Re: [gmx-users] Lincs all-bonds causing instability in otherwise stable system
Thanks Mark, A grompp warning about problematic constraints sounds like a good idea. DMSO is actually tetrahedral, not planar. Is that possible (and hopefully straightforward) to do with virtual sites? If it is, is there an example I could look at? Thanks, Cara From: mark.j.abra...@gmail.com Date: Wed, 20 May 2015 11:47:43 + To: gmx-us...@gromacs.org; gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Lincs all-bonds causing instability in otherwise stable system Hi, Sorry that was so painful for you. The LINCS documentation in the manual suggests that that combination of bonds becoming constraints won't work well. Perhaps we should add a 3-edge cycle detector to grompp? If you actually want a rigid planar DMSO, then three real atoms and a virtual site would be the best implementation. Mark On Wed, May 20, 2015 at 6:41 AM Cara Kreck cara.kr...@student.curtin.edu.au wrote: Hi everyone, I never got a reply to my message but I figured out the problem by myself. Just in case anyone else runs into a similar problem I thought I should explain what was wrong and share the solution. I was using a DMSO topology from the ATB that uses extra bonds to fix the geometry instead of angle or dihedral terms: [ moleculetype ] ; Name nrexcl DMSO 3 [ atoms ] ; nr type resnr resid atom cgnr chargemasstotal_charge 1 SDmso1DMSO S10.128 32.0600 2 ODmso1DMSO O1 -0.448 15.9994 3 CDmso1DMSO C10.160 15.0350 4 CDmso1DMSO C10.160 15.0350 ; 0.000 ; total charge of the molecule: 0.000 [ bonds ] ; ai aj funct c0 c1 122 0.1530 8.0400e+06 132 0.1938 4.9500e+06 142 0.1938 4.9500e+06 232 0.2794 2.3900e+06 242 0.2794 2.3900e+06 342 0.2912 2.1900e+06 This topology is fine to use with SHAKE but LINCS doesn't seem to be able to handle it. When I removed the extra bonds my simulations were able to run with all bonds constrained by LINCS. Then I found appropriate angle and dihedral parameters in the GROMOS ffbonded.itp file to control the geometry again. My topology file now looks like this: [ moleculetype ] ; Name nrexcl DMSO 3 [ atoms ] ; nr type resnr resid atom cgnr chargemasstotal_charge 1 SDmso1DMSO S10.128 32.0600 2 ODmso1DMSO O1 -0.448 15.9994 3 CDmso1DMSO C10.160 15.0350 4 CDmso1DMSO C10.160 15.0350 ; 0.000 ; total charge of the molecule: 0.000 [ bonds ] ; ai aj funct c0 c1 122 0.1530 8.0400e+06 132 0.1938 4.9500e+06 142 0.1938 4.9500e+06 [ angles ] ; ai aj ak funct angle fc 314297.40 469.00 3122 106.75 503.00 4122 106.75 503.00 [ dihedrals ] ; GROMOS improper dihedrals ; ai aj ak al funct angle fc 13422 35.26439 334.84617 ; tetrahedral centre I ran an energy minimisation of a single molecule with the new topology and its geometry overlapped the old one perfectly. So the problem was difficult to diagnose but easy to fix. Especially since I was able to energy minimise the individual molecules with all bonds constrained but the constraints went haywire when everything was combined in the full system. Hopefully I can at least save someone else from wasting 3 weeks trying to get a similar topology to work with LINCS. Cara From: cara.kr...@student.curtin.edu.au To: gromacs.org_gmx-users@maillist.sys.kth.se Date: Fri, 15 May 2015 14:31:16 +0800 Subject: [gmx-users] Lincs all-bonds causing instability in otherwise stable system I forgot to include an example of my mdp files. I've tried varying the timestep, running with and without pressure coupling, and obviously changing the constraints as outlined in the previous message: integrator = md dt = 0.001 ; 1fs nsteps = 10 ; 100ps comm_grps= DOPC !DOPC nstxout = 1000 nstvout = 0 nstlog = 1000 nstenergy= 1000 energygrps = DOPC !DOPC nstcalcenergy= 5 nstlist = 5 ns_type = grid pbc = xyz rlist= 0.8 coulombtype = Reaction-Field rcoulomb = 1.4 epsilon_rf = 62 vdwtype = Cut-off rvdw = 1.4 tcoupl = berendsen tc-grps = DOPC !DOPC
[gmx-users] How to proceed with molecule.itp file
Hi, I have made a molecule.itp file according to the chapter 5 of Gromacs Manual and existing entries in the ff directory I want to use. My problem is that I don't know how to continue, in theory I have to include it in the .top file but a .top file is produced by pdb2gmx which I cannot use because there isn't an entry in .rtp. Please help -- 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] pdb2gmx: Can I change the margin 10% to a higher value in the specbond.dat ?
Dear GROMACS experts, I am using pdb2gmx for a protein with 5 disulfind bond https://copy.com/kPLlSianI4LtohNy The distance between each Cys SG are: 0.203, 0.204, 0.204, 0.205, 0.167. As a result, 10% margin of any value of the reference length in specbond.dat cannot cover all of the 5 Cys SG distance. I understand that a typical disulfide bond should be about 2.05 Å in length. However, if I still want to keep them, can I change the 10% margin to a higher value (e.g. 15%)? Thank you very much. Yours sincerely Cheng (Thank you for Justin's reply at https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-May/097699.html Would it be possible if I can simply reply to you for the thread instead of creating a new one?) -- 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] tpr file portability
Dear All, I am generating .tpr file on my desktop (UBUNTU 14.04 X86_64) and running MD on Cray (suse-linux X86_64 )using Gromacs-5.0.5. It is mentioned on the Gromacs site is that Generally the tpr file is very portable between different machines. Is it valid in my case? Is there anything to worry about it? Please help. With best regards, Satyabrata Das -- 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] tpr file portability
Hi, There are no known issues with .tpr file portability. By design there should be none. Mark On Thu, May 21, 2015 at 11:41 AM Satyabrata Das satyabrata...@gmail.com wrote: Dear All, I am generating .tpr file on my desktop (UBUNTU 14.04 X86_64) and running MD on Cray (suse-linux X86_64 )using Gromacs-5.0.5. It is mentioned on the Gromacs site is that Generally the tpr file is very portable between different machines. Is it valid in my case? Is there anything to worry about it? Please help. With best regards, Satyabrata Das -- 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] .gro error
Hello, i'm working on membrane thickness in Martínez-Seara dppc article. When i use the following command: printf %s\n r 1-64 a P r 65-128 a P q|make_ndx -f dppc128_1.gro -o Dpp.ndx The following error appears: File Input/output error: dppc128_1.gro. Could you help me to solve it please? Alfonso -- 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] .gro error
On 5/21/15 2:30 PM, Poncho Arvayo Zatarain wrote: Hello, i'm working on membrane thickness in Martínez-Seara dppc article. When i use the following command: printf %s\n r 1-64 a P r 65-128 a P q|make_ndx -f dppc128_1.gro -o Dpp.ndx The following error appears: File Input/output error: dppc128_1.gro. Could you help me to solve it please? It means that file doesn't exist in the working directory. -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.
Re: [gmx-users] links errors at 700 or 800 K
On 5/21/15 10:24 AM, Christopher Neale wrote: Dear Users: I have a system with an 8-mer peptide in a box of water. After a 2-ns npt equilibration, I run 100 ns of nvt at various temperatures (300-800 K) in preparation for a REMD simulation. I am using velocity langevin for temperature control. Everything is fine for =600 K. Above that, I sometimes run into LINCS errors: ## Step 19126507, time 38253 (ps) LINCS WARNING I would say a 2-fs time step is destined to fail at such a high temperature. Almost certainly 1-fs (still in conjunction with constraints) would be more stable. relative constraint deviation after LINCS: rms 0.069230, max 0.677838 (between atoms 49 and 50) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 49 50 90.00. 0.1864 0. 46 48 90.00. 0.1722 0. ## with eventual crash: ## WARNING: Listed nonbonded interaction between particles 57 and 59 at distance 58.376 which is larger than the table limit 2.223 nm. Fatal error: 1 particles communicated to PME rank 0 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. This usually means that your system is not well equilibrated. ## I have verified this with three different force fields in gmx4.6.7 (charmm27, amber99sb-ildn, and opls). I have also seen this in gmx5 (only charmm27 force field tested so far in gmx5 -- the error snippits above are from that gmx 5 run). The gromacs 5 mdp file (with verlet cutoff scheme) is as follows: ## nsteps = 5000 constraints = all-bonds lincs-iter = 1 lincs-order = 6 constraint_algorithm = lincs integrator = sd dt = 0.002 tinit = 0 nstcomm = 1 nstxout = 0 nstvout = 0 nstfout = 0 nstxtcout = 10 nstenergy = 10 nstlist = 10 nstlog=0 ns_type = grid cutoff-scheme = verlet vdwtype = cut-off rlist = 1.2 rvdw = 1.2 rvdw-switch = 1.0 rcoulomb = 1.2 vdw-modifier = force-switch coulombtype = PME ewald-rtol = 1e-5 optimize_fft = yes fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 tc_grps = System tau_t = 1.0 ld_seed = -1 ref_t = 800 gen_temp = 800 gen_vel = yes unconstrained_start = no gen_seed = -1 Pcoupl = no ## I'm guessing that at high temperature I need to increase lincs-iter or lincs-order ? I'm asking because these errors are rare (1-3 out of 20 100-ns simulations will have such an error) so simply testing it is not that quick. Possibly, but dt itself is the more likely culprit. Simulating at 600-800 K is already taking a sledgehammer to the force field, anyway :) Very preliminary results suggest that gromacs5.0.5 with verlet cutoff scheme might have fewer such errors than gromacs 4.6.7 with the group cutoff scheme, possibly due to atoms moving out/in of the cutoff within the 20 fs between neighbourlist updates in the group scheme (3/20 crash with gmx4/group and 1/20 crashes with gmx5/verlet, but the variation between different force fields is on this order so I am not yet sure if the difference is significant). I will also note that I can get rid of these crashes by using constraints = h-bonds instead of constraints = all-bonds, though it has always been a mystery to me why constraints = h-bonds is stable (even at 300 K) with a 2 fs timestep so I am cautious about using that combination. I suppose that means you're getting distortion of bonds between heavy atoms, which is what causes the LINCS failures. Any unphysical geometries in these constraints = h-bonds runs? -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.
[gmx-users] Version 100 with version 83 program
I' m running Martínez Seara dppc tutorial and when i use echo 0|trjconv -f dppc128_1.xtc -s dppc128_1.tpr -o dppc128_1-ini.gro -dump 10 it appears the following error: Fatal error: reading tpx file (dppc128_1.tpr) version 100 with version 83 program. I' m using Gromacs 4.6.5 maybe it has to be with differente gromacs version. In that case, what can i do? Alfonso -- 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] Segmentation fault (core dumped) version 4.6.*
Dear Chris, Thanks a lot for your reply. Indeed, my first files were create by using gromacs 5, so i created all of the files again, but now using 4.6.3 version. Sadly the error is still appearing :/ (Even using gmxcheck) :-) gmxcheck (-: Option Filename Type Description -f traj.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt -f2 traj.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt -s1 top1.tpr Input, Opt. Run input file: tpr tpb tpa -s2 top2.tpr Input, Opt. Run input file: tpr tpb tpa -c topol.tpr Input, Opt. Structure+mass(db): tpr tpb tpa gro g96 pdb -e ener.edr Input, Opt. Energy file -e2 ener2.edr Input, Opt. Energy file -n index.ndx Input, Opt. Index file -mdoc.tex Output, Opt. LaTeX file Option Type Value Description -- -[no]h bool no Print help info and quit -[no]version bool no Print version info and quit -niceint0 Set the nicelevel -vdwfac real 0.8 Fraction of sum of VdW radii used as warning cutoff -bonlo real 0.4 Min. fract. of sum of VdW radii for bonded atoms -bonhi real 0.7 Max. fract. of sum of VdW radii for bonded atoms -[no]rmsdbool no Print RMSD for x, v and f -tol real 0.001 Relative tolerance for comparing real values defined as 2*(a-b)/(|a|+|b|) -abstol real 0.001 Absolute tolerance, useful when sums are close to zero. -[no]ab bool no Compare the A and B topology from one file -lastenerstring Last energy term to compare (if not given all are tested). It makes sense to go up until the Pressure. Segmentation fault (core dumped) Best, Carlos -- Carlos Navarro Retamal Bioinformatics Engineering Ph. D (c) Applied Sciences. Center of Bioinformatics and Molecular Simulations. CBSM University of Talca Av. Lircay S/N, Talca, Chile T: (+56) 712201 798 E: carlos.navarr...@gmail.com or cnava...@utalca.cl On May 21, 2015 at 6:30:22 PM, Christopher Neale (chris.ne...@alum.utoronto.camailto:chris.ne...@alum.utoronto.ca) wrote: Dear Carlos: Are you using a .top file from gromacs 5 with your gromacs 4 runs? If so, try regenerating your topology (and .itp files) using gromacs 4 (with GMXLIB set correctly). Not sure if that would even cause a problem, but it seems like it probably would and is the only thing that comes to mind. If that is not the issue, then do any of the other commands work without a segfault (e.g. gmxcheck)? Chris. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Carlos Navarro Retamal cnava...@utalca.cl Sent: 21 May 2015 11:55 To: gmx-us...@gromacs.org Subject: [gmx-users] Segmentation fault (core dumped) version 4.6.* Dear gmx users, In order to run my simulations, i usually used the 5.0.* version of gromacs without problems, but since i want to performed umbrella sampling simulations (and since the option pull_geometry=position is not available for the latest versions) For that, i installed the 4.6.7 version of gromacs. The installation went without issue, but every time i used a command from gromacs i got the Segmentation fault (core dumped) error: Like for example, by using this command line: grompp -f npt_production.mdp -c npt_equilibration.gro -p topol.top -o npt_production.tpr i got this: Option Filename Type Description -f npt_production.mdp Input grompp input file with MD parameters -po mdout.mdp Output grompp input file with MD parameters -c npt_equilibration.gro Input Structure file: gro g96 pdb tpr etc. -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc. -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc. -n index.ndx Input, Opt. Index file -p topol.top Input Topology file -pp processed.top Output, Opt. Topology file -o npt_production.tpr Output Run input file: tpr tpb tpa -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt -e ener.edr Input, Opt. Energy file -ref rotref.trr In/Out, Opt. Full precision trajectory: trr trj cpt Option Type Value Description -- -[no]h bool no Print help info and quit -[no]version bool no Print version info and quit -nice int 0 Set the nicelevel -[no]v bool no Be loud and noisy -time real -1 Take frame at or first after this time. -[no]rmvsbds bool yes Remove constant bonded interactions with virtual sites -maxwarn int 0 Number of allowed warnings during input processing. Not for normal use and may generate unstable systems -[no]zero
Re: [gmx-users] About Tabulated Potentials
On 5/21/15 8:36 AM, zhangzhengc wrote: Dear all, I want to add the Morse potential for nonbonded interactions between CH4 and CH4. I used three table files each contain seven columns to add the H to H, H to C, and C to C Morse form interactions. I set Coulombtype=user, vdwtype=user , and Dispcorr = no, and add energrps and energrps_table in the mdp file. However, when I did NVT simulations, I didnot get accurate pressure for my pure methane system. Actually the pressure is 20 I don't know much about tabulated potentials, but a question to get the ball rolling: How do you define accurate - from some previous run? Without tabulated potentials? If the latter, it means your tables are wrong with respect to whatever parameters gave the right behavior. -Justin Mpa smaller. Could you tell what is wrong with my set or what I missed in adding tabulated potentials? I tested the using of tabulated potentials with LJ form potential, It works very well. Look forward to your reply, Sincerely yours Zhengcai, -- == 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.
[gmx-users] Reading double-precision trr file using xdrfile
Dear Gromacs developers and users, I would like to read a .trr trajectory file in double-precision after running a simulation in double-precision, however reading the atomic positions etc with the xdrfile appears to yield only single precision. Are the trajectory position, velocity and forces not stored in double-precision in the trr file? Certainly the file size is much larger, so I imagine it's in double precision. xdrfile however is expecting only floats: extern int read_trr(XDRFILE *xd,int natoms,int *step,float *t,float *lambda, matrix box,rvec *x,rvec *v,rvec *f); (rvec is defined as typedef float rvec[DIM];) Is there any alternative to get them in double precision? Thank you for advice. Best regards, James -- 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] Version 100 with version 83 program
I' m running Martínez Seara dppc tutorial and when i use echo 0|trjconv -f dppc128_1.xtc -s dppc128_1.tpr -o dppc128_1-ini.gro -dump 10 it appears the following error: Fatal error: reading tpx file (dppc128_1.tpr) version 100 with version 83 program. I' m using Gromacs 4.6.5 maybe it has to be with differente gromacs version. In that case, what can i do? Alfonso -- 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] How to proceed with molecule.itp file
On 5/21/15 8:00 AM, Sotirios Dionysios I. Papadatos wrote: Hi, This indeed begins to clarify things but just to make sure I got it right. I want to simulate only a specific molecule from a protein, meaning I took the initial protein and deleted everything but the molecule. So I use the pdb2gmx to the molecule, I edit the topol.top that is produced (even in error a .top file is produced) and then I replace everything from the .itp file that I made.? Then I continue with the grompp command? Don't use pdb2gmx at all. You said you have an .itp file; this is already pretty much a .top as there are only small differences (.top is for a system, .itp is for a molecule, but in your case it sounds like molecule = system). See http://www.gromacs.org/Documentation/File_Formats/.itp_File The .top itself is as easy (if not easier) than the example already provided. Just do the following in a text editor to create a .top: 1. #include a parent force field (unless the .itp specifies all the parameters explicitly) 2. #include the molecule.itp file 3. Add a [system] directive with some name 4. Add a [molecules] directive that tells grompp there is 1 of your molecule That's all there is to it. -Justin From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Cara Kreck cara.kr...@student.curtin.edu.au Sent: Thursday, May 21, 2015 1:59 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] How to proceed with molecule.itp file Hi Sotirios, You need to either edit the .top file produced by pdb2gmx or make your own from scratch. You only need the pdb2gmx output if your system includes standard amino acids. If you have both a standard protein and a non-standard molecule, you should make a .pdb file with just the protein to use with pdb2gmx. I would then recommend you remove all the .top specific parts of this file and convert it to a .itp file for just the protein. Then make your own .top file using the bits you removed and link everything together. Alternatively you can just add to the include and molecule sections at the end of pdb2gmx's .top file. If you don't have any protein, don't bother with pdb2gmx at all. Here's an example DIY .top file: ; Forcefield files #include gromos53a6.ff/forcefield.itp #include ./lipids_vdw.itp ; Parameter set for DOPC #include ./dopc.itp ; Include DMSO topology #include ./dmso.itp ; Include water topology #include spc.itp [ system ] ; Name 128 DOPC in DMSO solution [ molecules ] ; name number DOPC 128 DMSO 496 SOL 7573 Make sure you use the molecule names defined in your .itp files and list the molecules in the same order that they appear in your coordinate file. Hope that helps, Cara From: si.papada...@edu.cut.ac.cy To: gromacs.org_gmx-users@maillist.sys.kth.se Date: Thu, 21 May 2015 07:13:00 + Subject: [gmx-users] How to proceed with molecule.itp file Hi, I have made a molecule.itp file according to the chapter 5 of Gromacs Manual and existing entries in the ff directory I want to use. My problem is that I don't know how to continue, in theory I have to include it in the .top file but a .top file is produced by pdb2gmx which I cannot use because there isn't an entry in .rtp. Please help -- 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. -- == 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.
Re: [gmx-users] How to proceed with molecule.itp file
Hi, This indeed begins to clarify things but just to make sure I got it right. I want to simulate only a specific molecule from a protein, meaning I took the initial protein and deleted everything but the molecule. So I use the pdb2gmx to the molecule, I edit the topol.top that is produced (even in error a .top file is produced) and then I replace everything from the .itp file that I made.? Then I continue with the grompp command? From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Cara Kreck cara.kr...@student.curtin.edu.au Sent: Thursday, May 21, 2015 1:59 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] How to proceed with molecule.itp file Hi Sotirios, You need to either edit the .top file produced by pdb2gmx or make your own from scratch. You only need the pdb2gmx output if your system includes standard amino acids. If you have both a standard protein and a non-standard molecule, you should make a .pdb file with just the protein to use with pdb2gmx. I would then recommend you remove all the .top specific parts of this file and convert it to a .itp file for just the protein. Then make your own .top file using the bits you removed and link everything together. Alternatively you can just add to the include and molecule sections at the end of pdb2gmx's .top file. If you don't have any protein, don't bother with pdb2gmx at all. Here's an example DIY .top file: ; Forcefield files #include gromos53a6.ff/forcefield.itp #include ./lipids_vdw.itp ; Parameter set for DOPC #include ./dopc.itp ; Include DMSO topology #include ./dmso.itp ; Include water topology #include spc.itp [ system ] ; Name 128 DOPC in DMSO solution [ molecules ] ; name number DOPC 128 DMSO 496 SOL 7573 Make sure you use the molecule names defined in your .itp files and list the molecules in the same order that they appear in your coordinate file. Hope that helps, Cara From: si.papada...@edu.cut.ac.cy To: gromacs.org_gmx-users@maillist.sys.kth.se Date: Thu, 21 May 2015 07:13:00 + Subject: [gmx-users] How to proceed with molecule.itp file Hi, I have made a molecule.itp file according to the chapter 5 of Gromacs Manual and existing entries in the ff directory I want to use. My problem is that I don't know how to continue, in theory I have to include it in the .top file but a .top file is produced by pdb2gmx which I cannot use because there isn't an entry in .rtp. Please help -- 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] About Tabulated Potentials
Dear all, I want to add the Morse potential for nonbonded interactions between CH4 and CH4. I used three table files each contain seven columns to add the H to H, H to C, and C to C Morse form interactions. I set Coulombtype=user, vdwtype=user , and Dispcorr = no, and add energrps and energrps_table in the mdp file. However, when I did NVT simulations, I didnot get accurate pressure for my pure methane system. Actually the pressure is 20 Mpa smaller. Could you tell what is wrong with my set or what I missed in adding tabulated potentials? I tested the using of tabulated potentials with LJ form potential, It works very well. Look forward to your reply, Sincerely yours Zhengcai, -- 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] Ligand covalently bound to protein: Best practice
Thanks for your comment and sorry for my weird english. I must have been in my thoughts :). I was also wondering if I attach covalently a protein to another protein or a large organic molecule through a residue in the middle of the sequence my approach would not work. Does anyone have a suggestion how setup a system like this? Thanks, Max On May 21, 2015, at 4:41 PM, Justin Lemkul jalem...@vt.edu wrote: On 5/21/15 4:30 PM, Ebert Maximilian wrote: Hi there, I am about to setup a protein ligand complex in which the the amino acid is covalently bound to the ligand. What I was about to do is to build an artificial amino acid (in this case serine) with the ligand attached to it an derive partial charges using antechamber or the RED server. Then while preparing the force field in GROMACS I would treat the serine was a new residue type with the new FF information. Is the a good practice? Sounds reasonable. -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. -- 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] Ligand covalently bound to protein: Best practice
On 5/21/15 4:51 PM, Ebert Maximilian wrote: Thanks for your comment and sorry for my weird english. I must have been in my thoughts :). I was also wondering if I attach covalently a protein to another protein or a large organic molecule through a residue in the middle of the sequence my approach would not work. Does anyone have a suggestion how setup a system like this? Why won't your approach work? The answer to this question is always the same: a modified residue in a biopolymer requires a modified .rtp entry. The details of how that works depends on the force field, but the net effect is the same. For linking proteins, that's what specbond.dat is for. The parametrization details depend on the kind of linkage. Isopeptides, disulfides, etc. are already handled easily. Other things require more effort. -Justin Thanks, Max On May 21, 2015, at 4:41 PM, Justin Lemkul jalem...@vt.edu wrote: On 5/21/15 4:30 PM, Ebert Maximilian wrote: Hi there, I am about to setup a protein ligand complex in which the the amino acid is covalently bound to the ligand. What I was about to do is to build an artificial amino acid (in this case serine) with the ligand attached to it an derive partial charges using antechamber or the RED server. Then while preparing the force field in GROMACS I would treat the serine was a new residue type with the new FF information. Is the a good practice? Sounds reasonable. -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. -- == 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.
[gmx-users] PMF calculation with constraint distance
Hi all, I started to calculate PMF between two ions in solution and I used constraint for pull option, instead of umbrella as I saw in Umbrella sampling Tutorial of Justin. This is the part of my mdp file! ; Pull code pull= constraint; Justin's value was umbrella pull_geometry = distance ; simple distance increase pull_dim= Y Y Y pull_start = no; Justin's value was yes pull_ngroups= 1 pull_group0 = CA_surf pull_group1 = carboxylate_carbon pull_init1 = 0.288 ; initial distance between pulling groups pull_rate1 = 0.001 ; 0.001 nm per ps pull_k1 = 1000 ; kJ mol^-1 nm^-2 I got the output and I tried to pull out with increasing the distance between two atoms and I have pullf.xvg file! I know that I can have the time evolution of constrained distance with g_dist from xtc file! I am wondering how to have the distance with corresponding constrained force? If I have the file contain forces and distances, I can integrate the force then I will have PMF. Could you help me that how I can manage this? Regards, Leila -- 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] PMF calculation with constraint distance
On 5/21/15 5:00 PM, leila salimi wrote: Hi all, I started to calculate PMF between two ions in solution and I used constraint for pull option, instead of umbrella as I saw in Umbrella sampling Tutorial of Justin. This is the part of my mdp file! ; Pull code pull= constraint; Justin's value was umbrella pull_geometry = distance ; simple distance increase pull_dim= Y Y Y pull_start = no; Justin's value was yes pull_ngroups= 1 pull_group0 = CA_surf pull_group1 = carboxylate_carbon pull_init1 = 0.288 ; initial distance between pulling groups pull_rate1 = 0.001 ; 0.001 nm per ps pull_k1 = 1000 ; kJ mol^-1 nm^-2 I got the output and I tried to pull out with increasing the distance between two atoms and I have pullf.xvg file! I know that I can have the time evolution of constrained distance with g_dist from xtc file! I am wondering how to have the distance with corresponding constrained force? If I have the file contain forces and distances, I can integrate the force then I will have PMF. This probably won't give you a very reliable PMF. You're effectively trying to use the Jarzynski method (albeit with a constraint rather than a harmonic potential) with one run (normally you have to do this many, many times), which won't give a correct result. Could you help me that how I can manage this? If you have the constraint force in pullf.xvg and the distance in another .xvg file, it's just a matter of using grep/awk to combine the two. Whether or not this means anything is another matter. Getting a PMF between ions is trivially simple with a harmonic potential. -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.
Re: [gmx-users] About Tabulated Potentials
On 5/21/15 3:46 PM, Zhengcai Zhang wrote: Dear Justin, Thank you for your reply. When I choose l-J form potential for the non-bonded interactions between CH4 and CH4 using the parameters from another paper, I can get system pressure (25.5Mpa) in accord with experimental value at same conditions. However, when I used tabulated potentials to add the morse form potentials, I got the pressure 5Mpa. I am confusing whether the tabulated potential works with the morse form potential. The tabulated potential does whatever you tell it; that's why it's there. I don't know anything about Morse potentials for nonbonded interactions; usually that's a bonded representation, so there's not much I can offer in the way of help. -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.
Re: [gmx-users] Version 100 with version 83 program
On 5/21/15 3:02 PM, Poncho Arvayo Zatarain wrote: I' m running Martínez Seara dppc tutorial and when i use echo 0|trjconv -f dppc128_1.xtc -s dppc128_1.tpr -o dppc128_1-ini.gro -dump 10 it appears the following error: Fatal error: reading tpx file (dppc128_1.tpr) version 100 with version 83 program. I' m using Gromacs 4.6.5 maybe it has to be with differente gromacs version. In that case, what can i do? Upgrade to the latest version. -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.
Re: [gmx-users] PMF calculation with constraint distance
Thanks Justin. Yes I have done PMF with Blue moon ensemble with DFT. Now I want to do the same with gromacs to have some knowledge about my FF parameters and compare with my DFT results! You meant I have to do with different configuration and average the forces? I am wondering that I did in DFT for each constrained distances around 15 ps MD and then I used averaged forces for each distances! Cheers, Leila On Thu, May 21, 2015 at 11:04 PM, Justin Lemkul jalem...@vt.edu wrote: On 5/21/15 5:00 PM, leila salimi wrote: Hi all, I started to calculate PMF between two ions in solution and I used constraint for pull option, instead of umbrella as I saw in Umbrella sampling Tutorial of Justin. This is the part of my mdp file! ; Pull code pull= constraint; Justin's value was umbrella pull_geometry = distance ; simple distance increase pull_dim= Y Y Y pull_start = no; Justin's value was yes pull_ngroups= 1 pull_group0 = CA_surf pull_group1 = carboxylate_carbon pull_init1 = 0.288 ; initial distance between pulling groups pull_rate1 = 0.001 ; 0.001 nm per ps pull_k1 = 1000 ; kJ mol^-1 nm^-2 I got the output and I tried to pull out with increasing the distance between two atoms and I have pullf.xvg file! I know that I can have the time evolution of constrained distance with g_dist from xtc file! I am wondering how to have the distance with corresponding constrained force? If I have the file contain forces and distances, I can integrate the force then I will have PMF. This probably won't give you a very reliable PMF. You're effectively trying to use the Jarzynski method (albeit with a constraint rather than a harmonic potential) with one run (normally you have to do this many, many times), which won't give a correct result. Could you help me that how I can manage this? If you have the constraint force in pullf.xvg and the distance in another .xvg file, it's just a matter of using grep/awk to combine the two. Whether or not this means anything is another matter. Getting a PMF between ions is trivially simple with a harmonic potential. -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. -- 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] Ligand covalently bound to protein: Best practice
Hi there, I am about to setup a protein ligand complex in which the the amino acid is covalently bound to the ligand. What I was about to do is to build an artificial amino acid (in this case serine) with the ligand attached to it an derive partial charges using antechamber or the RED server. Then while preparing the force field in GROMACS I would treat the serine was a new residue type with the new FF information. Is the a good practice? Thanks very much, Max -- 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] Ligand covalently bound to protein: Best practice
On 5/21/15 4:30 PM, Ebert Maximilian wrote: Hi there, I am about to setup a protein ligand complex in which the the amino acid is covalently bound to the ligand. What I was about to do is to build an artificial amino acid (in this case serine) with the ligand attached to it an derive partial charges using antechamber or the RED server. Then while preparing the force field in GROMACS I would treat the serine was a new residue type with the new FF information. Is the a good practice? Sounds reasonable. -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.
Re: [gmx-users] tpr file portability
Thank you sir. Best regards, Satyabrata Das -- 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] How to proceed with molecule.itp file
Hi Sotirios, You need to either edit the .top file produced by pdb2gmx or make your own from scratch. You only need the pdb2gmx output if your system includes standard amino acids. If you have both a standard protein and a non-standard molecule, you should make a .pdb file with just the protein to use with pdb2gmx. I would then recommend you remove all the .top specific parts of this file and convert it to a .itp file for just the protein. Then make your own .top file using the bits you removed and link everything together. Alternatively you can just add to the include and molecule sections at the end of pdb2gmx's .top file. If you don't have any protein, don't bother with pdb2gmx at all. Here's an example DIY .top file: ; Forcefield files #include gromos53a6.ff/forcefield.itp #include ./lipids_vdw.itp ; Parameter set for DOPC #include ./dopc.itp ; Include DMSO topology #include ./dmso.itp ; Include water topology #include spc.itp [ system ] ; Name 128 DOPC in DMSO solution [ molecules ] ; name number DOPC 128 DMSO 496 SOL 7573 Make sure you use the molecule names defined in your .itp files and list the molecules in the same order that they appear in your coordinate file. Hope that helps, Cara From: si.papada...@edu.cut.ac.cy To: gromacs.org_gmx-users@maillist.sys.kth.se Date: Thu, 21 May 2015 07:13:00 + Subject: [gmx-users] How to proceed with molecule.itp file Hi, I have made a molecule.itp file according to the chapter 5 of Gromacs Manual and existing entries in the ff directory I want to use. My problem is that I don't know how to continue, in theory I have to include it in the .top file but a .top file is produced by pdb2gmx which I cannot use because there isn't an entry in .rtp. Please help -- 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] pdb2gmx: Can I change the margin 10% to a higher value in the specbond.dat ?
Hi Cheng, You can add another entry for a disulfide bond with a different length. Cheers, Tsjerk On Thu, May 21, 2015 at 11:31 AM, Zhang, Cheng c.zhang...@ucl.ac.uk wrote: Dear GROMACS experts, I am using pdb2gmx for a protein with 5 disulfind bond https://copy.com/kPLlSianI4LtohNy The distance between each Cys SG are: 0.203, 0.204, 0.204, 0.205, 0.167. As a result, 10% margin of any value of the reference length in specbond.dat cannot cover all of the 5 Cys SG distance. I understand that a typical disulfide bond should be about 2.05 Å in length. However, if I still want to keep them, can I change the 10% margin to a higher value (e.g. 15%)? Thank you very much. Yours sincerely Cheng (Thank you for Justin's reply at https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-May/097699.html Would it be possible if I can simply reply to you for the thread instead of creating a new one?) -- 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. -- Tsjerk A. Wassenaar, Ph.D. -- 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 nuance in gmx5 (avoiding file INSTALL cannot find gmx)
You can't install into the build tree, AFAIK that's not allowed! Install into a clean target directory instead. Also, you mkdir source; mv * source step is just weird. Why move the source around? Instead you can simply create a build directory - this can even be in the source tree just as the uiqck and dirty install steps suggest: http://www.gromacs.org/Documentation/Installation_Instructions_5.0#quick-and-dirty-installation -- Szilárd On Thu, May 21, 2015 at 5:11 PM, Christopher Neale chris.ne...@alum.utoronto.ca wrote: Dear Users: This is just a note about compiling gromacs 5 so that the solution can be found by others if they need it. I used to compile gromacs like this: download and unpack tarball cd gromacs-5.0.5 mkdir source mv * source mkdir exec cd exec ** run my build script from here, using CMAKE_INSTALL_PREFIX=$(pwd) However, that no longer works. What happens is that make creates ./bin/gmx and then make install removes ./bin/gmx and then complains that it does not exist: CMake Error at src/programs/cmake_install.cmake:42 (file): file INSTALL cannot find /project2/p/pomes/cneale/GPC/exe/intel/gromacs-5.0.5/exec/bin/gmx. Call Stack (most recent call first): src/cmake_install.cmake:40 (include) cmake_install.cmake:48 (include) My solution was to build in a separate directory from either the source or the executable: download and unpack tarball cd gromacs-5.0.5 mkdir source mv * source mkdir exec build cd build ** run my build script from here, using CMAKE_INSTALL_PREFIX=$(pwd)/../exec Perhaps this is standard practice. Anyway, my original procedure works for gmx4.6.7 but not gmx5.0.5 so I thought I would report it. Note that this is separate from the issue that some have reported where a CMAKE_INSTALL_PREFIX using $(pwd) did not install but using the explicit path worked (I tested the explicit paths and got the same error that I report above). Chris. -- 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] pdb2gmx: can we use a file to specify the protonation instead of using -inter?
Dear GROMACS experts, Can I ask is there a more efficient way to deal with the -inter option in the pdb2gmx command? Now, I have to manually assign individual protonation status one by one, which takes a very long time. Sometimes I make a mistake and I have to re-do all of them again. Would it be possible if the command line can link to a file, which specifies the protonation for individual residues? Thank you very much. Yours sincerely Cheng -- 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] links errors at 700 or 800 K
Dear Users: I have a system with an 8-mer peptide in a box of water. After a 2-ns npt equilibration, I run 100 ns of nvt at various temperatures (300-800 K) in preparation for a REMD simulation. I am using velocity langevin for temperature control. Everything is fine for =600 K. Above that, I sometimes run into LINCS errors: ## Step 19126507, time 38253 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.069230, max 0.677838 (between atoms 49 and 50) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 49 50 90.00. 0.1864 0. 46 48 90.00. 0.1722 0. ## with eventual crash: ## WARNING: Listed nonbonded interaction between particles 57 and 59 at distance 58.376 which is larger than the table limit 2.223 nm. Fatal error: 1 particles communicated to PME rank 0 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. This usually means that your system is not well equilibrated. ## I have verified this with three different force fields in gmx4.6.7 (charmm27, amber99sb-ildn, and opls). I have also seen this in gmx5 (only charmm27 force field tested so far in gmx5 -- the error snippits above are from that gmx 5 run). The gromacs 5 mdp file (with verlet cutoff scheme) is as follows: ## nsteps = 5000 constraints = all-bonds lincs-iter = 1 lincs-order = 6 constraint_algorithm = lincs integrator = sd dt = 0.002 tinit = 0 nstcomm = 1 nstxout = 0 nstvout = 0 nstfout = 0 nstxtcout = 10 nstenergy = 10 nstlist = 10 nstlog=0 ns_type = grid cutoff-scheme = verlet vdwtype = cut-off rlist = 1.2 rvdw = 1.2 rvdw-switch = 1.0 rcoulomb = 1.2 vdw-modifier = force-switch coulombtype = PME ewald-rtol = 1e-5 optimize_fft = yes fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 tc_grps = System tau_t = 1.0 ld_seed = -1 ref_t = 800 gen_temp = 800 gen_vel = yes unconstrained_start = no gen_seed = -1 Pcoupl = no ## I'm guessing that at high temperature I need to increase lincs-iter or lincs-order ? I'm asking because these errors are rare (1-3 out of 20 100-ns simulations will have such an error) so simply testing it is not that quick. Very preliminary results suggest that gromacs5.0.5 with verlet cutoff scheme might have fewer such errors than gromacs 4.6.7 with the group cutoff scheme, possibly due to atoms moving out/in of the cutoff within the 20 fs between neighbourlist updates in the group scheme (3/20 crash with gmx4/group and 1/20 crashes with gmx5/verlet, but the variation between different force fields is on this order so I am not yet sure if the difference is significant). I will also note that I can get rid of these crashes by using constraints = h-bonds instead of constraints = all-bonds, though it has always been a mystery to me why constraints = h-bonds is stable (even at 300 K) with a 2 fs timestep so I am cautious about using that combination. Please let me note in advance that although 800K is quite hot, this is the system that I am trying to fix. Thank you for your assistance, Chris. -- 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] pdb2gmx: can we use a file to specify the protonation instead of using -inter?
Dear Cheng: You can define protonation states like this: echo 0 1 2 | pdb2gmx -ff amber99sb-ildn -water tip3p -his That will give you, in order for three HIS residues: 0. H on ND1 only (HID) 1. H on NE2 only (HIE) 2. H on ND1 and NE2 (HIP) You can also use -inter, but you'll need to do a dry-run to see what order gmx asks you for these things in. From my tests, it follow an order that is first residue type (in order: LYS, ARG, GLN, ASP, GLU, HIS, disulfide bonds) and for each of these, order by residue number. Chris. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Zhang, Cheng c.zhang...@ucl.ac.uk Sent: 21 May 2015 10:38 To: gromacs.org_gmx-users@maillist.sys.kth.se Cc: Zhang, Cheng Subject: [gmx-users] pdb2gmx: can we use a file to specify the protonation instead of using -inter? Dear GROMACS experts, Can I ask is there a more efficient way to deal with the -inter option in the pdb2gmx command? Now, I have to manually assign individual protonation status one by one, which takes a very long time. Sometimes I make a mistake and I have to re-do all of them again. Would it be possible if the command line can link to a file, which specifies the protonation for individual residues? Thank you very much. Yours sincerely Cheng -- 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] build nuance in gmx5 (avoiding file INSTALL cannot find gmx)
Dear Users: This is just a note about compiling gromacs 5 so that the solution can be found by others if they need it. I used to compile gromacs like this: download and unpack tarball cd gromacs-5.0.5 mkdir source mv * source mkdir exec cd exec ** run my build script from here, using CMAKE_INSTALL_PREFIX=$(pwd) However, that no longer works. What happens is that make creates ./bin/gmx and then make install removes ./bin/gmx and then complains that it does not exist: CMake Error at src/programs/cmake_install.cmake:42 (file): file INSTALL cannot find /project2/p/pomes/cneale/GPC/exe/intel/gromacs-5.0.5/exec/bin/gmx. Call Stack (most recent call first): src/cmake_install.cmake:40 (include) cmake_install.cmake:48 (include) My solution was to build in a separate directory from either the source or the executable: download and unpack tarball cd gromacs-5.0.5 mkdir source mv * source mkdir exec build cd build ** run my build script from here, using CMAKE_INSTALL_PREFIX=$(pwd)/../exec Perhaps this is standard practice. Anyway, my original procedure works for gmx4.6.7 but not gmx5.0.5 so I thought I would report it. Note that this is separate from the issue that some have reported where a CMAKE_INSTALL_PREFIX using $(pwd) did not install but using the explicit path worked (I tested the explicit paths and got the same error that I report above). Chris. -- 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] Generate the water box
Dear all, I can generate the cubic box or the rectangular box with gmx solvate -cs water.gro -box but I would like to have the octahedron box.I try many way but I can not. How I can do it? Thank a lot Tuong Vy 2015-05-21 1:49 GMT+09:00 Justin Lemkul jalem...@vt.edu: On 5/20/15 11:55 AM, 姚懿 wrote: genbox without adding a protein. More specifically (and for 5.0): gmx solvate -cs water.gro -box (whatever size is needed) -Justin On Wed, May 20, 2015 at 9:56 AM, Vy Phan phanvy120...@gmail.com wrote: Dear Gromacs Users, Can I generate only water on the Gromacs? I need water box only. Thank you Tuong Vy -- 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. -- == 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. -- 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] Re generate a tpr file
i'm trying to use the following command echo 0|trjconv -f dppc128_1.xtc -s dppc128_1.tpr -o dppc128_1-ini.gro -dump 10 but it appears the following error reading tpx file (dppc128_1.tpr) version 100 with version 83 program. I'm doing Martinez Seara tutorial and in the article uses 4.0.2 gromacs and i'm using gromacs version 4.6.5. How can i re generate the article in my 4.6.5 version? Alfonso -- 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] About Tabulated Potentials
Dear Justin, Thank you for your reply. When I choose l-J form potential for the non-bonded interactions between CH4 and CH4 using the parameters from another paper, I can get system pressure (25.5Mpa) in accord with experimental value at same conditions. However, when I used tabulated potentials to add the morse form potentials, I got the pressure 5Mpa. I am confusing whether the tabulated potential works with the morse form potential. Best, Zhengcai 在 2015年5月22日，01:54，Justin Lemkul jalem...@vt.edu 写道： On 5/21/15 8:36 AM, zhangzhengc wrote: Dear all, I want to add the Morse potential for nonbonded interactions between CH4 and CH4. I used three table files each contain seven columns to add the H to H, H to C, and C to C Morse form interactions. I set Coulombtype=user, vdwtype=user , and Dispcorr = no, and add energrps and energrps_table in the mdp file. However, when I did NVT simulations, I didnot get accurate pressure for my pure methane system. Actually the pressure is 20 I don't know much about tabulated potentials, but a question to get the ball rolling: How do you define accurate - from some previous run? Without tabulated potentials? If the latter, it means your tables are wrong with respect to whatever parameters gave the right behavior. -Justin Mpa smaller. Could you tell what is wrong with my set or what I missed in adding tabulated potentials? I tested the using of tabulated potentials with LJ form potential, It works very well. Look forward to your reply, Sincerely yours Zhengcai, -- == 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.
[gmx-users] Version 100 with version 83 program
I' m running Martínez Seara dppc tutorial and when i use echo 0|trjconv -f dppc128_1.xtc -s dppc128_1.tpr -o dppc128_1-ini.gro -dump 10 it appears the following error: Fatal error: reading tpx file (dppc128_1.tpr) version 100 with version 83 program. I' m using Gromacs 4.6.5 maybe it has to be with differente gromacs version. In that case, what can i do? Alfonso -- 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 nuance in gmx5 (avoiding file INSTALL cannot find gmx)
Chris, On Thu, May 21, 2015 at 5:50 PM, Christopher Neale chris.ne...@alum.utoronto.ca wrote: Dear Szilárd: I report it only because it is allowed in gmx4 builds (or at least it works, I am not sure whether or not is it allowed). By now allowed I meant that things will likely break if you do that (@others: please confirm if I remember correctly this is indeed prone to break with CMake). Additionally, I spoke up because this is also a bad practice. The build and installation directory trees serve different purposes and have different, but potentially overlapping structure. Hence, you can easily end up with a disastrous mess if e.g. the install process modifies or deletes a file that the build tree generated. I move the source because I often have many modified source trees that I rename to keep things straight. You could still do that if e.g. you structure things like this: GROMACS-5.0.5 /source /build /install The quick and dirty method that you cite presumes that one has root access, which is very unlikely on the places that most simulations are run. The http://www.gromacs.org/Documentation/Installation_Instructions_5.0#typical-gromacs-installation section below that does have a note about -DCMAKE_INSTALL_PREFIX=xxx to install GROMACS to a non-standard location (default /usr/local/gromacs) but that gives no suggestions on how to use it and based on my experience I presume that -DCMAKE_INSTALL_PREFIX=$(pwd) would give a similar error if applied to the quick and dirty method. Exactly, -DCMAKE_INSTALL_PREFIX is all you need to add to the configure line to avoid needing root access. Perhaps we should add that to the quick and dirty steps. Not sure why does it make things easier to put the installation in the same place where you configured - which is supposed to be just a staging area, nothing more. However, we should probably note this issue in the install guide. My intention is not to try to get gromacs to change the build procedure. Just to report something that worked once that no longer works and to include a snippit from the relevant error message so that it is searchable. Sure, documenting issue it is always beneficial for the gmx community, so thanks for the note! Cheers, -- Szilárd 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 Szilárd Páll pall.szil...@gmail.com Sent: 21 May 2015 11:24 To: Discussion list for GROMACS users Cc: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] build nuance in gmx5 (avoiding file INSTALL cannot find gmx) You can't install into the build tree, AFAIK that's not allowed! Install into a clean target directory instead. Also, you mkdir source; mv * source step is just weird. Why move the source around? Instead you can simply create a build directory - this can even be in the source tree just as the uiqck and dirty install steps suggest: http://www.gromacs.org/Documentation/Installation_Instructions_5.0#quick-and-dirty-installation -- Szilárd On Thu, May 21, 2015 at 5:11 PM, Christopher Neale chris.ne...@alum.utoronto.ca wrote: Dear Users: This is just a note about compiling gromacs 5 so that the solution can be found by others if they need it. I used to compile gromacs like this: download and unpack tarball cd gromacs-5.0.5 mkdir source mv * source mkdir exec cd exec ** run my build script from here, using CMAKE_INSTALL_PREFIX=$(pwd) However, that no longer works. What happens is that make creates ./bin/gmx and then make install removes ./bin/gmx and then complains that it does not exist: CMake Error at src/programs/cmake_install.cmake:42 (file): file INSTALL cannot find /project2/p/pomes/cneale/GPC/exe/intel/gromacs-5.0.5/exec/bin/gmx. Call Stack (most recent call first): src/cmake_install.cmake:40 (include) cmake_install.cmake:48 (include) My solution was to build in a separate directory from either the source or the executable: download and unpack tarball cd gromacs-5.0.5 mkdir source mv * source mkdir exec build cd build ** run my build script from here, using CMAKE_INSTALL_PREFIX=$(pwd)/../exec Perhaps this is standard practice. Anyway, my original procedure works for gmx4.6.7 but not gmx5.0.5 so I thought I would report it. Note that this is separate from the issue that some have reported where a CMAKE_INSTALL_PREFIX using $(pwd) did not install but using the explicit path worked (I tested the explicit paths and got the same error that I report above). Chris. -- 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
[gmx-users] Fatal error tpx file
I' m running Martínez Seara dppc tutorial and when i use echo 0|trjconv -f dppc128_1.xtc -s dppc128_1.tpr -o dppc128_1-ini.gro -dump 10 it appears the following error: Fatal error: reading tpx file (dppc128_1.tpr) version 100 with version 83 program. I' m using Gromacs 4.6.5 maybe it has to be with differente gromacs version. In that case, what can i do? Alfonso -- 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 nuance in gmx5 (avoiding file INSTALL cannot find gmx)
Dear Szilárd: I report it only because it is allowed in gmx4 builds (or at least it works, I am not sure whether or not is it allowed). I move the source because I often have many modified source trees that I rename to keep things straight. The quick and dirty method that you cite presumes that one has root access, which is very unlikely on the places that most simulations are run. The http://www.gromacs.org/Documentation/Installation_Instructions_5.0#typical-gromacs-installation section below that does have a note about -DCMAKE_INSTALL_PREFIX=xxx to install GROMACS to a non-standard location (default /usr/local/gromacs) but that gives no suggestions on how to use it and based on my experience I presume that -DCMAKE_INSTALL_PREFIX=$(pwd) would give a similar error if applied to the quick and dirty method. My intention is not to try to get gromacs to change the build procedure. Just to report something that worked once that no longer works and to include a snippit from the relevant error message so that it is searchable. 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 Szilárd Páll pall.szil...@gmail.com Sent: 21 May 2015 11:24 To: Discussion list for GROMACS users Cc: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] build nuance in gmx5 (avoiding file INSTALL cannot find gmx) You can't install into the build tree, AFAIK that's not allowed! Install into a clean target directory instead. Also, you mkdir source; mv * source step is just weird. Why move the source around? Instead you can simply create a build directory - this can even be in the source tree just as the uiqck and dirty install steps suggest: http://www.gromacs.org/Documentation/Installation_Instructions_5.0#quick-and-dirty-installation -- Szilárd On Thu, May 21, 2015 at 5:11 PM, Christopher Neale chris.ne...@alum.utoronto.ca wrote: Dear Users: This is just a note about compiling gromacs 5 so that the solution can be found by others if they need it. I used to compile gromacs like this: download and unpack tarball cd gromacs-5.0.5 mkdir source mv * source mkdir exec cd exec ** run my build script from here, using CMAKE_INSTALL_PREFIX=$(pwd) However, that no longer works. What happens is that make creates ./bin/gmx and then make install removes ./bin/gmx and then complains that it does not exist: CMake Error at src/programs/cmake_install.cmake:42 (file): file INSTALL cannot find /project2/p/pomes/cneale/GPC/exe/intel/gromacs-5.0.5/exec/bin/gmx. Call Stack (most recent call first): src/cmake_install.cmake:40 (include) cmake_install.cmake:48 (include) My solution was to build in a separate directory from either the source or the executable: download and unpack tarball cd gromacs-5.0.5 mkdir source mv * source mkdir exec build cd build ** run my build script from here, using CMAKE_INSTALL_PREFIX=$(pwd)/../exec Perhaps this is standard practice. Anyway, my original procedure works for gmx4.6.7 but not gmx5.0.5 so I thought I would report it. Note that this is separate from the issue that some have reported where a CMAKE_INSTALL_PREFIX using $(pwd) did not install but using the explicit path worked (I tested the explicit paths and got the same error that I report above). Chris. -- 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] Segmentation fault (core dumped) version 4.6.*
Dear gmx users, In order to run my simulations, i usually used the 5.0.* version of gromacs without problems, but since i want to performed umbrella sampling simulations (and since the option pull_geometry=position is not available for the latest versions) For that, i installed the 4.6.7 version of gromacs. The installation went without issue, but every time i used a command from gromacs i got the Segmentation fault (core dumped) error: Like for example, by using this command line: grompp -f npt_production.mdp -c npt_equilibration.gro -p topol.top -o npt_production.tpr i got this: Option Filename Type Description -f npt_production.mdp Inputgrompp input file with MD parameters -po mdout.mdp Output grompp input file with MD parameters -c npt_equilibration.gro InputStructure file: gro g96 pdb tpr etc. -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc. -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc. -n index.ndx Input, Opt. Index file -p topol.top InputTopology file -pp processed.top Output, Opt. Topology file -o npt_production.tpr Output Run input file: tpr tpb tpa -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt -e ener.edr Input, Opt. Energy file -ref rotref.trr In/Out, Opt. Full precision trajectory: trr trj cpt Option Type Value Description -- -[no]h bool no Print help info and quit -[no]version bool no Print version info and quit -niceint0 Set the nicelevel -[no]v bool no Be loud and noisy -timereal -1 Take frame at or first after this time. -[no]rmvsbds bool yes Remove constant bonded interactions with virtual sites -maxwarn int0 Number of allowed warnings during input processing. Not for normal use and may generate unstable systems -[no]zerobool no Set parameters for bonded interactions without defaults to zero instead of generating an error -[no]renum bool yes Renumber atomtypes and minimize number of atomtypes Segmentation fault (core dumped) That is not telling me anything useful :/ I tried also installing the 4.6.3, but sadly i have the same problems with this version. Hope someone can help me. Best, Carlos -- Carlos Navarro Retamal Bioinformatics Engineering Ph. D (c) Applied Sciences. Center of Bioinformatics and Molecular Simulations. CBSM University of Talca Av. Lircay S/N, Talca, Chile T: (+56) 712201 798 E: carlos.navarr...@gmail.com or cnava...@utalca.cl -- 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] Segmentation fault (core dumped) version 4.6.*
Dear Carlos: Are you using a .top file from gromacs 5 with your gromacs 4 runs? If so, try regenerating your topology (and .itp files) using gromacs 4 (with GMXLIB set correctly). Not sure if that would even cause a problem, but it seems like it probably would and is the only thing that comes to mind. If that is not the issue, then do any of the other commands work without a segfault (e.g. gmxcheck)? Chris. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Carlos Navarro Retamal cnava...@utalca.cl Sent: 21 May 2015 11:55 To: gmx-us...@gromacs.org Subject: [gmx-users] Segmentation fault (core dumped) version 4.6.* Dear gmx users, In order to run my simulations, i usually used the 5.0.* version of gromacs without problems, but since i want to performed umbrella sampling simulations (and since the option pull_geometry=position is not available for the latest versions) For that, i installed the 4.6.7 version of gromacs. The installation went without issue, but every time i used a command from gromacs i got the Segmentation fault (core dumped) error: Like for example, by using this command line: grompp -f npt_production.mdp -c npt_equilibration.gro -p topol.top -o npt_production.tpr i got this: Option Filename Type Description -f npt_production.mdp Inputgrompp input file with MD parameters -po mdout.mdp Output grompp input file with MD parameters -c npt_equilibration.gro InputStructure file: gro g96 pdb tpr etc. -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc. -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc. -n index.ndx Input, Opt. Index file -p topol.top InputTopology file -pp processed.top Output, Opt. Topology file -o npt_production.tpr Output Run input file: tpr tpb tpa -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt -e ener.edr Input, Opt. Energy file -ref rotref.trr In/Out, Opt. Full precision trajectory: trr trj cpt Option Type Value Description -- -[no]h bool no Print help info and quit -[no]version bool no Print version info and quit -niceint0 Set the nicelevel -[no]v bool no Be loud and noisy -timereal -1 Take frame at or first after this time. -[no]rmvsbds bool yes Remove constant bonded interactions with virtual sites -maxwarn int0 Number of allowed warnings during input processing. Not for normal use and may generate unstable systems -[no]zerobool no Set parameters for bonded interactions without defaults to zero instead of generating an error -[no]renum bool yes Renumber atomtypes and minimize number of atomtypes Segmentation fault (core dumped) That is not telling me anything useful :/ I tried also installing the 4.6.3, but sadly i have the same problems with this version. Hope someone can help me. Best, Carlos -- Carlos Navarro Retamal Bioinformatics Engineering Ph. D (c) Applied Sciences. Center of Bioinformatics and Molecular Simulations. CBSM University of Talca Av. Lircay S/N, Talca, Chile T: (+56) 712201 798 E: carlos.navarr...@gmail.com or cnava...@utalca.cl -- 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.
