Re: [gmx-users] solute tempering (REST2)
Hi, You can patch Gromacs with Plumed and use hrex: * generate a full .top file of your system (with -pp in the grompp command) * open your .top and add "_" in the second column (type) of each atom you want to apply REST2 in the [ atoms ] section of the moleculetype * use the command "plumed partial_tempering ..." as described in https://www.plumed.org/doc-v2.5/user-doc/html/hrex.html to create all the scaled topologies * use grompp to generate all the tpr * run gromacs. The website above suggest the use of multi which doesn't work anymore. Something like this should work "gmx mdrun -multidir run0 run1 run2 run3 -deffnm NPT -plumed Plumed.dat -replex 200 -hrex" (where you have created the folders run0, run1, run2 and run3, and in each one there is the corresponding file NPT.tpr). You need the file Plumed.dat even if it can be empty Nicolas Le dim. 12 janv. 2020 à 23:02, hind ahmed a écrit : > Dear All, > Is there a tutorial for solute tempering (REST2) in gromacs or any clear > guide to apply this method? > > Regards, > > Thank you > > Sent from my Huawei tablet > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Calculation of RMSF
Thank you for your answer. As Mala said, since it is called the reference structure, I was thinking that the RMSF was computed with respect to this structure and not the average structure. Is there any way with Gromacs to compute RMSF exactly with respect to a given structure? If I want to study a crystal of protein for force field validation (as in https://pubs.acs.org/doi/abs/10.1021/jp105813j), I would like to compute RMSF exactly with respect to the XRay structure first. If not with Gromacs, does someone know a way to do it with something else (cpptraj, mdanalysis, mdtraj?) Thank you Nicolas Le ven. 29 nov. 2019 à 14:22, Justin Lemkul a écrit : > > > On 11/29/19 5:53 AM, Mala L Radhakrishnan wrote: > > Hi, > > > > I am confused a bit by this answer -- isn't the file specified by -s used > > for defining the rmsf (this is what is called the "reference" structure > in > > the documentation, and I have found that my results do vary using a > > different "-s" file)...? Or is that just used for fitting and then the > > average of the resulting fitted structures is used for the rmsf? > > Specifically, what is the "-s" uased for in this case? > > It is used for fitting. RMSF is simply the standard deviation of > position, so an average structure is computed from the selected frames > and the RMSF is computed from it. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Calculation of RMSF
Dear all, I am puzzled by the way RMSF are computed. For a given trajectory (nothing fancy, just a regular protein): (1) I have computed RMSF 5 times for two frames i.e. Frame 1/2, 3/4, 5/6, 7/8 and 9/10, each time using the same pdb reference (if I compute RMSF for a single frame I sometimes have -nan, that's why I did it for couple of frames) (2) I have then computed RMSF for the 10 frames at the same time (1-10). I would expect that the average of RMSF^2 for (1) would equal RMSF^2 for (2), but that's not the case. To give you some numbers for 4 Calpha carbons: Avg of case (1) case (2) 0,000722 0,001673 0,000417 0,001197 0,000400 0,001096 0,000768 0,001910 It doesn't seem to be a rounding issue, neither a systematic difference. Can anyone please help me understand these differences? Thank you Nicolas PS: in case someone suggests that the problem may come from pbc because the protein would be split in two, it is not the case, the protein is whole. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Periodic saving of checkpoint file
Hi Mark, Thank you for your answer. I didn't know this option. From what I have read, eneconv is for reading parameters for Nose-Hoover or Parrinello-Rahman coupling. Thus, if I am doing first an NVT simulation with the velocity-rescale thermostat or a Langevin dynamics, I don't need the .edr file, right ? Can you please confirm that this is enough to prepare the tpr from the time 50ps of the NVT simulation: gmx grompp -v -f NVE.mdp -n Index.ndx -o NVE.tpr -c NVT.gro -t NVT.trr -time 50 -p Protein.top -po NVE_mdout.mdp Thank you Le lun. 5 nov. 2018 à 17:50, Mark Abraham a écrit : > Hi, > > Since you are anyway intending to change the ensemble, you can just use > nstxout, nstvout and nstenergy to write output every 10ps. That content is > equivalent to that of the checkpoint. Use trjconv and eneconv afterwards to > split those up, and use them as inputs to grompp -e -t along with the > regular inputs. > > Mark > > On Mon, Nov 5, 2018 at 5:14 PM Nicolas Cheron < > nicolas.cheron.bou...@gmail.com> wrote: > > > Dear all, > > > > I would like to run a long NVT simulation and save a checkpoint file > every > > 10ps (in order to then run short NVE simulations from each checkpoint). > Is > > there a way to save a .cpt file every 10ps in an automatic way? > > > > I can do it with other program, for example with Amber "ntwr=-5000" will > > save a new restart file every 5000 steps. For now with Gromacs, the only > > thing I have found is to write a loop where at each step I extend the > > simulation time of 10ps with convert-tpr, perform the 10ps simulation, > save > > the .cpt, and then loop again. > > > > Thanks for your help. > > > > Nicolas > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Periodic saving of checkpoint file
Dear all, I would like to run a long NVT simulation and save a checkpoint file every 10ps (in order to then run short NVE simulations from each checkpoint). Is there a way to save a .cpt file every 10ps in an automatic way? I can do it with other program, for example with Amber "ntwr=-5000" will save a new restart file every 5000 steps. For now with Gromacs, the only thing I have found is to write a loop where at each step I extend the simulation time of 10ps with convert-tpr, perform the 10ps simulation, save the .cpt, and then loop again. Thanks for your help. Nicolas -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Extension on different machines (CPU/GPU
Hi Mark, Thank you for the quick answer. However, the problem is not only a problem of reproducibility of a single simulation. To make sure that I have converged results with proper sampling, I am performing each time 10 simulations of the same system with different positions of the solvent molecules and different initial velocities. For the 10 simulations, I had reached a plateau at 250ns for the parameters I am looking at. When extending to the GPU machine, for the 10 simulations I see these parameters increasing. For other sets of simulations with the same solute but different water:glycerol molar fractions, the plateau stays stable until 300ns and I never saw this kind of increase. That's why I was wondering if there is a big red flag when extending simulations on another machine or switching from CPU to GPU. Thank you. Nicolas Le mar. 5 juin 2018 à 10:43, Mark Abraham a écrit : > Hi, > > You'll basically never get a reproducible trajectory > http://www.gromacs.org/Documentation/Terminology/Reproducibility. If your > conclusions would depend on the configurations in any single trajectory, > you'll have a hard time demonstrating that those conclusions are valid > reflection of reality. > > Mark > > On Tue, Jun 5, 2018 at 10:37 AM Nicolas Cheron < > nicolas.cheron.bou...@gmail.com> wrote: > > > Dear all, > > > > I ran a 250ns simulation with Gromacs 5.1.2 on a machine with only CPUs. > I > > then wanted to extend the simulation to 300ns, and copied the .tpr and > the > > .cpt to another machine with GPUs (also running Gromacs 5.1.2). I > observed > > strange results, so I decided to also extend the simulation (from 250ns) > on > > the first machine to compare. > > > > Different results are obtained for the 2 extensions (that were started > from > > the same .tpr and .cpt) on the 2 different machines/architectures. Is it > a > > known behaviour, and one should never proceed like this? Is it due to > > CPU/GPU, or only the fact that machines are different and the same would > > have happened on another CPU machine? > > > > Thank you > > > > Nicolas > > > > PS: I am looking at a solute in a water:glycerol mixture. By "different > > results" I mean that the number of water (or glycerol) around the solute > > are different at all time steps > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Extension on different machines (CPU/GPU
Dear all, I ran a 250ns simulation with Gromacs 5.1.2 on a machine with only CPUs. I then wanted to extend the simulation to 300ns, and copied the .tpr and the .cpt to another machine with GPUs (also running Gromacs 5.1.2). I observed strange results, so I decided to also extend the simulation (from 250ns) on the first machine to compare. Different results are obtained for the 2 extensions (that were started from the same .tpr and .cpt) on the 2 different machines/architectures. Is it a known behaviour, and one should never proceed like this? Is it due to CPU/GPU, or only the fact that machines are different and the same would have happened on another CPU machine? Thank you Nicolas PS: I am looking at a solute in a water:glycerol mixture. By "different results" I mean that the number of water (or glycerol) around the solute are different at all time steps -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Charmm topologies for DHF/NADPH
Dear all, I am searching for topology files in Gromacs format for the NADPH cofactor and the dihydrofolate (DHF) ligand that would be compatible with the Charmm27 force field. Does anyone here have them and woud kindly accept to send them to me? If you have them in another format than Gromacs, I am also interested. Thanks a lot. Nicolas -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] gmx select
Dear all, I am a little bit lost with the use of select. I am looking at a protein in a water:glycerol mixture. I would like to count how many glycerol molecules there are within 3Angstrom of the protein. I first used the following command to count the central atom (named C2): gmx select -s File.gro -f File.xtc -n Index.ndx -os Gly-0.3.xvg -xvg none -select "name C2 and within 0.3 of group Protein" This gives me on average over the trajectory 3.3. Then I wanted to count for the center of mass of glycerols, which shouldn't be too far from the central atom: gmx select -s File.gro -f File.xtc -n Index.ndx -os Gly-0.3.xvg -xvg none -select "res_com of resname GOL and within 0.3 of group Protein" There I found 58.4. I got the same result with whole_res_com than with res_com, and with Gromacs 5.1.1, 5.1.2 and 2016. I am surprised by the difference. I suspect that the second command counts all the atoms. Can someone please tell me if the last command is correct, and if not tell me what would be the correct use of select to count the number of center of mass of the glycerol molecules that have their center of mass within 0.3nm of the protein. Thank you Nicolas PS: I posted this question on the list a week ago but not sure it went through, sorry for the double posting -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Use of gmx select
Dear all, I am a little bit lost with the use of select. I would like to count how many water molecules there are within 3Angstrom of a protein. I first used the following command to count the oxygen atoms: gmx select -s File.gro -f File.xtc -n Index.ndx -os Wat-0.3.xvg -xvg none -select "name OW and within 0.3 of group Protein" Then I wanted to count for the center of mass with: gmx select -s File.gro -f File.xtc -n Index.ndx -os Wat-0.3.xvg -xvg none -select "res_com of resname SOL and within 0.3 of group Protein" I have found significantly different values (in the order of 20%) which surprises me. Can you please confirm me that the last command is correct, and if not tell me what would be the correct use of select to count the number of water molecules that have their center of mass within 0.3nm of the protein. Thank you Nicolas -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] HID error in amber14sb.ff
Hi, I had this problem and wrote to Viet Man who uploaded the force field. I am quoting his answer: I have found the error come from HIP residues, diheral angle CB-CG-CD2-ND1 (= CT-CC-CW-NA). It causes by missing the improper dihedral angle information. To solve it, you may open file ffbonded.itp and add below line under line 730th NA CW CC CT 4 180.00 4.60240 2 Nicolas 2016-08-16 20:28 GMT+02:00 Mark Abraham : > Hi, > > Please search the archives - you're not the first person to notice that > with the user-contributed port of amber14, but nobody's reported back where > the problem might be. > > Mark > > On Tue, Aug 16, 2016 at 7:48 PM Hongbin Wan wrote: > > > Hi all, > > > > I am trying to run MD simulations with *amber14sb.ff (downloaded from > > gromacs forcefiled web)* > > > > However, it always shows * No default Improper Dih. types *for HID when > to > > use grompp. Could anyone tell me how to solve this issue? > > > > I had tried other forcefields, and they worked well. > > > > Thanks!! > > -Hongbin > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Looking for the source of the H-REMD slowdown when decoupling a lot of atoms
See: https://groups.google.com/forum/#!topic/plumed-users/eJ0xpnHPb_s and https://github.com/GiovanniBussi/plumed2/tree/v2.2-hrex Nicolas 2016-04-02 12:09 GMT+02:00 Mark Abraham : > Hi, > > On Fri, Apr 1, 2016 at 11:39 PM Christopher Neale < > chris.ne...@alum.utoronto.ca> wrote: > > > Dear developers: > > > > Is it possible with only a small amount of work to modify calc_delta() in > > src/programs/mdrun/repl_ex.cpp to add another case to re->type such that > > the program sends the coordinates to the alternate .tpr information and > > evaluates the energy completely? > > > This is approximately what the implementation of plumed does. > > This would allow for arbitrary exchanges, including bizarre things like > > exchanging the cutoff distance or whatever (not what I want to do -- I'm > > just emphasizing the generality of this approach). It will certainly cost > > some communication and compute cycles to do this, but for e.g. I > currently > > have a 12x slowdown using the free energy architecture while decoupling > 5K > > atoms. So if I do an exchange attempt every 500 steps, we're still > breaking > > even if this complete energy re-evaluation takes 5,500x longer than a > > regular integration step -- and I don't see how it could possibly take > > anywhere near that long assuming bMultiEx==FALSE. > > > > One can also implement such schemes as a script that calls grompp and mdrun > -rerun before relaunching whatever simulation. Horrible, but probably > better. > > Possible problems that I can imagine are: > > (a) the functions for a complete re-evaluation don't exist (either the > > communication of coordinates or the energy evaluation) > > > > The code's not modular enough for that, yet. > > (b) some issues with changes in temperature or pressure > > > > Yes, such state is not well organised. > > (c) the coordinates that are required to do this evaluation no longer exist > > because the energy evaluation functions are coupled to the timestep so we > > really need to pass them the coordinates of the previous timestep. > > > > No, those are separate stages, because there are multiple parts of the code > computing forces. > > Any suggestions are really appreciated > > > > Updating plumed for 5.1 is easily the path of least resistance, if it can > do the job. > > Mark > > Thank you, > > Chris. > > > > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Michael > > Shirts > > Sent: 31 March 2016 14:00 > > To: Discussion list for GROMACS users > > Subject: Re: [gmx-users] Looking for the source of the H-REMD slowdown > > when decoupling a lot of atoms > > > > > One more question: why does the free energy code have to use its own > > kernel? I realize that I'm going to sound like an idiot here, but why > can't > > one just tweak parameters outside of the kernel and then have the > optimized > > kernel do the dynamics? I presume that one has to step outside of the > > kernel to do the replica exchanges, so why can't the code just use the > > optimized kernel to do the dynamics between exchanges? > > > > The optimized energy code only codes very specific interactions; > > vanilla Coulomb, and Lennard-Jones. If it coded the more general > > interactions (such as soft-core) it would be significantly slower. > > > > We've come up with some ways to handle free energy calculations with > > optimized inner loops (I think we're talking about the same thing Mark > > -- though we should coordinate to be sure), but that will take a > > little time. > > > > One alternate possibility would be to create N replicas of the system, > > with slightly different parameters, but where all systems use the > > standard functional form, and then combine the results internall. For > > something like REST2, then this could work, since one is only linearly > > scaling the interactions between two parts A and B of the system; so > > it would be possible to represent each system as a separate physical > > system. This could work fairly well for small numbers of replicas, > > though might have some problems with large numbers of replicas. If > > each replica was an entire new system, it could make replica exchange > > quite slow, since calculating the energies of a given configuration > > with a different replica's energy function would be very costly. > > > > Right now, for alchemical interactions, there are only two > > representations of the system, and then lambda interpolates between > > the two representations of the systems to create the alchemical > > intermediates. Changing the way the code is structured would again > > require some significant changes and time. > > > > On Thu, Mar 31, 2016 at 10:49 AM, Christopher Neale > > wrote: > > > Dear Szilárd, Mark, and Michael: > > > > > > Thank you for your suggestions. > > > > > > 1. I did use the icc compiler > > > 2. I tested usage of nstlist=10 by setting verl
[gmx-users] Regression test 4.6.7
Dear all, I am looking for the file regressiontests-4.6.7.tar.gz. I can't find it online, the previous links are done. Can someone please either send it to me or tell me where to find it? Thanks a lot. Nicolas -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Roadmap for new features
Dear all, Is there a place where the planned/hoped new features of Gromacs are listed? I am wondering if there is a chance that EVB, HREX (without the need to use plumed) or new QM/MM interface will be available at some point. I know that the developers are busy, but I am wondering what is in their mind. Thank you. Nicolas -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Build fails with AVX2_256 on Intel Xeon CPU E5-2680 v3
Hi, After installing the last version of binutils, it worked. Thanks for the tip. Nicolas PS: Just in case, to be able to install binutils I had to follow the instructions given here https://forums.opensuse.org/showthread.php/508627-Compiling-Binutils-error-%E2%80%98TARGET_ALIAS%E2%80%99-undeclared-(first-use-in-this-function)-Work-Around 2016-01-25 19:54 GMT+01:00 Koji Tanaka : > Hi Nicolas, have you installed the latest binutils before going through the > installation? I used gcc/5.3.0, but the versions you've tried should work > fine, too. > > Koji > > On Mon, Jan 25, 2016 at 12:56 PM, Nicolas Cheron < > nicolas.cheron.bou...@gmail.com> wrote: > > > Hi, > > > > All my installations are made from a clean build directory. I am > > using CentOS release 6.6 and the CPU is Intel Xeon CPU E5-2650 v3 @ > > 2.30GHz. Here is the exact list of command that I have used (as I said, I > > have also tried with gcc4.9.3 and gcc5.2): > > > > module purge > > module load gcc/4.8.5 > > cd /home2/ncheron/Programs/ > > cp 00-Install/gromacs-5.1.1.tar.gz . > > tar zxf gromacs-5.1.1.tar.gz > > rm gromacs-5.1.1.tar.gz > > cd /home2/ncheron/Programs/gromacs-5.1.1 > > umask 022 > > mkdir build > > cd /home2/ncheron/Programs/gromacs-5.1.1/build > > mkdir /home2/ncheron/Programs/Gromacs5.1.1 > > > > > CMAKE_PREFIX_PATH=/home2/ncheron/Programs/LibXml_2.9.2:/home2/ncheron/Programs/Boost_1.60.0 > > cmake .. -DGMX_OPENMP=ON -DGMX_THREAD_MPI=ON -DGMX_MPI=OFF -DGMX_GPU=OFF > > -DGMX_DOUBLE=OFF -DGMX_BUILD_MDRUN_ONLY=ON > > -DCMAKE_INSTALL_PREFIX=/home2/ncheron/Programs/Gromacs5.1.1 > > -DGMX_BUILD_OWN_FFTW=ON > > > > > -DGMX_BUILD_OWN_FFTW_URL=/home2/ncheron/Programs/00-Install/fftw-3.3.4.tar.gz > > -DGMX_DEFAULT_SUFFIX=OFF -DGMX_BINARY_SUFFIX=_Dell > -DGMX_LIBS_SUFFIX=_Dell > > -DGMX_SIMD=AVX2_256 > > make -j4 > > make install > > > > The error file says: > > CMake Error at cmake/gmxManageSimd.cmake:271 (message): > > Cannot find AVX2 compiler flag. Use a newer compiler, or choose AVX > SIMD > > (slower). > > Call Stack (most recent call first): > > CMakeLists.txt:645 (gmx_manage_simd) > > > > > > The output file says: > > -- The C compiler identification is GNU 4.8.5 > > -- The CXX compiler identification is GNU 4.8.5 > > -- Check for working C compiler: /usr/local/gcc/4.8.5/bin/gcc > > -- Check for working C compiler: /usr/local/gcc/4.8.5/bin/gcc -- works > > -- Detecting C compiler ABI info > > -- Detecting C compiler ABI info - done > > -- Detecting C compile features > > -- Detecting C compile features - done > > -- Check for working CXX compiler: /usr/local/gcc/4.8.5/bin/g++ > > -- Check for working CXX compiler: /usr/local/gcc/4.8.5/bin/g++ -- works > > -- Detecting CXX compiler ABI info > > -- Detecting CXX compiler ABI info - done > > -- Detecting CXX compile features > > -- Detecting CXX compile features - done > > -- Try OpenMP C flag = [-fopenmp] > > -- Performing Test OpenMP_FLAG_DETECTED > > -- Performing Test OpenMP_FLAG_DETECTED - Success > > -- Try OpenMP CXX flag = [-fopenmp] > > -- Performing Test OpenMP_FLAG_DETECTED > > -- Performing Test OpenMP_FLAG_DETECTED - Success > > -- Found OpenMP: -fopenmp > > -- Performing Test CFLAGS_WARN > > -- Performing Test CFLAGS_WARN - Success > > -- Performing Test CFLAGS_WARN_EXTRA > > -- Performing Test CFLAGS_WARN_EXTRA - Success > > -- Performing Test CFLAGS_WARN_UNDEF > > -- Performing Test CFLAGS_WARN_UNDEF - Success > > -- Performing Test CFLAGS_WARN_REL > > -- Performing Test CFLAGS_WARN_REL - Success > > -- Performing Test CFLAGS_EXCESS_PREC > > -- Performing Test CFLAGS_EXCESS_PREC - Success > > -- Performing Test CFLAGS_COPT > > -- Performing Test CFLAGS_COPT - Success > > -- Performing Test CFLAGS_NOINLINE > > -- Performing Test CFLAGS_NOINLINE - Success > > -- Performing Test CXXFLAGS_WARN > > -- Performing Test CXXFLAGS_WARN - Success > > -- Performing Test CXXFLAGS_WARN_EXTRA > > -- Performing Test CXXFLAGS_WARN_EXTRA - Success > > -- Performing Test CXXFLAGS_WARN_UNDEF > > -- Performing Test CXXFLAGS_WARN_UNDEF - Success > > -- Performing Test CXXFLAGS_WARN_REL > > -- Performing Test CXXFLAGS_WARN_REL - Success > > -- Performing Test CXXFLAGS_EXCESS_PREC > > -- Performing Test CXXFLAGS_EXCESS_PREC - Success > > -- Performing Test CXXFLAGS_COPT > > -- Performing Test CXXFLAGS_COPT - Success > > -- Performing Test CXXFLAGS_NOINLINE > > -- Performing Test CXXFLAGS_NOIN
Re: [gmx-users] Build fails with AVX2_256 on Intel Xeon CPU E5-2680 v3
> Hi, > > That shouldn't happen. What does the terminal output when you run cmake in > a clean build tree? > > Mark > > On Sun, 24 Jan 2016 21:59 Nicolas Cheron > wrote: > > > Hi, > > > > I have faced the same problem, with gcc 4.8.3, 4.9.1 and 5.2. I ended up > > asking for SIMD=AVX_256. So I assume there is something else going wrong. > > > > Nicolas > > > > 2016-01-24 20:59 GMT+01:00 Mark Abraham : > > > > > Hi, > > > > > > Like the *5.1* installation instructions and that error suggest, you > > need a > > > recent compiler. The "stable" compilers in distros like centos are > > merely a > > > euphemism for outdated, if you want to run fast on new hardware. > > > > > > Mark > > > > > > On Sun, 24 Jan 2016 16:47 Koji Tanaka wrote: > > > > > > > Hello Gromacs Community, > > > > > > > > I'm trying to build Gromacs with SIMD=AVX2_256 support, but it fails. > > > > Instead, if I pick AVX_256, the build will finish okay. > > > > > > > > However, according to the documentation( > > > > http://www.gromacs.org/Documentation/Installation_Instructions_5.0), > > > > AVX2_256 is the right option for the Intel Xeon CPU E5-2680 v3 > > (Haswell). > > > > Does anyone have the same problem? > > > > > > > > My environment is; > > > > - CentOS 6.7 > > > > - Gromacs 5.1.1 > > > > - OpenMPI 1.10.1 > > > > > > > > The error message is; > > > > --- > > > > CMake Error at cmake/gmxManageSimd.cmake:271 (message): > > > > Cannot find AVX2 compiler flag. Use a newer compiler, or choose AVX > > > SIMD > > > > (slower). > > > > Call Stack (most recent call first): > > > > CMakeLists.txt:645 (gmx_manage_simd) > > > > > > > > > > > > Also, I found the following error in build/CMakeFiles/CMakeError.log > > > > --- > > > > Run Build Command:/usr/bin/gmake "cmTryCompileExec1019102511/fast" > > > > /usr/bin/gmake -f CMakeFiles/cmTryCompileExec1019102511.dir/build.make > > > > CMakeFiles/cmTryCompileExec1019102511.dir/build > > > > gmake[1]: Entering directory > > > `/tmp/gromacs-5.1.1/build/CMakeFiles/CMakeTmp' > > > > /usr/bin/cmake -E cmake_progress_report > > > > /tmp/gromacs-5.1.1/build/CMakeFiles/CMakeTmp/CMakeFiles 1 > > > > Building C object CMakeFiles/cmTryCompileExec1019102511.dir/src.c.o > > > > /opt/openmpi/1.10.1/bin/mpicc -Wundef -Wextra > > > > -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall > > > > -Wno-unused -Wunused-value -Wunused-p > > > > arameter -D_callconv___regcall -o > > > > CMakeFiles/cmTryCompileExec1019102511.dir/src.c.o -c > > > > /tmp/gromacs-5.1.1/build/CMakeFiles/CMakeTmp/src.c > > > > /tmp/gromacs-5.1.1/build/CMakeFiles/CMakeTmp/src.c:1: error: expected > > > ‘=’, > > > > ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘f’ > > > > /tmp/gromacs-5.1.1/build/CMakeFiles/CMakeTmp/src.c: In function ‘main’: > > > > /tmp/gromacs-5.1.1/build/CMakeFiles/CMakeTmp/src.c:1: warning: implicit > > > > declaration of function ‘f’ > > > > gmake[1]: *** [CMakeFiles/cmTryCompileExec1019102511.dir/src.c.o] > > Error 1 > > > > gmake[1]: Leaving directory > > > `/tmp/gromacs-5.1.1/build/CMakeFiles/CMakeTmp' > > > > gmake: *** [cmTryCompileExec1019102511/fast] Error 2 > > > > > > > > > > > > Any comment/suggestion would be appreciated! > > > > > > > > Thanks a lot, > > > > Koji > > > > -- > > > > Gromacs Users mailing list > > > > > > > > * Please search the archive at > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > > posting! > > > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > * For (un)subscribe requests visit > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archi
Re: [gmx-users] Build fails with AVX2_256 on Intel Xeon CPU E5-2680 v3
Hi, I have faced the same problem, with gcc 4.8.3, 4.9.1 and 5.2. I ended up asking for SIMD=AVX_256. So I assume there is something else going wrong. Nicolas 2016-01-24 20:59 GMT+01:00 Mark Abraham : > Hi, > > Like the *5.1* installation instructions and that error suggest, you need a > recent compiler. The "stable" compilers in distros like centos are merely a > euphemism for outdated, if you want to run fast on new hardware. > > Mark > > On Sun, 24 Jan 2016 16:47 Koji Tanaka wrote: > > > Hello Gromacs Community, > > > > I'm trying to build Gromacs with SIMD=AVX2_256 support, but it fails. > > Instead, if I pick AVX_256, the build will finish okay. > > > > However, according to the documentation( > > http://www.gromacs.org/Documentation/Installation_Instructions_5.0), > > AVX2_256 is the right option for the Intel Xeon CPU E5-2680 v3 (Haswell). > > Does anyone have the same problem? > > > > My environment is; > > - CentOS 6.7 > > - Gromacs 5.1.1 > > - OpenMPI 1.10.1 > > > > The error message is; > > --- > > CMake Error at cmake/gmxManageSimd.cmake:271 (message): > > Cannot find AVX2 compiler flag. Use a newer compiler, or choose AVX > SIMD > > (slower). > > Call Stack (most recent call first): > > CMakeLists.txt:645 (gmx_manage_simd) > > > > > > Also, I found the following error in build/CMakeFiles/CMakeError.log > > --- > > Run Build Command:/usr/bin/gmake "cmTryCompileExec1019102511/fast" > > /usr/bin/gmake -f CMakeFiles/cmTryCompileExec1019102511.dir/build.make > > CMakeFiles/cmTryCompileExec1019102511.dir/build > > gmake[1]: Entering directory > `/tmp/gromacs-5.1.1/build/CMakeFiles/CMakeTmp' > > /usr/bin/cmake -E cmake_progress_report > > /tmp/gromacs-5.1.1/build/CMakeFiles/CMakeTmp/CMakeFiles 1 > > Building C object CMakeFiles/cmTryCompileExec1019102511.dir/src.c.o > > /opt/openmpi/1.10.1/bin/mpicc -Wundef -Wextra > > -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall > > -Wno-unused -Wunused-value -Wunused-p > > arameter -D_callconv___regcall -o > > CMakeFiles/cmTryCompileExec1019102511.dir/src.c.o -c > > /tmp/gromacs-5.1.1/build/CMakeFiles/CMakeTmp/src.c > > /tmp/gromacs-5.1.1/build/CMakeFiles/CMakeTmp/src.c:1: error: expected > ‘=’, > > ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘f’ > > /tmp/gromacs-5.1.1/build/CMakeFiles/CMakeTmp/src.c: In function ‘main’: > > /tmp/gromacs-5.1.1/build/CMakeFiles/CMakeTmp/src.c:1: warning: implicit > > declaration of function ‘f’ > > gmake[1]: *** [CMakeFiles/cmTryCompileExec1019102511.dir/src.c.o] Error 1 > > gmake[1]: Leaving directory > `/tmp/gromacs-5.1.1/build/CMakeFiles/CMakeTmp' > > gmake: *** [cmTryCompileExec1019102511/fast] Error 2 > > > > > > Any comment/suggestion would be appreciated! > > > > Thanks a lot, > > Koji > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Confusion on improper dihedrals and Urey-Bradley (lost when converting from Amber with acpype)
Dear all, 10 days ago I had this question regarding the conversion of force fields with acpype. After a thorough analysis (via single points between Amber and Gromacs), I have reached the conclusion that acpype can't be use blindly for the conversion of CHARMM22/27 force field in the Amber format (prmtop) to Gromacs. Please note that I have found that acpype is working smoothly when converting Amber force fields in the Amber format to Gromacs and is very useful for that purpose. However, Urey-Bradley terms and improper dihedrals in the CHARMM22/27 force fields are not taken into account properly by acpype. I just wanted to report this in case other people find the same problem. Nicolas 2015-10-09 14:21 GMT+02:00 Alan : > Nicolas, if you have created your files in Amber, then the conversion to > GROMACS should be fine. You can find some details about it in > https://code.google.com/p/acpype/wiki/TestingAcpypeAmb2gmx > > Alan > > On 9 October 2015 at 12:39, Justin Lemkul wrote: > > > > > > > On 10/8/15 11:48 AM, Nicolas Cheron wrote: > > > >> Dear all, > >> > >> I am joining a project where people are using the CHARMM22 force field. > >> They converted a .prmtop file from Amber to Gromacs format with acpype. > In > >> the output topology, there are no Urey-Bradley potentials or improper > >> dihedrals (for example, all the [ angle ] functions are of type 1 and > none > >> are 5 and all the [ dihedrals ] function are of type 9 and none are 2). > >> > >> I am confused, and I am wondering if something went missing when using > >> acpype? Do you know how acpype handle this part of the amber topology? > Or > >> did acpype converted the Urey-Bradley and improper dihedrals from the > >> .prmtop to other kind of functions? For an angle A-B-C with > Urey-Bradley, > >> I > >> thought it would be possible to have a force as if there was a bond > >> between > >> A and C but I didn't find anything like that in the topology. > >> > >> The manual says about Urey-Bradley potential "Although this can be > easily > >> written as a simple sum of two terms, it is convenient to have it as a > >> single entry in the topology file and in the output as a separate energy > >> term" but I am not sure to understand if that means that Gromacs > >> developers > >> have prefered to keep it as a single entry or not. > >> > >> > > Yes, it is a single entry. > > > > Not all U-B angles in CHARMM have an explicit 1-3 term, but if the > > conversion is simply nixing those that exist, clearly the conversion is > > being done wrong. If impropers are present yet disappearing, this is > more > > evidence that the program is not designed to do what you want it to, or > > that there is some problem with the input itself. > > > > The simplest test is to do a single-point energy in AMBER and GROMACS and > > compare the outcome to determine if the newly generated topology is > > sensible. If there's a mismatch, find a better method of conversion. > > > > -Justin > > > > -- > > == > > > > Justin A. Lemkul, Ph.D. > > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > > > Department of Pharmaceutical Sciences > > School of Pharmacy > > Health Sciences Facility II, Room 629 > > University of Maryland, Baltimore > > 20 Penn St. > > Baltimore, MD 21201 > > > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > http://mackerell.umaryland.edu/~jalemkul > > > > == > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > -- > Alan Wilter SOUSA da SILVA, DSc > Bioinformatician, UniProt > European Bioinformatics Institute (EMBL-EBI) > European Molecular Biology Laboratory > Wellcome Trust Genome Campus > Hinxton > Cambridge CB10 1SD > United Kingdom > Tel: +44 (0)1223 494588 > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Unified topology
Dear all, Someone gave me a topology file for a system which was converted from Amber (with the CHARMM27 force field). When I compare (via a single point) with a topology coming from pdb2gmx, I find some differences between the energetic values. I would like to find the cause. The topology from pdb2gmx has the following format: #include "charmm27.ff/forcefield.itp" (...) [ bonds ] ; aiaj functc0c1c2c3 1 2 1 1 3 1 wheras the one I have been given has the following format: [ bonds ] ; ai aj funct r k 2 1 11.0400e-013.3723e+05 ;HT1 - N 3 1 11.0400e-013.3723e+05 ;HT2 - N Is there any option in pdb2gmx or grompp to tell the program to write all the parameters in the latter format? This would help me to compare parameters one by one. I have tried the -pp option of grompp but it "only" gathers everything and I still have the same format. If not possible, do you have any suggestions? Thank you for your help or any hints. Nicolas -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Confusion on improper dihedrals and Urey-Bradley (lost when converting from Amber with acpype)
Dear all, I am joining a project where people are using the CHARMM22 force field. They converted a .prmtop file from Amber to Gromacs format with acpype. In the output topology, there are no Urey-Bradley potentials or improper dihedrals (for example, all the [ angle ] functions are of type 1 and none are 5 and all the [ dihedrals ] function are of type 9 and none are 2). I am confused, and I am wondering if something went missing when using acpype? Do you know how acpype handle this part of the amber topology? Or did acpype converted the Urey-Bradley and improper dihedrals from the .prmtop to other kind of functions? For an angle A-B-C with Urey-Bradley, I thought it would be possible to have a force as if there was a bond between A and C but I didn't find anything like that in the topology. The manual says about Urey-Bradley potential "Although this can be easily written as a simple sum of two terms, it is convenient to have it as a single entry in the topology file and in the output as a separate energy term" but I am not sure to understand if that means that Gromacs developers have prefered to keep it as a single entry or not. Thanks for your help Nicolas -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Gromacs and Gcc5.2
Dear all, I am wondering if there is an official statement regarding compiling Gromacs with gcc5.2.0 (or any gcc from the 5.x branch). Is it recommended or not? Should we expect improvements? I have tried quickly some small benchmarks (with Gromacs 4.6.3 and Gromacs 5.1) and found improvement on ns/day between 1 and 3% (with respect to gcc4.8.5). Also, during compilation I get several warnings such as: In file included from /usr/local/openmpi-gnu/include/mpi.h:253:0, from /home2/ncheron/Programs/gromacs-5.1/src/gromacs/utility/gmxmpi.h:59, from /home2/ncheron/Programs/gromacs-5.1/src/gromacs/legacyheaders/types/commrec.h:45, from /home2/ncheron/Programs/gromacs-5.1/src/gromacs/legacyheaders/gmx_ga2la.h:40, from /home2/ncheron/Programs/gromacs-5.1/src/gromacs/domdec/domdec_constraints.cpp:55: /usr/local/openmpi-gnu/include/mpi_portable_platform.h:374:34: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] _STRINGIFY(__GNUC__)"."_STRINGIFY(__GNUC_MINOR__)"."_STRINGIFY(__GNUC_PATCHLEVEL__) I don't think it is relevant and I am not worried about it, but just wanted to check with you. Thank you. Nicolas -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] problem with chimera opening gromacs 4.6.5 trajectories
Which Chimera version are you using? Have you tried the latest (at least 1.8)? http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.8.html : "support added for Gromacs 4.6 trajectories" Nicolas 2014-04-23 14:02 GMT-04:00 Rafael I. Silverman y de la Vega : > Hi all > I have been having problems getting chimera to open 4.6 trajectories. It > opens trajectory files from gromacs 4.5 just fine. (well, at least some > chimera builds open the trajecotries). > I tried using gromacs 4.5 trjconv to make xtc readable by chimera, but, of > course that didnt work on the trr made by 4.6. > Will gromacs 5.0 make chimera readable files, or should I go bother the > chimera developers? > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
