignacio -- 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] Velocities in trjconv 4.5.5
--- On Mon, 23/4/12, francesco oteri francesco.ot...@gmail.com wrote: Hi Ignacio,actually .cpt contains velocities and, to extract a .gro containing them, you can try to use editconf. Thank you, Francesco. editconf doesn't appear to read .cpt files, trjconv does. But my problem is that trjconv does not write velocities in the output .gro file in the 4.5.5 version, while it does in the 4.5.3 version. -- 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] Velocities in trjconv 4.5.5
Hi all, I'm trying to get a .gro file with velocities. This command line works in 4.5.3: $ trjconv -f file.cpt -s file.tpr -o file.gro -pbc mol -center -boxcenter zero -ur compact -ndec 6 But in 4.5.5 the output .gro file is written without the velocities, even though the -vel option is listed as yes in the terminal. Has this been changed on purpose? Is there a way to get the old behaviour? If you wonder why I want this, I want to continue a simulation where the coordinates of a frozen part of the system are slightly changed, so I need a file with coordinates and velocities, and then modify the coordinates. Thanks, Ignacio -- 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] Velocities in trjconv 4.5.5
--- On Mon, 23/4/12, Alex Marshall amars...@uwo.ca wrote: I'm pretty sure .cpt files don't store velocity information. Try using a trr file instead. Well, I'm pretty sure .cpt files do store velocities: 1. What good would be checkpoint files without velocities? 2. It works with version 4.5.3 3. gmxcheck -f file.cpt says, for both 4.5.3 and 4.5.5: Step 1 Time 1 Lambda 1 Coords 1 Velocities 1 Forces 0 Box 1 -- 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] Velocity autocorrelation
--- On Sun, 1/4/12, Ignacio Fernández Galván jel...@yahoo.com wrote: Maybe instead of individual atoms, I should analyze the VACF of the center of mass of each molecule, and the rotational ACF. The latter I know how to do it. Is there an easy way to calculate the former? Silly me, I should have tried the -mol flag for g_velacc from the beginning, how did I miss it? The shape that results is exactly what I was expecting. However, I'm not completely sure what this flag does. Does it compute the velocity (and its autocorrelation) for the center of mass of each molecule? Does it compute some kind of average per molecule? Something else? I also tried a workaround: first generate the the centers of mass trajectory with g_traj -oxt -com, and then try to calculate the corresponding VACF with g_velacc... but g_traj does not write center of mass velocities in the trajectory, hmmm -- 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] Velocity autocorrelation
--- On Fri, 30/3/12, David van der Spoel sp...@xray.bmc.uu.se wrote: No need, I think it is just fine! What your seeing is the average vacf per atom, and apparently there are correlations between the vibrations which cause the oscillation. In theory both VACF should be the same but they are relatively close. A longer simulation is always good of course. But how can I extract a meaningful relaxation time from there? Maybe instead of individual atoms, I should analyze the VACF of the center of mass of each molecule, and the rotational ACF. The latter I know how to do it. Is there an easy way to calculate the former? Anyway, in this case it makes sense to divide the system in molecules, because that's what it is, but if it were say a protein, what would be the best way to analize the VACF and get some meaningful relaxation time? Thank you, Ignacio -- 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] Velocity autocorrelation
--- On Thu, 29/3/12, Krzysztof Kuczera kkucz...@ku.edu wrote: You probably need to save velocities at least every 10 fs; look at your plot on a fine enough time scale - say 0-1 ps range probably running in NVE ensemble would help as well Thanks for your suggestion. I was already saving velocities every 10 fs. I tried with a NVE ensemble, but the behaviour is the same. I have uploaded a sample velocity ACF here: http://djelibeibi.unex.es/files/vac_NVE.xvg That's the autocorrelation file for CN atoms in acetonitrile. I have also uploaded the corresponding mdp file: http://djelibeibi.unex.es/files/dinamica_NVE.mdp I still don't know how to properly analyze this, I would say that I want the amplitude to drop to almost zero, and that would mean a relaxation time of ~5-6 ps. But is this the correct/expected behaviour? Thank you, Ignacio -- 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] Velocity autocorrelation
--- On Fri, 30/3/12, David van der Spoel sp...@xray.bmc.uu.se wrote: Why are you freezing part of the system? I want a given molecule (20 atoms) to be rigid. Is there a better way that works for any kind of molecule (not just water)? I believe freezing it should be equivalent to keeping it rigid and removing the center of mass motion. The VAC looks ok doesn't it? How many molecules? My concern is it doesn't look like the typical VAC I find in the literature (as in http://www.compsoc.man.ac.uk/~lucky/Democritus/Theory/vaf.html), and I don't know how to quantitatively analyze this function. There are 459 solvent (acetonitrile) molecules. Not too many, I know, but it's box size of ~40 Å. What is the temperature of your system? Around 295 K. Is it starting from an equilibrated liquid? Yes, or so I believe. I run a 50 ps equilibration first, and use the resulting checkpoint with -t Thank you, Ignacio -- 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] Velocity autocorrelation
--- On Fri, 30/3/12, David van der Spoel sp...@xray.bmc.uu.se wrote: There are 459 solvent (acetonitrile) molecules. Not too many, I know, but it's box size of ~40 Å. And how are you treating the linear angle? Nothing special. I built an OPLS-AA topology with 5 bonds, 7 angles, 3 dihedral and 3 pairs (http://djelibeibi.unex.es/files/ACN.itp). Visual inspection of the conformations shows an almost linear CN group in every molecule, and g_angle gives an average of 177, and a distribution that looks fine to me. Is it starting from an equilibrated liquid? Yes, or so I believe. I run a 50 ps equilibration first, and use the resulting checkpoint with -t Have you checked the diffusion constant to test whether it is liquid? You can do that from the VACF and from the mean square displacement. From g_msd I get a D of around 5.6e-5 cm^2/s which looks about the right order of magnitude? (Default OPLS-AA acetonitrile is not very good, anyway.) Integrating the VACF gives 4.8e-5 cm^2/s Perhaps I should try with a larger system / longer simulation? I can provide all the input files if needed. Thanks, Ignacio -- 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] Velocity autocorrelation
Dear all, I'm trying to estimate the correlation time for my system, for the purpose of selecting a number of uncorrelated configurations and setting a good value for nstxout. My systems are usually small molecules in molecular liquids (water, methanol, acetonitrile, cyclohexane...). As a first approach, I calculate the velocity autocorrelation function for the pure liquid (or for a group containing only the solvent in a simulation of the full system). I expect to find a function more or less like the one shown here: http://www.compsoc.man.ac.uk/~lucky/Democritus/Theory/vaf.html. But instead I get a line that rapidly oscillates around 0, with an amplitude that progressively vanishes. I think I understand this behaviour, as it would be due to intramolecular vibrations or librations, but I don't find samples of this in the literature. My question is how can analyze this and extract some correlation time? How could I get some smooth function like the one shown in the above link? Am I doing something wrong? Is there another way to estimate a good value for nstxout? Any help or pointers to where to find it would be appreciated. Thank you, Ignacio -- 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] Reading starting velocities
Hi all, I was wondering if it's possible to start a simulation by reading the starting configuration from a file and the initial velocities from somewhere else. The goal is being able to continue a simulation of a mostly equilibrated system, but where I change slightly the coordinates of some atoms (in particular, of some frozen atoms). The closer I could get to that was modifying the final .gro file of the first simulation, which includes coordinates and velocities. But the precision of the .gro file is relatively low. I tried using both a .gro (without velocities) and .cpt files for starting the new simulation, but initial velocities are then assigned as 0.000. I also tried trjconv to convert the .cpt to .gro with higher precision (-ndec), but only coordinates are written in this case (although I explicitly added -vel). I guess I could manually add the velocities after getting them with gmxdump, but is there some other more straightforward way? Thanks, Ignacio -- 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] Using groups in the mdp file
--- On Mon, 6/2/12, Ignacio Fernández Galván jel...@yahoo.com wrote: The .gro file does not contain any mention to ACX, but I believe it's not needed, as long as it's in the .top, right? It seems that default group names are generated not from moleculetype names, but from residue names. At least that's what it says in http://www.gromacs.org/Documentation/Gromacs_Utilities/make_ndx: default index groups are already generated (entire system, 9 groups for proteins, and one for every other *residue name*). In my case, if I use GLC (residue) for energygrps instead of ACX (molecule), it works fine. -- 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: Gromacs analysis tools for Namd output
--- On Tue, 7/2/12, Kunze, Micha micha.kunze...@ucl.ac.uk wrote: cant help you with the plugin issue, but have you instead tried loading the dcd trajectory into vmd and save it as trr? No need to open it with VMD. You can use catdcd (http://www.ks.uiuc.edu/Development/MDTools/catdcd/) to do the conversion: catdcd -o output.trr -otype trr input.dcd -- 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] Using groups in the mdp file
Hi all, I have a system with a molecule called ACX plus water (molecules called SOL), but when I try to use ACX as a group name in the .mdp file, grompp says such a group does not exist: --- Program grompp, VERSION 4.5.5 Source code file: readir.c, line: 1320 Fatal error: Group ACX not found in index file. Group names must match either [moleculetype] names or custom index group names,in which case you must supply an index file to the '-n' option of grompp. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- However, the .top file is, I believe, correct, it contains these lines: [ moleculetype ] ; Namenrexcl ACX 3 and then [atoms], [bonds], etc. It ends with: [ molecules ] ; Compound#mols ACX 1 SOL 2139 and that's not a problem. It's when I try to use ACX as a group name, as in: energy_grps = ACX that I get the error. What am I doing wrong? Is there any option I must activate to enable using molecule names as groups? Thanks, Ignacio -- 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] Using groups in the mdp file
--- On Mon, 6/2/12, Justin A. Lemkul jalem...@vt.edu wrote: Perhaps the OP can provide the original grompp command and whether or not the -n flag was invoked. An incorrect index file can also give this error, I believe, if it does not contain the desired group. I'm not using an index file. The grompp command line is simply: grompp -f dinamica.mdp -c equilibrar.gro -p topol-mod.top -o dinamica.tpr The .gro file does not contain any mention to ACX, but I believe it's not needed, as long as it's in the .top, right? energy_grps = ACX This is an incorrect keyword that should have raised a fatal error. The proper keyword is energygrps. Perhaps both energy_grps and energygrps are valid? I tried with energygrps and I get the same error as with energy_grps, and both work if I use SOL instead of ACX. -- 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] Getting nonbonded interactions from gmxdump
Hi all, I'm trying to extract the nonbonded interaction parameters for a whole system from the text dump generated by gmxdump (-s topol.tpr). I get it the relevant section is something like this: atnr=7 ntypes=50 functype[0]=LJ_SR, c6= 2.34487536e-03, c12= 4.69342376e-06 functype[1]=LJ_SR, c6= 2.94705760e-03, c12= 4.75720708e-06 functype[2]=LJ_SR, c6= 5.42534457e-04, c12= 3.83789740e-07 ... All is fine with that, except that I see nowhere the correspondence between the functypes and the nonbonded pairs. In principle, I assume the first n^2 functypes correspond to the interactions between the n atomtypes (7 in this case). But is there a guarantee that the nonbonded parameters are always listed first in the functypes (and, after them, there come the bonded parameters)? Thanks, Ignacio -- 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] Rigid structure and flexible structure present in sing system
chris.ne...@utoronto.ca wrote: If you simply want to know how to freeze one structure, then use freeze groups and energy exclusions without pressure coupling, or use position restraints and refcoordscaling=com with position restraints, or create an elastic network of restraints. Is it really not possible (or conducting to wrong results) to do NPT simulations with freeze groups? I did some tests with just a freeze group (a single molecule with no bonds with the rest of the system), and it caused a blow-up, indeed. But excluding all intramolecular interactions, for example using the 5 bond type and a large enough nrexcl value, or explicitly listing all exclusions in the topology, seemed to fix it. The coordinates of the frozen molecule do not change when the box grows or sinks... So, my conclusion was that NPT with a frozen molecule is possible, as long as no intramolecular terms are included. Am I wrong? Ignacio -- 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] Is there still interest in rigid-body simulation?
From: Adam Herbst ad...@cornell.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Mon, 28 March, 2011 0:02:17 Subject: [gmx-users] Is there still interest in rigid-body simulation? Hi all, I have seen a few posts on gmx-users indicating a desire to treat certain atom groups as rigid bodies in MD simulations. I just started implementing this, and so far I have it working for translational forces (not rotation, though this should be simple to add), even when the group is split over multiple processors. At the moment I have the rigid body groups specified as freeze groups in the mdp file, but there could be a separate option. Would anyone else find this useful? I would warmly welcome this feature! :) -- 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] Performance in ia64 and x86_64
I wrote: It seems the x86_64 processor has 4 cores and 8 threads support (http://ark.intel.com/Product.aspx?id=37104), so the machine has probably two physical processors. I thought MPI was only needed if there was network communication involved, as in a cluster, but not in SMP, which is what both machines are (single memory, single OS), I guess I was wrong. I'll try compiling with MPI. Well, I've compiled mdrun with MPI (with fortran kernels in the ia64), and run my test system in both machines, with a single processor. The results are still worrying (to me). This is a 50 time step (0.5 ns) simulation with 1500 water molecules, not a big system, but it still takes some hours: x86_64: 3.147 ns/day ia64: 0.507 ns/day Is this difference normal? Am I doing anything wrong? what further data should I provide? The compilation in both machines was quite straightforward (once I had solved the library and path issues). Thanks Ignacio -- 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] Performance in ia64 and x86_64
Carsten Kutzner wrote: With Fortran kernels I got a performance of 0.31 ns/day for an 80,000 atom system (with PME) on an Altix 4700, so your 0.5 ns/day for 1,500 waters seems too slow to me. What processor is this? Are you shure you are using the Fortran and not the C kernels? I don't have physical access to the ia64, and I don't know the details, but /proc/cpuinfo says: model name : Dual-Core Intel(R) Itanium(R) Processor 9140N cpu MHz: 1598.00 And as for the kernels in the log: Configuring nonbonded kernels... Configuring standard C nonbonded kernels... Configuring single precision Fortran kernels... Whereas for the x86_64 it's: model name : Intel(R) Xeon(R) CPU E5540 @ 2.53GHz cpu MHz : 1600.000 Configuring nonbonded kernels... Configuring standard C nonbonded kernels... Testing x86_64 SSE2 support... present. -- 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] Performance in ia64 and x86_64
Hi all, I'm compiling and testing gromacs 4.5.3 in different machines, and I'm wondering if it's normal that the ia64 is much slower than the x86_64 I don't know full details of the machines, because I'm not the administrator or owner, but /proc/cpuinfo says: ia64 (128 cores): Dual-Core Intel(R) Itanium(R) Processor 9140N x86_64 (16 cores): Intel(R) Xeon(R) CPU E5540 @ 2.53GHz Just looking at the GHz, one is 2.5 and the other is 1.4, so I'd expect some difference, but not a tenfold one: with 8 threads (mdrun -nt 8) I get 0.727 hours/ns on the x86_64, but 7.607 hours/ns on the ia64. (With 4 threads, it's 1.3 and 13.7). I compiled both cases with gcc, although different versions, and default options. I had read assembly or fortran kernels could help with ia64, but fortran is apparently incompatible with threads, and when I tried with assembly the mdrun seemed stuck (no timestep output was written). Is this normal? Is there something else I'm missing? Also, in the x86_64 system I get much lower performance with 12 or 16 threads, I guess that could be because of the cores/processors, but I don't know what's the exact configuration of the machine. Again: is this normal? Thanks, Ignacio -- 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] Performance in ia64 and x86_64
Original Message From: Mark Abraham mark.abra...@anu.edu.au We can't say with the information given. For best performance, the number of threads cannot exceed the number of physical cores available to one processor. To go higher, you need to compile and use GROMACS with MPI, not threading. If the IA64 is dual core then you are not measuring anything useful. You also need to be sure you're measuring for a decent length of time - a few minutes at least. It seems the x86_64 processor has 4 cores and 8 threads support (http://ark.intel.com/Product.aspx?id=37104), so the machine has probably two physical processors. I thought MPI was only needed if there was network communication involved, as in a cluster, but not in SMP, which is what both machines are (single memory, single OS), I guess I was wrong. I'll try compiling with MPI. Thanks, Ignacio -- 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] Visualizing non-rectangular boxes
--- [EMAIL PROTECTED] wrote: Yes. I use 3.3.1. Try installing that. If it works fine with 3.3.1 and not with 3.3.2 then submit a bugzilla. OK, I think I found it. Indeed, it works with 3.3.1 but not with 3.3.2. After checking the source code, it works with 3.3.2 if I use this command line: trjconv -f b.gro -s b.tpr -pbc atom -ur compact -o c.gro (note: -pbc atom) There is a small confusion, because the help text for trjconv says: Option -ur sets the unit cell representation for options mol, res and inbox of -pbc. But the inbox option is not allowed for -pbc. Instead it should say atom (which translates to bInBox in the source). ___ Want ideas for reducing your carbon footprint? Visit Yahoo! For Good http://uk.promotions.yahoo.com/forgood/environment.html ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Visualizing non-rectangular boxes
Hi all, I'm trying to set up a simulation with a rhombic dodecahedron cell shape, for that I use editconf with the -bt dodecahedron option. Now I'd like to visually check the system configuration with a program such as VMD, but when I open the .gro files, I see the equivalent rectangular box used in the simulation (I guess). How can I generate a configuration file (.gro, .pdb, .trr...) with the dodecahedron shape? I tried with: trjconv -ur compact -s topol.tpr -f config.gro -o filenew.pdb but when I open filenew.pdb with VMD I still see the rectangular box. Am I missing anything? Thanks Ignacio ___ Want ideas for reducing your carbon footprint? Visit Yahoo! For Good http://uk.promotions.yahoo.com/forgood/environment.html ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Visualizing non-rectangular boxes
--- [EMAIL PROTECTED] wrote: Your trjconv command seems fine. Is config.gro actually a dodecahedron? $tail -1 config.gro Does it look like a dodecahedron? 3.02251 3.02251 2.13022 0.0 0.0 0.0 0.0 1.51125 1.51125 Or does it look more rectanguar? 18.84582 18.63005 22.03044 It is a dodecahedron, as far as I can see. The last line says: 3.44971 3.44971 2.43931 0.0 0.0 0.0 0.0 1.72486 1.72486 ___ Want ideas for reducing your carbon footprint? Visit Yahoo! For Good http://uk.promotions.yahoo.com/forgood/environment.html ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Visualizing non-rectangular boxes
--- sebastien santini [EMAIL PROTECTED] wrote: I think you should use: editconf -f config.gro -o config.pdb -visbox 1 1 1 donot forget to remove the MODEL 1 and ENDMDL from the file if you want to see the box with pymol. it works fine for me With that, I get the same configuration (the shape occupied by the molecules is still rectangular), but also an elongated dodecahedron drawn with CONECT lines in the pdb... ___ Want ideas for reducing your carbon footprint? Visit Yahoo! For Good http://uk.promotions.yahoo.com/forgood/environment.html ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Visualizing non-rectangular boxes
--- [EMAIL PROTECTED] wrote: Here's a test. Copy this into a file and chmod +x it and then run it and vmd c.gro. Is it dodecahedron? It should be. Hmm... No, it is still a rectangular box. I was preparing a simple test similar to yours, but it's now unnecessary (interestingly, I had the same touch empty.mpd line ;)). VMD is version 1.8.6, so it's recent enough, and molden also shows the same rectangular box (plus the triclinic box wireframe). Gromacs is version 3.3.2, just compiled some days ago in a Mandriva 2007.1 system. It seems there is some problem here. Ignacio ___ Want ideas for reducing your carbon footprint? Visit Yahoo! For Good http://uk.promotions.yahoo.com/forgood/environment.html ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] backup files
Pedro, looks like gmx-tools allways want an .extension for input files, so how about renaming all # files, or at least remove the last # ? try this: (quick and dirty) rename \#conf.gro.1# #1.conf.gro \#conf.gro.1# rename \#conf.tpr.1# #1.conf.tpr \#conf.tpr.1# rename \#conf.edr.1# #1.conf.edr \#conf.edr.1# rename \#conf.xtc.1# #1.conf.xtc \#conf.xtc.1# rename \#conf.trr.1# #1.conf.trr \#conf.trr.1# For renaming a single file, use mv, rename can rename multiple files (some additional escaping might be needed): (remove all the .1#) rename .1# \#conf* (change the initial # into #1.) rename # #1. \#conf* ___ The all-new Yahoo! Mail goes wherever you go - free your email address from your Internet provider. http://uk.docs.yahoo.com/nowyoucan.html ___ 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] MANPATH setting in GMXRC.bash
Hi all, I'm using Gromacs 3.3.1 in Mandriva 2007, and I'm having an issue with the definitions in GMXRC.bash. The problem is that, with the default settings, I lose the standard directories searched by man, i.e., typing man bash says command not found. Without sourcing GMXRC.bash, it works, and so it does if I add an empty string to MANPATH (prefixing a colon, for instance). I realise adding empty strings is a security problem in PATH (since that means current directory), but it might be desirable in MANPATH (I don't know about LD_LIBRARY_PATH). Ignacio ___ Copy addresses and emails from any email account to Yahoo! Mail - quick, easy and free. http://uk.docs.yahoo.com/trueswitch2.html ___ 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] MANPATH setting in GMXRC.bash
--- Ansgar Esztermann [EMAIL PROTECTED] wrote: settings, I lose the standard directories searched by man, i.e., typing man bash says command not found. Without sourcing That does not seem to be a MANPATH problem but rather a PATH problem: searching for an unknown man page yields No manual entry rather than Command not found -- the latter happens if the command man itself is not found. O, gosh!... I wrote it from the top of my head and made a stupid mistake. The actual message is, of course, No manual entry for bash, and it's fixed by export MANPATH=:$MANPATH. GMXRC.bash, it works, and so it does if I add an empty string to MANPATH (prefixing a colon, for instance). Did you compile Gromacs for yourself, or is it included with Mandriva? If you compiled it for yourself, where did you install, i.e. what --prefix did you give to configure? I compiled it myself, I didn't write any explicit --prefix, so config.log says it's --prefix=/usr (gromacs is installed in /usr/local/gromacs). Instead of just make install, I used checkinstall, which does the same, but builds an rpm package. I don't know if it works differently for other versions of man/bash, but in my case, if MANPATH is empty, changing it to something else without adding an empty string is not nice. Thanks Ignacio ___ To help you stay safe and secure online, we've developed the all new Yahoo! Security Centre. http://uk.security.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
Re: [gmx-users] Free energy calculation, parallel or sequential lambda runs ?
--- David Mobley [EMAIL PROTECTED] wrote: What I've shown in my work is that at some particular lambda values, there maybe worse sampling problems than at any other lambda value. This means that you may need to run longer at that particular lambda value in order to get adequate statistics. Unless you stop and analyze each of your lambda values before going on, noticing this later would mean you would need to go back and re-start the simulation of all of the subsequent lambda values, since the first time you didn't, you didn't use the correct ending structure. I still don't see it. I mean, I don't think I would need to rerun anything (except the particular lambda value). The fact that I'm using the final structure of a lambda run to start the equilibration of the next lambda is not really so important, I mean it doesn't *have to* be the final structure, it's only some structure that would probably be a better starting point than the global initial structure (lambda=0). Say, for instance, I want to run a TI with lambda=0, 0.1, 0.2 ... 1.0. I optimize, equilibrate and run with lambda=0; then I take the final structure, set lambda=0.1, equilibrate and run; take the final structure, set lambda=0.2, equilibrate and run; etc. Then I may find I need more sampling, and I decide I will run a simulation at lambda=0.15, I would take the final structure from lambda=0.1, equilibrate and run. But I would not change anything in the rest of the simulations, the one with lambda=0.2 is already done and it's fine. Is it really important that the initial structure prior to equilibration comes from lambda=0.1 or lambda=0.15? And if all I do is running a longer simulation at lambda=0.1, the effect would probably be even lower, I'd just leave the simulation at lambda=0.2 as it is. You seem to mean that, if I create this new lambda=0.15 I would have to rerun 0.2 with a new starting structure (still, with an equilibration period). Sure, the results would be different, but not significantly so (it would only be a different trajectory), and not worse than starting with a structure obtained with lambda=0. Am I still missing something? Thanks Ignacio ___ Try the all-new Yahoo! Mail. The New Version is radically easier to use The Wall Street Journal http://uk.docs.yahoo.com/nowyoucan.html ___ 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] strange new H-H bond formation during MD
--- Mark Abraham [EMAIL PROTECTED] wrote: Right, so like I said earlier, you're not giving it your topology, because you're loading from a .gro file. Instead, VMD is making stuff up Incidentally, you can disable this behaviour by loading the file in VMD with mol new myfile.gro autobonds 0 (or something like that). 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] Free energy, frozen atoms and exclusions
Hi all, I'm trying to calculate solvation free energies and I've found something strange. The thing is I'm interested in free energy of rigid molecules (I consider other contributions separately), typically a small solute molecule in water. I'm making a test with methanol. The setup is a frozen methanol molecule in a box of of water molecules. Since I'm considering rigid molecules, I create an .itp file with no bonded terms, just atoms (with charges and LJ). The methanol molecule is called MOH, and I have this in the .mdp: energy_grps = MOH energygrp_excl = MOH MOH freezegrps = MOH freezedim= y y y which should freeze the methanol and disregard all nonbonded terms between the methanol atoms (and there are no bonded terms). Well, after the usual equilibration and such, I get this output for the initial configuration with lambda=1: LJ (SR): 5.70341e+03 Coulomb (SR): -3.65377e+04 ... dVpot/dlambda: 2.81161e+02 It seems right, but after simulation for several lambda values I get a free energy of around 10 times what I would expect. Now I repeat exactly the same simulation, but adding all pairs of methanol atoms in the [exclusions] of the .itp file. For the same initial configuration as before, I get this: LJ (SR): 5.70341e+03 Coulomb (SR): -3.65377e+04 ... dVpot/dlambda: 2.14385e+00 (the only difference is in dVpot/dlambda). This (if I extrapolate) would give a much more sensible value for the free energy. As far as I could understand, having energygrp_excl = MOH MOH should be the same as putting all atoms in the [exclusions] section, but it obviously isn't, at least when it comes to calculating dVpot/dlambda. Is there something I'm missing? A bug/feature in the code? A limitation? Thanks in advance PS. As a side question, I'd say that, if I have a frozen molecule it would be best *not* to remove the center of mass motion (not even of the rest of the system). Am I right? ___ Try the all-new Yahoo! Mail. The New Version is radically easier to use The Wall Street Journal http://uk.docs.yahoo.com/nowyoucan.html ___ 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] Free energy, frozen atoms and exclusions
--- Berk Hess [EMAIL PROTECTED] wrote: Is there something I'm missing? A bug/feature in the code? A limitation? If you are using PME, the mesh contribution is not excluded when using energygrp_excl, grompp should give you a warning about this. Adding all the pairs as exclusions solves this problem. Thanks. Would that account for such a large difference, considering it's a neutral molecule (and at lambda=1, with no partial charges)? Well... since it's the derivative, and that means the free energy change from lambda=0 to lambda=1... yes that could be it. Is this mentioned in the manual? 'Cause I read about the [exclusions] section and it gives the advice to use energygrp_excl, but doesn't warn about this. Would normal Ewald or reaction field work as (I) expected? I guess I will keep using PME anyway, if it's as easy as adding the [exclusions]. But why do you want to freeze the methonal? Things would be much easier with a free methanol. At the moment this is only a test. I need the method to work for arbitrary molecules for which there are no force field parameters, only LJ. The atomic charges and intramolecular contributions I get them from other QM/MM calculations. I also need to compare with other rigid-body simulations. I'm not saying this is the best way to calculate free energies, but it's the way I need now :) Thanks a lot for the reply! PS. The manual mentions using no for comm_mode, but grompp prefers none instead. ___ All New Yahoo! Mail Tired of [EMAIL PROTECTED]@! come-ons? Let our SpamGuard protect you. http://uk.docs.yahoo.com/nowyoucan.html ___ 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
