Re: [gmx-users] Forces are large - How to track down the culprit
Hi Shay, sorry for the late comment - let me guess, you compiled Gromacs in double precision? :) Greetings Steffen Is this reproducible? Yes. I've taken the same simulation and had it re-run and got the same error at the exact same frame (frame 693, which is timeframe 6930). You could try to fork off a tpr file using tpbconv -f -e -s -o just before this happens and rerun it. I did something similar to what you suggest before posting here: Oddly enough the Warning did not occur: I ran the simulation up to 6000ps and then continued the simulation to another 4000ps and the simulation ran correctly and without any problems. It can also be combined by input parameters, e.g. too large time step, too infrequent neighborsearching etc., use of cutoffs. If no other suggestions I'll try working that angle too, since a lot of my simulations are running with very similar mdp parameters without problems. Thanks again for your prompt reply, -Shay Shay Amram wrote: Of course. I'm using version 3.3.3 of GROMACS. -Shay -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham Sent: Tuesday, December 30, 2008 02:59 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Forces are large - How to track down the culprit Shay Amram wrote: Greetings dear Gromacs users, I have recently been simulating a POPG membrane* in water (SPC). Several of my simulations after running well into the 10ns and 20ns are sometimes getting a Forces for atom X are large. I'm rather unsure as to the cause of this situation. Moreover, as far as I can tell from viewing the simulation, the system _does NOT_ explode (as may be suggested by wiki.gromacs and some previous answers to this kind of situation). The rest of the simulation looks much as it did in the beginning. I would be interested (and thankful!) to hear any of your opinions as to why I'm getting this message (or how to catch the culprit), and more importantly, how to prevent it from happening in the future. During this version-transitive period, it's always right to report the GROMACS version that you're using. It would normally be right to be using the most recent version (4.0.2) if encountering problems. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dipl.-Chem. Steffen Wolf Fellow of the Ruhr-University Research School Department of Biophysics University of Bochum ND 04/67 44780 Bochum Germany Tel: +49 (0)234 32 28363 Fax: +49 (0)234 32 14626 E-Mail: sw...@bph.rub.de Web: http://www.bph.rub.de ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Problems with parallelisation of GROMACS on a Mac Pro (OS X)
Hi Alan, thanks for the hint!!! Seems like it really was a problem with lammpi. The download from FINK worked beautifully, and GROMACS/open mpi works perfectly. Cheers Steffen Steffen, if don't intend to use GMX double precision, why not use Gromacs from FINK? It's all there. Use ommpi also, instead of lammpi (seems broken in Fink too). Then you can do something like: # with openmpi, for a dual core grompp -f em.mdp -c Complex_b4em.pdb -p Complex.top -o em.tpr -np 2 om-mpirun -n 2 mdrun_mpi -v -deffnm em grompp -f md.mdp -c em.gro -p Complex.top -o md.tpr -np 2 -sort -shuffle om-mpirun -n 2 mdrun_mpi -v -deffnm md Cheers, Alan On Thu, Jul 31, 2008 at 4:40 PM, [EMAIL PROTECTED] wrote: Hi all, I'm having trouble with the compilation of GROMACS on a Mac Pro (OS X). It's a machine with two Quad-Core Intel Xeon, so 8 nodes in all. As compiler I used the programs delivered with the Xcode tools 3.0 and for parallelisation the LAM/MPI package delivered with the Xcode tools. The problem now is: If I try to start a job on the 8 nodes, the program is started 8 times (one time each node) instead of one time and distributed on 8 nodes. The result is the same for GROMACS 3.3.1, 3.3.3 and the recent CVS. Does anybody have a suggestion? Is the problem more related to LAM then to GROMACS? Greetings Steffen -- Dipl.-Chem. Steffen Wolf Fellow of the Ruhr-University Research School Department of Biophysics University of Bochum ND 04/67 44780 Bochum Germany Tel: +49 (0)234 32 28363 Fax: +49 (0)234 32 14626 E-Mail: [EMAIL PROTECTED] Web: http://www.bph.rub.de ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Analysis of mutants
Hi Sundar, general advice: check the literature on what other people did to get insight into similar problems. This should give you a good overview what can be done by MD - and what can't. Interaction and fluctuation can be assessed via energy analysis (g_energy, one energygroup per amino acid), and distance plots (g_dist). Fluctuations are distinguishable via the RMSF analysis (g_rmsf). And: check the manual + the GROMACS wiki again. greetings Steffen hi people, I am new to gromacs. I am running gromacs (version 3.3.1) for a protein and its 3 mutants. I am not having any problems in the run. I would like to focus my analysis on 3-4 amino acids specifically. Can anyone please tell me some good commands or a link where I can check how these amino acids are interacting, how these amino acids are fluctuating etc. I searched the manual but I am not sure which commands to use. Also, I think it is better to get some help from people who have done this type of analysis many times. I am waiting for your reply. Thank you -- Dipl.-Chem. Steffen Wolf Fellow of the Ruhr-University Research School Department of Biophysics University of Bochum ND 04/67 44780 Bochum Germany Tel: +49 (0)234 32 28363 Fax: +49 (0)234 32 14626 E-Mail: [EMAIL PROTECTED] Web: http://www.bph.rub.de ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] cholesterol distortion
Hi Jian, seems like there's something seriously wrong with the topology of the cholesterols - check if the angles impropers are set and reasonable. Cheers Steffen Hi, all: I got the initial structure of a DPPC bilayer from Dr. Karttunen's website, use the parameters (hopefully) from their paper: Patra, Karttunen, Hyvönen, Falck, Lindqvist, Vattulainen, Biophys. J. *84*, 3636-3645 (2003) to run for 100ns then replace some DPPC molecules with cholesterols, do the energy minimization, run for 20ns and the cholesterols are distorted as shown in the attached file. Here are parameters for the pure DPPC run which I deem important: nstcomm = 1 comm_grps= DPPC SOL nstlist = 10 ns_type = grid pbc = xyz rlist= 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = Cutoff rvdw = 1.0 ewald_rtol = 1e-5 optimize_fft = yes tcoupl = Berendsen tau_t= 0.1 0.1 tc_grps = DPPC SOL ref_t= 323 323 pcoupl = Berendsen pcoupltype = semiisotropic tau_p= 1 1 compressibility = 4.5e-5 4.5e-5 ref_p= 1.01.0 gen_vel = yes gen_temp = 325 gen_seed = 173529 constraints = all-bonds constraint_algorithm = LINCS lincs_order = 4 For the DPPC-CHOL combined system I only changed corresponding sections to: comm_grps= DPPC CHOL SOL tau_t= 0.1 0.1 0.1 tc_grps = DPPC CHOL SOL ref_t= 323 323 323 Any suggestion is appreciated. Thank you. Jian ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dipl.-Chem. Steffen Wolf Fellow of the Ruhr-University Research School Department of Biophysics University of Bochum ND 04/67 44780 Bochum Germany Tel: +49 (0)234 32 28363 Fax: +49 (0)234 32 14626 E-Mail: [EMAIL PROTECTED] Web: http://www.bph.rub.de ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] information for analysis
Hi Pragya, well: -Surface area / lipid: = x(box)*y(box) / half the number of lipids in your box -order parameter: see the g_order-tool -3rd one I can't say, but a general hint: Search on www.gromacs.org in the mailing list archive, most of these topic has been discussed a thousand times before. Greetings Steffen hello users please can you tell me how to calculate surface area per lipid, orer parameters, area per head group of lipid from simulation thanks in advance Post free auto ads on Yello Classifieds now! Try it now! http://ss1.richmedia.in/recurl.asp?pid=255 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dipl.-Chem. Steffen Wolf Fellow of the Ruhr-University Research School Department of Biophysics University of Bochum ND 04/67 44780 Bochum Germany Tel: +49 (0)234 32 28363 Fax: +49 (0)234 32 14626 E-Mail: [EMAIL PROTECTED] Web: http://www.bph.rub.de ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] make_hole error installation
Hi Landry, well: make_hole just works with Gromacs version 3.1.4 - download this old version from the gromacs homepage, start from the beginning, and everything should work fine. J'espere que ca t'aide Steffen Hi I try to install gromacs with make_hole utility so I download the gromacs-3.3.2.tar.gz, I uncompress it, I download the mdrun_make_hole.tar.gz and uncompress it in the gromacs folder. After the ./configure command which completed successfully, I run the make command and I get the following error (the same that pragya chohan http://www.gromacs.org/pipermail/gmx-users/2007-November/030613.html ): nonbonded.c: In function 'do_nonbonded': nonbonded.c:272: error: 'esolSPC' undeclared (first use in this function) nonbonded.c:272: error: (Each undeclared identifier is reported only once nonbonded.c:272: error: for each function it appears in.) nonbonded.c:276: error: 'esolTIP4P' undeclared (first use in this function) nonbonded.c:472: error: 'enlistWATER' undeclared (first use in this function) nonbonded.c:476: error: 'enlistWATERWATER' undeclared (first use in this function) nonbonded.c: In function 'do_nonbonded14': nonbonded.c:542: error: 'eelRF_NEC' undeclared (first use in this function) nonbonded.c:569: error: 'epbcFULL' undeclared (first use in this function) make[5]: *** [nonbonded.lo] Error 1 make[5]: Leaving directory `/usr/local/gromacs-3.3.2/src/gmxlib/nonbonded' make[4]: *** [all-recursive] Error 1 make[4]: Leaving directory `/usr/local/gromacs-3.3.2/src/gmxlib/nonbonded' make[3]: *** [all-recursive] Error 1 make[3]: Leaving directory `/usr/local/gromacs-3.3.2/src/gmxlib' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/usr/local/gromacs-3.3.2/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/usr/local/gromacs-3.3.2/src' make: *** [all-recursive] Error 1 However, after, I get no error when I install gromacs without the make_hole utility, so the problem comes from make_hole... Thanks in advance -- Dipl.-Chem. Steffen Wolf Fellow of the Ruhr-University Research School Department of Biophysics University of Bochum ND 04/67 44780 Bochum Germany Tel: +49 (0)234 32 28363 Fax: +49 (0)234 32 14626 E-Mail: [EMAIL PROTECTED] Web: http://www.bph.rub.de ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] b-factor
Hi Tang, read carefully: http://www.pdb.org/robohelp_f/#site_navigation/general_faq.htm and get yourself prepared in how a pdb file is set up. If you want to do simulations, get started with knowing the basics first. Cheers Steffen Dear all, I have got a pdb file by command g_rmsf and option -oq, and the content of the file is like this: TITLE Protein in water REMARKTHIS IS A SIMULATION BOX CRYST1 148.918 148.918 148.428 59.89 59.89 90.00 P 1 1 MODEL1 ATOM 47354 CA ALA I9967 60.915 88.765 42.075 1.00 92.09 ATOM 47364 CA GLY I9968 60.037 91.017 39.099 1.00 31.09 ATOM 47371 CA PHE I9969 59.892 94.727 38.149 1.00 13.34 ATOM 47391 CA LYS I9970 56.778 96.973 38.146 1.00 13.59 ATOM 47413 CA ALA I9971 57.412 100.730 38.292 1.00 8.88 ATOM 47423 CA GLY I9972 55.243 102.910 40.429 1.00 8.42 ATOM 47430 CA VAL I9973 55.349 104.629 43.777 1.00 6.96 ATOM 47446 CA LYS I9974 55.039 102.584 47.023 1.00 10.56 ATOM 47468 CA ASP I9975 53.919 102.844 50.642 1.00 8.59 ATOM 47480 CA TYR I9976 56.618 101.675 53.096 1.00 5.41 ATOM 47501 CA ARG I9977 54.179 100.074 55.607 1.00 6.66 ATOM 47525 CA LEU I9978 53.642 97.083 53.329 1.00 10.59 ATOM 47544 CA THR I9979 57.043 95.266 53.147 1.00 10.24 ATOM 47558 CA TYR I9980 59.307 96.919 55.730 1.00 4.74 ATOM 47579 CA TYR I9981 57.141 96.770 58.853 1.00 4.52 ATOM 47600 CA THR I9982 57.423 93.001 59.524 1.00 5.61 ATOM 47613 CA PRO I9983 55.634 91.722 62.707 1.00 11.23 ATOM 47628 CA ASP I9984 56.655 88.019 62.809 1.00 13.38 ATOM 47640 CA TYR I9985 60.439 88.728 62.349 1.00 9.58 Could you tell me which column should be the b-factor? B-factor is the thermal deviation of the atom, and could you tell me how the gromacs gives the values of b-factor for each atom in detail? Thank you! Tang Jiaowei ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dipl.-Chem. Steffen Wolf Fellow of the Ruhr-University Research School Department of Biophysics University of Bochum ND 04/67 44780 Bochum Germany Tel: +49 (0)234 32 28363 Fax: +49 (0)234 32 14626 E-Mail: [EMAIL PROTECTED] Web: http://www.bph.rub.de ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How Long to Equlibrate?
Hi Mark, well, equilibration is a tricy thing: Most simple would be the answer when all observables level off, but one can wait eternally for that. I usually go the folloing way: a) has the total system energy levelled off / does it not fall anymore but oscillates around a certain value? b) are the interaction energies for the part of my system of interest stable (for you: the protein/protein or protein/solvent terms) not changin anymore / oscillating around a mean value? An other painfull truth: don't expect anything like an equilibration within 100 ps. After 2 ns most of the system creation effects (too high order of solvent, lacking protein solvation etc.) will vanish, but then comes the interesting part where the small but important changes happen. In general: You NEVER can be sure that your system is equillibrated, there might be changes even after 100 ns. A reasonable time scale for simulations would be ca. 10 ns (if you can afford it computationally), and see what you can gain as information out of this trajectory. Hope this helps you - it's not really a cheerful positive answer, but even in silico, nature is a bitch... ;) Steffen I have a 290+ residue protein and I recently ran a 200 ps simulation in a water box with electrostatic cutoff at approximately half the value of the box dimension. Since there is no heating stage in the dynamics, I am wondering what guidelines there are for knowing when to evaluate data from the simulation. There are some interesting features to the RMSD plot I would like to investigate. But I am not sure I can analyze the last 100 ps of the dynamics or not. Any help would be greatly appreciated. Thanks! Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dipl.-Chem. Steffen Wolf Fellow of the Ruhr-University Research School Department of Biophysics University of Bochum ND 04/67 44780 Bochum Germany Tel: +49 (0)234 32 28363 Fax: +49 (0)234 32 14626 E-Mail: [EMAIL PROTECTED] Web: http://www.bph.rub.de ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] water molecules in vacuum simulation.
Hi Anwar, the answer is: Yes, sure. CU Steffen Dear users, Is it possible to perform an invacuum simulation with few constrained water molecules? I dont want to use the explicit solvent, but want to use the crystallographic water molecules in protein and perform invacuum simulation. regards Anwar -- Mohd Anwaruddin Project Assistant C/o DR.H.A.Nagarajaram Lab of Computational Biology and Bioinformatics Center for DNA Fingerprinting and Diagnostics(CDFD) Nacharam Hyderabad-500 076 INDIA. Tel: +91-8413-235467,68,69,70 ext 2019 [EMAIL PROTECTED] --- - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dipl.-Chem. Steffen Wolf Department of Biophysics University of Bochum ND 04/67 44780 Bochum Germany Tel: +49 (0)234 32 28363 Fax: +49 (0)234 32 14626 E-Mail: [EMAIL PROTECTED] Web: http://www.bph.rub.de ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] position restraints crashing
Alan Dodd wrote: No, minimisation was without PR. Surely minimisation with PR would *increase* bad contacts, rather than removing them? I've tried running for a while under normal MD, successfully and without LINCS errors, then taking the endpoint and running under PR, but it still crashes almost instantaneously, so it's unlikely to just be a matter of energies or bad contacts, I'd have thought? Yes, so it looks that minimization ended at a metastable point, which was surmounted by a free MD run but kept by the PR and therefore caused the system to crash. Which minimization algorithm did you use? Steep or CG? -- Dipl.-Chem. Steffen Wolf Department of Biophysics University of Bochum ND 04/67 44780 Bochum Germany Tel: +49 (0)234 32 28363 Fax: +49 (0)234 32 14626 E-Mail: [EMAIL PROTECTED] Web: http://www.bph.rub.de ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] POPC simulation
Hi Arindam, you've simply got to switch two lines in the *.top file: lipid.itp has to be called by the topology before popc.itp, as it contains the information on atomtypes for GROMACS. So: #include lipid.itp #include popc.itp should work just fine. Greetings Steffen -- Dipl.-Chem. Steffen Wolf Department of Biophysics University of Bochum ND 04/67 44780 Bochum Germany Tel: +49 (0)234 32 28363 Fax: +49 (0)234 32 14626 E-Mail: [EMAIL PROTECTED] Web: http://www.bph.rub.de ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Topology question
Anthony Cruz wrote: Hi users: I made a small molecule topology using the PRODRG topology generation server but I want to use it with the G43a1 GROMOS96 43a1 Forcefield. How I could change the parameters from GROMACS to GROMOS??? thanks Anthony ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Hi Anthony, search for a mail by christian burisch on this topic, posted on the list yesterday... -- Dipl.-Chem. Steffen Wolf Department of Biophysics University of Bochum ND 04/67 44780 Bochum Germany Tel: +49 (0)234 32 28363 Fax: +49 (0)234 32 14626 E-Mail: [EMAIL PROTECTED] Web: http://www.bph.rub.de ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Req for script to make rtp entro of ligand with ffoplsa compatiable
Hi Raja, an entry for a molecule in the rtp database you have to create on your own - the principles how to explain your ligand to Gromacs is simple, just take a look onto the aminoacids in there and how they are described. Will take you some time (roughly some days probably), but it will work. An other possibility would be to write an *.itp file especially for your ligand, which I find a better solution. This is described in the manual. Some kind of simple topology creater is the PRODRG Server () - there you can create a topology for your ligand. Bye Steffen -- Dipl.-Chem. Steffen Wolf Department of Biophysics University of Bochum ND 04/67 44780 Bochum Germany ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Protein out of water box
Prasad Gajula wrote: Dear Gromacs Users, When I use the genbox after editconf , most of the protein is out of water. Even with 'trjconv' after the simulations I cant see any change, as suggested by other gromacs users. Pls some one give me an idea... thank you very much! best regards Gajula ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Hi Gajula, maybe a stupid question, but: is your simulation box larger than the protein itself, as it has to be? Steffen -- Dipl.-Chem. Steffen Wolf Department of Biophysics University of Bochum ND 04/67 44780 Bochum Germany ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] LINCS Warning using mdrun
Gaurav Chopra wrote: Hi I get the following error when using mdrun for a protein in solution. I have checked the structure and everything looks fine to me. Could you suggested anything else I could do. Step -2, time -0.004 (ps) LINCS WARNING relative constraint deviation after LINCS: max 0.126305 (between atoms 892 and 894) rms 0.007000 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 898899 41.60.1015 0.0997 0.1010 898900 38.10.1038 0.0984 0.1010 starting mdrun 'HEADER Output set 125 with rmsf= .982 of 1nkd.cl_nH_tir.pdb in water' 10 steps,200.0 ps. Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max 3.372058 (between atoms 894 and 895) rms 0.239340 bonds that rotated more than 30 degrees: Thanks gaurav ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Hi Gaurav, what is your stepsize during the simulation? what is constrained? And have you run a minimization before starting the simulation? hear from you soon Steffen -- Dipl.-Chem. Steffen Wolf Department of Biophysics University of Bochum ND 04/67 44780 Bochum Germany ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
