[gmx-users] Gromacs 4.5.5 GPU Error
Hi all, I am trying to get the GPU version of gromacs running. I manage to install OpenMM, compile and install mdrun-gpu. However when I ran mdrun-gpu on any of the benchmark files, I got this: ./run.sh: line 2: 14224 Floating point exception/usr/local/gromacs-4.5.5-cuda/bin/mdrun-gpu -v Any idea what goes wrong here? -- Regards, THChew -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] gromacs 4.5.5 cygwin installation error message
Dear All, For the fftw3 I use the following configuration: ./configure --disable-threads --enable-float --enable-sse For the gromacs I use the following configuration: ./configure --disable-threads But in the gromacs I get the following new error message. I am looking forward to getting your reply on how to solve the problem. Cheers, Wholly /bin/sh ../../../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I../../../src -I/usr/include/libxml2 -I../../../include -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 -fexcess-precision=fast -MT slasd3.lo -MD -MP -MF .deps/slasd3.Tpo -c -o slasd3.lo slasd3.c make[4]: execvp: /bin/sh: Bad address ../../../libtool: fork: retry: Resource temporarily unavailable ../../../libtool: fork: retry: Resource temporarily unavailable ../../../libtool: fork: retry: Resource temporarily unavailable ../../../libtool: fork: retry: Resource temporarily unavailable ../../../libtool: fork: Resource temporarily unavailable Makefile:529: recipe for target `slasd3.lo' failed make[4]: *** [slasd3.lo] Error 254 make[4]: Leaving directory `/cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src/gmxlib/gmx_lapack' Makefile:599: recipe for target `all-recursive' failed make[3]: *** [all-recursive] Error 1 make[3]: Leaving directory `/cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src/gmxlib' Makefile:302: recipe for target `all-recursive' failed make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src' Makefile:238: recipe for target `all' failed make[1]: *** [all] Error 2 make[1]: Leaving directory `/cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src' Makefile:347: recipe for target `all-recursive' failed make: *** [all-recursive] Error 1 - Forwarded Message - From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, 12 March 2012 1:21 PM Subject: Re: [gmx-users] gromacs 4.5.5 cygwin installation error message On 12/03/2012 1:18 PM, Peter C. Lai wrote: Oops I just saw this. Yeah it could be --enable-shared is broken on this for cygwin, since the build is breaking during linking. Yes, that is possible. In an unrelated note, is running gromacs in cygwin supposed to be faster than running it in a unix/linux virtual machine with paravirt I/O? I'm not aware that anyone's compared them. Mark On 2012-03-12 11:21:26AM +1100, Mark Abraham wrote: On 12/03/2012 8:14 AM, Wholly Peach wrote: Dear All, For fftw, I use the following configure, ./configure --enable-threads --enable-float --enable-sse --prefix=/home/ABC/fftw If /home/ABC exists, and you then did make and make install and they both succeeded then you will be able to see that /home/ABC/fftw exists and has stuff in it. You will have built non-shared libraries however. For gromacs, I use the following configure, ./configure --with-fft=fftw3 --disable-threads --prefix=/home/ABC/GROMACS --enable-shared LDFLAGS='-L/home/ABC/fftw/lib' CPPFLAGS='-I/home/ABC/fftw/include' If the FFTW installation worked, then this should work. Possibly you will need to choose --enable-shared for both, or --disable-shared for both - I'm not sure. Mark But in the make step of gromacs, I still got a series of error message. I am looking forward to getting some suggesrions to solve it. Cheers, Wholly ... .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2489): undefined reference to `_fftwf_destroy_plan' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x249f): undefined reference to `_fftwf_destroy_plan' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x24b5): undefined reference to `_fftwf_destroy_plan' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x24cb): more undefined references to `_fftwf_destroy_plan' follow .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2506): undefined reference to `_fftwf_free' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2512): undefined reference to `_fftwf_free' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x251e): undefined reference to `_fftwf_free' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x25ce): undefined reference to `_fftwf_execute_dft' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x268e): undefined reference to `_fftwf_execute_dft' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2755): undefined reference to `_fftwf_execute_dft_c2r' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2770): undefined reference to `_fftwf_execute_dft_r2c' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2825): undefined reference to `_fftwf_execute_dft_c2r' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2840): undefined reference to `_fftwf_execute_dft_r2c' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x28ee): undefined reference to `_fftwf_execute_dft' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x29b5): undefined reference to `_fftwf_execute_dft_c2r'
[gmx-users] Re:g_enemat
Dear All, I was going to use g_enemat to make my life easier than splitting things up into individual files for a break down of multiple components in a trajectory (multiple protein domains and atooms, etc...I indexed before the run rather complex or long depending on your point of view). When I use g_enemat_d with a 2 group set as a test I get the following; dat file 2 sans-p 3b Opened traj_5.edr as double precision energy file Will read groupnames from inputfile Read 2 groups group 0WARNING! could not find group (null):sans-p-sans-p (0,0)in energy file WARNING! could not find group (null):sans-p-3b (0,1)in energy file group 1WARNING! could not find group (null):3b-3b (1,1)in energy file Will select half-matrix of energies with 6 elements Last energy frame read 200 time 4000.000 Will build energy half-matrix of 2 groups, 6 elements, over 201 frames While typing at your keyboard, suddenly... ...nothing happens. WARNING: Not Implemented Yet ---If I switch the above around to 3b then sans-p I get two extra Warning of LJ:3b-3b and Coul:3b-3b not found--- if I use g_energy with out the double percission I get the following; Opened traj_5.edr as double precision energy file Will read groupnames from inputfile Read 2 groups group 1 Will select half-matrix of energies with 6 elements Last energy frame read 200 time 4000.000 Will build energy half-matrix of 2 groups, 6 elements, over 201 frames While typing at your keyboard, suddenly... ...nothing happens. WARNING: Not Implemented Yet Not implemented yet sounds pretty clear. If however g_enemat is implemented already (as I read the manual on it), then can somone please let me know how to get it to work? A note, I did look at all the groups in the file using g_energy_d and the groups it complains about above in all cases are included in the .edr file? It just cant see them? I should add, nothing gets written out either. Any help is appriciated, Sincerely, Stephan Watkins -- NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! Jetzt informieren: http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: gmx-users Digest, Vol 95, Issue 60
Hi, so further to my last email, I have run a quick test on my desktop machine (4 cores, 12Gb RAM). It seems that when running the parrinello-rahman barostat with domain decomposition (-dd 2 2 1) that I'm still getting memory leak (this time with GNU compilers). I followed proper equilibration with the berendsen barostat (although I didn't think this was the problem) and also added the constraints = all-bonds line, but this has made no difference to my results (I'm using [ constraints ] in my topology file). To give an idea of the rate of memory loss, initial memory consumption was 0.1% total memory per process, which rose steadily to 0.5% total memory after 5 minutes. After 17mins, memory consumption is 1.7% total memory and rising. Running with -pd, memory usage is constant at 0.1% total memory. The system is 328 TIP4P/ice + 64 all-atomic methane. This problem has occurred for me on different architectures and with different compilers (and different system sizes). It would be good if anybody familiar with the source could take a look, or if anybody knows any compiler flags that would prevent memory leak. Thanks, Steve On 9 March 2012 13:32, Stephen Cox stephen.cox...@ucl.ac.uk wrote: On 9 March 2012 13:03, gmx-users-requ...@gromacs.org gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Re: GROMACS stalls for NPT simulation when using -npmeand -dd flags (Mark Abraham) 2. Error Message in Make clean command for installation. (a a) 3. Re: Error Message in Make clean command for installation. (Mark Abraham) -- Message: 1 Date: Fri, 09 Mar 2012 23:42:33 +1100 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] GROMACS stalls for NPT simulation when using -npme and -dd flags To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4f59fab9.6010...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 9/03/2012 9:43 PM, Stephen Cox wrote: Dear users, I'm trying to run an isotropic NPT simulation on a cubic cell containing TIP4P/ice water and methane. I'm using the Parrinello-Rahman barostat. I've been playing around with the different decomposition flags of mdrun to get better performance and scaling and have found that the standard -npme (half number of cores) works pretty well. I've also tried using the -dd flags, and I appear to get decent performance and scaling. However, after a few nanoseconds (corresponding to about 3 hours run time), the program just stalls; no output and no error messages. I realise NPT may cause domain decompositon some issues if the cell vectors vary wildly, but this isn't happening in my system. Has anybody else experienced issues with domain decomposition and NPT simulations? If so, are there any workarounds? For the moment, I've had to resort to using -pd, which is giving relatively poor performance and scaling, but at least it isn't dying! I'm using GROMACS 4.5.5 with an intel compiler (I followed the instructions online, with static linking) and using the command: #!/bin/bash -f # --- #$ -V #$ -N test #$ -S /bin/bash #$ -cwd #$ -l vf=2G #$ -pe ib-ompi 32 #$ -q infiniband.q mpirun mdrun_mpi -cpnum -cpt 60 -npme 16 -dd 4 2 2 Below is my grompp.mdp. Thanks, Steve P.S. I think that there may be an issue with memory leak that occurs for domain decomposition with NPT. I seem to remember seeing this happening on my desktop and my local cluster. I don't see this with NVT simulations. This would be consistent with the lack of error message: I've just run a short test run and the memory usage was climbing streadily. ; run control integrator = md dt = 0.002 nsteps = -1 comm_mode = linear nstcomm= 10 ; energy minimization emtol = 0.01 emstep = 0.01 ; output control nstxout = 0 nstvout = 0 nstfout = 0 nstlog= 0 nstcalcenergy = 2500 nstenergy = 2500 nstxtcout = 2500 ; neighbour searching nstlist= 1 ns_type= grid pbc= xyz periodic_molecules = no rlist = 0.90 ; electrostatics coulombtype = pme rcoulomb= 0.90 ; vdw vdwtype = cut-off rvdw = 0.90 dispcorr = ener ; ewald fourierspacing = 0.1 pme_order = 4
Re: [gmx-users] Umbrella Sampling - Ligand Protein
Steven Neumann wrote: On Sun, Mar 11, 2012 at 10:13 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Steven Neumann wrote: Hi Justin, As you advised I reduced number of my windows and I obtined histogram: http://speedy.sh/2b9dT/histo.__JPG http://speedy.sh/2b9dT/histo.JPG Which looks really good. The corresponding profile: http://speedy.sh/y8Ssz/__profile.JPG http://speedy.sh/y8Ssz/profile.JPG I do not understand it. Does my deltaG of binding correspond to everything above 0 kcal/mol which is 6 kcal/mol? DeltaG = the free energy difference between the final and initial states. So that's up to you to decide. Your curve is rather rough and the energy minimum potentially still ill-defined. The histograms indicate that the sampling overlap is likely fine, you just may need a bit more sampling in each window to smooth things out. Also make use of the error estimates that g_wham can provide; they can be quite informative (and necessary). -Justin Thank you Justin. In each window I run the simulation of 10 ns. Do you think that making it 20 ns will make the profile more smooth? It's no use to blindly guess. It's up to you to assess the convergence of your simulations and decide on an appropriate time frame. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: questions about Principal Component Analysis
Hi Thomas, Whether or not it makes sense to do PCA on the domain only depends on the question you ask. It may well make sense if you aim at characterizing the intra-domain motions. But be aware that you will view those motions within the context of the rest of the protein. It is quite likely that the internal motions depend on the interaction with the surroundings. Concerning the cosine content, there indeed seems to ba a transition. But that is already evident from your RMSD plot. A lot of stuff is still happening in the second half of the simulation. To see if the last part of your simulation is in a (local) equilibrium, you can calculate the average structure from that part, say the alst 10 or 20 ns, and determine the RMSD against the average. The RMSD should then decrease towards the average and level off or oscillate around it to assure you've reached some sort of equilibrium. On the basis of that you could then decide whether it's worthwhile performing PCA on that part only. Cheers, Tsjerk On Sat, Mar 10, 2012 at 3:18 PM, Thomas Evangelidis teva...@gmail.com wrote: Regarding my second question, I have been experimenting with the cosine content using different portions of the trajectory and these are the results I got for the first principal component: proj-ev1_coscont_0-5ns.xvg 0.0174761 proj-ev1_coscont_0-10ns.xvg 0.0283423 proj-ev1_coscont_0-15ns.xvg 4.16906e-06 proj-ev1_coscont_0-20ns.xvg 0.0689592 proj-ev1_coscont_0-25ns.xvg 0.161691 proj-ev1_coscont_0-30ns.xvg 0.298431 proj-ev1_coscont_0-35ns.xvg 0.535732 proj-ev1_coscont_0-40ns.xvg 0.767029 proj-ev1_coscont_0-45ns.xvg 0.885829 proj-ev1_coscont_0-50ns.xvg 0.906473 proj-ev1_coscont_5-50ns.xvg 0.8823 proj-ev1_coscont_10-50ns.xvg 0.751018 proj-ev1_coscont_15-50ns.xvg 0.537473 proj-ev1_coscont_20-50ns.xvg 0.357136 proj-ev1_coscont_25-50ns.xvg 0.145889 proj-ev1_coscont_30-50ns.xvg 0.0150995 proj-ev1_coscont_35-50ns.xvg 0.00123905 proj-ev1_coscont_40-50ns.xvg 0.00675679 proj-ev1_coscont_45-50ns.xvg 0.0105643 The total time I have run the simulation was 70ns, but judging from the steep increase of the RMSD (RMSD plot attached), I decided to exclude the first 20ns from the analysis. Hence the cosine content values above correspond to the last 50ns and the counting starts from the 20th ns. Clearly the convergence of the last 50ns is not good (proj-ev1_coscont_0-50ns.xvg: 0.906473), but the PC1 plot (attached) shows a steep decrease at ~30ns which looks like a conformational transition. It is also evident that the cosine content decreases drastically approximately at that point (25-50ns: 0.145889, 30-50ns.xvg: 0.0150995, 35-50ns.xvg: 0.00123905, etc.) and reached values that are not bad. Unfortunately, extending the simulation is not an option due to lack of time (I am forced to finish the manuscript soon). So would you recommend doing essential dynamics for the last 20ns? I would GREATLY appreciate any comments!!! Thomas On 7 March 2012 21:56, Thomas Evangelidis teva...@gmail.com wrote: Dear GROMACS community, I have two questions regarding PCA. I have run MD simulations for 70 ns for a protein of 1100 amino acids, of which I decided - based on the RMSD - to analyze the last 50. 1) The protein consists of 5 domains, out of which only one is of interest in this study. Is it right to do draw conclusion from PCA restricted that domain (400 aa)? 2) How can I find out if the simulation time is sufficient to do PCA? Thanks in advance for any feedback. Thomas -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Generation of the Distance Restraints
Dear Gromacs users! I want to perform constrained MD simulation of my protein with inclusion of some experimental restraints. 1) I found that genrest cpmmand could be usefull for the generation of the distance restrictions wich I could use in my constrined simulation. Also in manual I've found that command like genrestr -f b2ar.gro -disre -index.ndx -o test.itp will produce some distance restricted matrix of the whole groups presented in the index.ndx file. So how I could select to contrain selected residues within selected distance by means the index file? E.g I've manually point out 2 residues in index.ndx. I waant to preserve between that residues some desired distance D wich I've obtaine from the experimental data. How I could do it via genrestr and waht addition flags should I use for that purpose ? 2) Is there any way to apply gradually the desired dist.resrs during MDrun to prevent some artifacts in my system wich would occur due to the rapid application of the dis.res ( e.g in cases where the conformation of the started structure and that wich I'd obtained fter application of the restrains are slightly different)? Thanks for help, James -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Generation of the Distance Restraints
I think you can make an index file using make_ndx where you specify the atoms you want to restraint. Hope this can help. Francesca 2012/3/12 James Starlight jmsstarli...@gmail.com: Dear Gromacs users! I want to perform constrained MD simulation of my protein with inclusion of some experimental restraints. 1) I found that genrest cpmmand could be usefull for the generation of the distance restrictions wich I could use in my constrined simulation. Also in manual I've found that command like genrestr -f b2ar.gro -disre -index.ndx -o test.itp will produce some distance restricted matrix of the whole groups presented in the index.ndx file. So how I could select to contrain selected residues within selected distance by means the index file? E.g I've manually point out 2 residues in index.ndx. I waant to preserve between that residues some desired distance D wich I've obtaine from the experimental data. How I could do it via genrestr and waht addition flags should I use for that purpose ? 2) Is there any way to apply gradually the desired dist.resrs during MDrun to prevent some artifacts in my system wich would occur due to the rapid application of the dis.res ( e.g in cases where the conformation of the started structure and that wich I'd obtained fter application of the restrains are slightly different)? Thanks for help, James -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Generation of the Distance Restraints
Francesca, Yes I suppose this is good aproach for the generation of position restricktions on the desired atoms. But I want to restrain the distance between selected pairs of atoms ( e.g between C-alpha- C-alpha atoms of two different residues). Also I want to restrain some dihedral angles in the desired rotameric forms. In literature I've found that peple have dome the same things in Gromacs but I could not find detailed algorithm of such methodology :( James 12 марта 2012 г. 18:05 пользователь francesca vitalini francesca.vitalin...@gmail.com написал: I think you can make an index file using make_ndx where you specify the atoms you want to restraint. Hope this can help. Francesca 2012/3/12 James Starlight jmsstarli...@gmail.com: Dear Gromacs users! I want to perform constrained MD simulation of my protein with inclusion of some experimental restraints. 1) I found that genrest cpmmand could be usefull for the generation of the distance restrictions wich I could use in my constrined simulation. Also in manual I've found that command like genrestr -f b2ar.gro -disre -index.ndx -o test.itp will produce some distance restricted matrix of the whole groups presented in the index.ndx file. So how I could select to contrain selected residues within selected distance by means the index file? E.g I've manually point out 2 residues in index.ndx. I waant to preserve between that residues some desired distance D wich I've obtaine from the experimental data. How I could do it via genrestr and waht addition flags should I use for that purpose ? 2) Is there any way to apply gradually the desired dist.resrs during MDrun to prevent some artifacts in my system wich would occur due to the rapid application of the dis.res ( e.g in cases where the conformation of the started structure and that wich I'd obtained fter application of the restrains are slightly different)? Thanks for help, James -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Generation of the Distance Restraints
On 13/03/2012 1:13 AM, James Starlight wrote: Francesca, Yes I suppose this is good aproach for the generation of position restricktions on the desired atoms. But I want to restrain the distance between selected pairs of atoms ( e.g between C-alpha- C-alpha atoms of two different residues). The help for genrestr -disre says that this is exactly what it does... use an index group to make distance restraints. Also I want to restrain some dihedral angles in the desired rotameric forms. In literature I've found that peple have dome the same things in Gromacs but I could not find detailed algorithm of such methodology :( There can't be a walk-through of everything anybody might ever do, unfortunately. Manual chapter 4 talks about the functional forms available. There's a table in section 5.5 that describes how to construct the line of a [ moleculetype ] section. That's all you need to know if have a general understanding of how the .top file works (elsewhere in chapter 5). Mark James 12 ? 2012 ?. 18:05 francesca vitalini francesca.vitalin...@gmail.com mailto:francesca.vitalin...@gmail.com ???: I think you can make an index file using make_ndx where you specify the atoms you want to restraint. Hope this can help. Francesca 2012/3/12 James Starlight jmsstarli...@gmail.com mailto:jmsstarli...@gmail.com: Dear Gromacs users! I want to perform constrained MD simulation of my protein with inclusion of some experimental restraints. 1) I found that genrest cpmmand could be usefull for the generation of the distance restrictions wich I could use in my constrined simulation. Also in manual I've found that command like genrestr -f b2ar.gro -disre -index.ndx -o test.itp will produce some distance restricted matrix of the whole groups presented in the index.ndx file. So how I could select to contrain selected residues within selected distance by means the index file? E.g I've manually point out 2 residues in index.ndx. I waant to preserve between that residues some desired distance D wich I've obtaine from the experimental data. How I could do it via genrestr and waht addition flags should I use for that purpose ? 2) Is there any way to apply gradually the desired dist.resrs during MDrun to prevent some artifacts in my system wich would occur due to the rapid application of the dis.res ( e.g in cases where the conformation of the started structure and that wich I'd obtained fter application of the restrains are slightly different)? Thanks for help, James -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Generation of the Distance Restraints
On 13/03/2012 12:54 AM, James Starlight wrote: Dear Gromacs users! I want to perform constrained MD simulation of my protein with inclusion of some experimental restraints. 1) I found that genrest cpmmand could be usefull for the generation of the distance restrictions wich I could use in my constrined simulation. Also in manual I've found that command like genrestr -f b2ar.gro -disre -index.ndx -o test.itp ... which should read -n index.ndx. Please get in the habit of copying and pasting actual command lines that you have observed to function like you think they do :-). Then you won't mis-type something sometime that will cause everyone to waste their time. will produce some distance restricted matrix of the whole groups presented in the index.ndx file. So how I could select to contrain selected residues within selected distance by means the index file? E.g I've manually point out 2 residues in index.ndx. I waant to preserve between that residues some desired distance D wich I've obtaine from the experimental data. How I could do it via genrestr and waht addition flags should I use for that purpose ? You need an index file that has a group or groups that do what you want. Some details on the webpage. Since you know already the 2 atoms you care about, you can make it in a text editor faster than writing this email :-) Or indeed just constructing a [ distance_restraints ] section of the [ moleculetype ] in consultation with the information in chapters 4 and 5 faster still. 2) Is there any way to apply gradually the desired dist.resrs during MDrun to prevent some artifacts in my system wich would occur due to the rapid application of the dis.res ( e.g in cases where the conformation of the started structure and that wich I'd obtained fter application of the restrains are slightly different)? Only by choosing a gentle restraint at first and picking a time interval at which to increase it. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Generation of the Distance Restraints
James Starlight wrote: Francesca, Yes I suppose this is good aproach for the generation of position restricktions on the desired atoms. But I want to restrain the distance between selected pairs of atoms ( e.g between C-alpha- C-alpha atoms of two different residues). How many restraints do you need to create? If they are this simple, you can write them yourself using a text editor in conjunction with manual section 4.3.4. Using genrestr is only really helpful when you require a network of distance restraints between the atoms of a given group. If there are only a few to create, it's actually more work to use make_ndx and genrestr than it is to fire up your favorite text editor. Also I want to restrain some dihedral angles in the desired rotameric forms. See manual section 4.3.3 and http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints. In literature I've found that peple have dome the same things in Gromacs but I could not find detailed algorithm of such methodology :( All relevant equations are provided in the manual, and examples are provided either there or on the Gromacs site. If you need further information, ask a specific question related to what you can't find or don't understand. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Umbrella Sampling - Ligand Protein
On Sun, Mar 11, 2012 at 10:13 PM, Justin A. Lemkul jalem...@vt.edu wrote: Steven Neumann wrote: Hi Justin, As you advised I reduced number of my windows and I obtined histogram: http://speedy.sh/2b9dT/histo.**JPG http://speedy.sh/2b9dT/histo.JPG Which looks really good. The corresponding profile: http://speedy.sh/y8Ssz/**profile.JPGhttp://speedy.sh/y8Ssz/profile.JPG I do not understand it. Does my deltaG of binding correspond to everything above 0 kcal/mol which is 6 kcal/mol? DeltaG = the free energy difference between the final and initial states. So that's up to you to decide. Your curve is rather rough and the energy minimum potentially still ill-defined. The histograms indicate that the sampling overlap is likely fine, you just may need a bit more sampling in each window to smooth things out. Also make use of the error estimates that g_wham can provide; they can be quite informative (and necessary). -Justin Thank you Justin. In each window I run the simulation of 10 ns. Do you think that making it 20 ns will make the profile more smooth? Steven -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Umbrella Sampling - Ligand Protein
On Mon, Mar 12, 2012 at 11:06 AM, Justin A. Lemkul jalem...@vt.edu wrote: Steven Neumann wrote: On Sun, Mar 11, 2012 at 10:13 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Steven Neumann wrote: Hi Justin, As you advised I reduced number of my windows and I obtined histogram: http://speedy.sh/2b9dT/histo._**_JPGhttp://speedy.sh/2b9dT/histo.__JPG http://speedy.sh/2b9dT/histo.**JPGhttp://speedy.sh/2b9dT/histo.JPG Which looks really good. The corresponding profile: http://speedy.sh/y8Ssz/__**profile.JPGhttp://speedy.sh/y8Ssz/__profile.JPG http://speedy.sh/y8Ssz/**profile.JPGhttp://speedy.sh/y8Ssz/profile.JPG I do not understand it. Does my deltaG of binding correspond to everything above 0 kcal/mol which is 6 kcal/mol? DeltaG = the free energy difference between the final and initial states. So that's up to you to decide. Your curve is rather rough and the energy minimum potentially still ill-defined. The histograms indicate that the sampling overlap is likely fine, you just may need a bit more sampling in each window to smooth things out. Also make use of the error estimates that g_wham can provide; they can be quite informative (and necessary). -Justin Thank you Justin. In each window I run the simulation of 10 ns. Do you think that making it 20 ns will make the profile more smooth? It's no use to blindly guess. It's up to you to assess the convergence of your simulations and decide on an appropriate time frame. -Justin Thank you Justin. Is there any way to find out after deltaG the entropic contribution to binding free energy? Steven -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Umbrella Sampling - Ligand Protein
Steven Neumann wrote: On Mon, Mar 12, 2012 at 11:06 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Steven Neumann wrote: On Sun, Mar 11, 2012 at 10:13 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Steven Neumann wrote: Hi Justin, As you advised I reduced number of my windows and I obtined histogram: http://speedy.sh/2b9dT/histo.JPG http://speedy.sh/2b9dT/histo.__JPG http://speedy.sh/2b9dT/histo.__JPG http://speedy.sh/2b9dT/histo.JPG Which looks really good. The corresponding profile: http://speedy.sh/y8Ssz/profile.JPG http://speedy.sh/y8Ssz/__profile.JPG http://speedy.sh/y8Ssz/__profile.JPG http://speedy.sh/y8Ssz/profile.JPG I do not understand it. Does my deltaG of binding correspond to everything above 0 kcal/mol which is 6 kcal/mol? DeltaG = the free energy difference between the final and initial states. So that's up to you to decide. Your curve is rather rough and the energy minimum potentially still ill-defined. The histograms indicate that the sampling overlap is likely fine, you just may need a bit more sampling in each window to smooth things out. Also make use of the error estimates that g_wham can provide; they can be quite informative (and necessary). -Justin Thank you Justin. In each window I run the simulation of 10 ns. Do you think that making it 20 ns will make the profile more smooth? It's no use to blindly guess. It's up to you to assess the convergence of your simulations and decide on an appropriate time frame. -Justin Thank you Justin. Is there any way to find out after deltaG the entropic contribution to binding free energy? Probably, but having never done it I can't offer any specific guidance. Perhaps others on the list can. I would certainly suggest you seek a protocol in the literature; I feel sure that I've seen such endeavors. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Literature reading on DispCorr for energy and pressure
Hi, Only if you have time, can you please recommend literature reading on how long-range dispersion corrections are computed? I have been using DispCorr = EnerPres for my simulations, which are in the NPT ensemble. When I search through this user's list, I find frequent mention of the fact that DispCorr = EnerPres is useful for obtaining the correct system density at the end of an NPT simulation. I have the general idea that dispersion correction corrects for the cut-off of the Lennard-Jones potential ( for example, http://lists.gromacs.org/pipermail/gmx-users/2003-August/006717.html ), which is always attractive at long range. Perhaps this is (very roughly, very qualitatively) analogous to the Ewald summation, which is a sort of electrostatic correction to correct for the cut-off of the Coulomb interaction? However, I would be interested in more details about how this correction to the Lennard-Jones potential is accomplished, and what approximations it introduces and assumptions it makes. Section 4.8 of the manual gives many details, but I am curious if you can recommend any review-type articles about this correction. Thank you very much for your time! Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] pull code - i-motif constant velocity pull
Hello All, I am trying to apply pull code on DNA I-motif structure which is 4 stranded DNA with the pair of 2 parallel duplexes arranged in anti-parallel manner. I have followed the tutorial by Justin Lemkul it works well but I have to select the fixed and pull group on different chains together and they may different atoms. Like H5T on 2 chains as well as H3T on 2 others Both for pull and fixed groups on 4 different chain. For further if someone want to have a look RCSB code is 225D. I would be grateful if anyone can of some help here :) Thank You Regards Raghav -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Literature reading on DispCorr for energy and pressure
Hi, This paper comes to mind: Accurate and Efficient Corrections for Missing Dispersion Interactions in Molecular Simulations Shirts, Mobley, Chodera and Pande J. Phys. Chem. B 2007, 111, 13052-13063 Cheers Tom Andrew DeYoung wrote: Hi, Only if you have time, can you please recommend literature reading on how long-range dispersion corrections are computed? I have been using DispCorr = EnerPres for my simulations, which are in the NPT ensemble. When I search through this user's list, I find frequent mention of the fact that DispCorr = EnerPres is useful for obtaining the correct system density at the end of an NPT simulation. I have the general idea that dispersion correction corrects for the cut-off of the Lennard-Jones potential ( for example, http://lists.gromacs.org/pipermail/gmx-users/2003-August/006717.html ), which is always attractive at long range. Perhaps this is (very roughly, very qualitatively) analogous to the Ewald summation, which is a sort of electrostatic correction to correct for the cut-off of the Coulomb interaction? However, I would be interested in more details about how this correction to the Lennard-Jones potential is accomplished, and what approximations it introduces and assumptions it makes. Section 4.8 of the manual gives many details, but I am curious if you can recommend any review-type articles about this correction. Thank you very much for your time! Andrew DeYoung Carnegie Mellon University -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] pdb file
Dear Gromacs Specialists, I need pdb file of tiofen, but I didn't find it!!! Can I change pdb file of one compound that is as same as tiofen (for example pyrrole) and give it to PRODRG for obtain gro file and topology file of tiofen? Please help me. Thanks in advance. Best Regards Dina -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] pdb file
dina dusti wrote: Dear Gromacs Specialists, I need pdb file of tiofen, but I didn't find it!!! Can I change pdb file of one compound that is as same as tiofen (for example pyrrole) and give it to PRODRG for obtain gro file and topology file of tiofen? There are numerous methods for producing coordinate files. See, for instance: http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] pdb file
Thank you very much from your response. Best Regards Dina From: Justin A. Lemkul jalem...@vt.edu To: dina dusti dinadu...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, March 12, 2012 10:02 PM Subject: Re: [gmx-users] pdb file dina dusti wrote: Dear Gromacs Specialists, I need pdb file of tiofen, but I didn't find it!!! Can I change pdb file of one compound that is as same as tiofen (for example pyrrole) and give it to PRODRG for obtain gro file and topology file of tiofen? There are numerous methods for producing coordinate files. See, for instance: http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] pdb file
A neat way to get generic coordinates of organic molecules like this is using Jmol: 1) go to http://chemapps.stolaf.edu/jmol/docs/examples-12/new.htm?USESIGNED This requires Sun/Oracle Java plugin activated in the browser and asks for permission to trust the signed applet. Alternatively one could use the Jmol Application instead. 2) type the following two commands into the cmd textbox (or the Jmol console) load $Thiophene ; write coords ? ; The first one will load the structure and the second one will open a Save-File dialog to ask for the filename to save it on your hard disk. Quoting Bob Hanson (currently the lead Jmol developer): If you can name it [and if it is organic] [...] you can probably get it. Cheers, Oliver On Mon, Mar 12, 2012 at 12:42, dina dusti dinadu...@yahoo.com wrote: Thank you very much from your response. Best Regards Dina From: Justin A. Lemkul jalem...@vt.edu To: dina dusti dinadu...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, March 12, 2012 10:02 PM Subject: Re: [gmx-users] pdb file dina dusti wrote: Dear Gromacs Specialists, I need pdb file of tiofen, but I didn't find it!!! Can I change pdb file of one compound that is as same as tiofen (for example pyrrole) and give it to PRODRG for obtain gro file and topology file of tiofen? There are numerous methods for producing coordinate files. See, for instance: http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources -Justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] There was 1 error in input file(s)
Hi everybody I want to build a simulation box fill of water and some SDS molecules. To do this at first I fill the box with SDS molecules without their Na+ ions. Then I filled the simulation box with water molecules. After that, I want to replace some water molecules with Na+ ions. I ran the following commands: genbox -ci SDS.pdb -nmol 10 -box 2 2 1.9 -p topol.top -o SDS-box.gro genbox -cp SDS-box.gro -cs spc216.gro -p topol.top -o SDSWater.gro grompp -f ions.mdp -c SDSWater.gro -p topol.top -o ions.tpr But to run the last command I receive the following error: Fatal error: There was 1 error in input file(s) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I managed to get two hours of work done before work (E. Lindahl) Would you please help me, Thanks Saly -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] There was 1 error in input file(s)
On 2012-03-12 22:56, saly jackson wrote: Hi everybody I want to build a simulation box fill of water and some SDS molecules. To do this at first I fill the box with SDS molecules without their Na+ ions. Then I filled the simulation box with water molecules. After that, I want to replace some water molecules with Na+ ions. I ran the following commands: genbox -ci SDS.pdb -nmol 10 -box 2 2 1.9 -p topol.top -o SDS-box.gro genbox -cp SDS-box.gro -cs spc216.gro -p topol.top -o SDSWater.gro grompp -f ions.mdp -c SDSWater.gro -p topol.top -o ions.tpr But to run the last command I receive the following error: you managed to cut the essential information before this, that would help you to fix the problem yourself. Fatal error: There was 1 error in input file(s) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I managed to get two hours of work done before work (E. Lindahl) Would you please help me, Thanks Saly -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Ques
Dear gmx users: I would like to apply electric field to my simulation box. I have already read the manual and I added this into mpd file as manual told: ; Electric fields = 7.1e-10V/nm ; Format is number of terms (int) and for all terms an amplitude (real) = ; and a phase angle (real) = E_x = 1.0 7.1e-10 0 ;E_xt= ;E_y = ;E_yt= ;E_z = ;E_zt= as I know, this line E_x = 1.0 7.1e-10 0 would add x direction 7.1e-10V/nm electric field, but in the MD simulation log file the three number is efield-x: n = 1 a = 0.00e+00 phi = 7.10e-10 efield-xt: n = 0 efield-y: n = 0 efield-yt: n = 0 efield-z: n = 0 efield-zt: n = 0 why phi = 7.10e-10 and a=0? Are a and phi the strength of the electric field and phase of the cosine? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] help on replica exchange dynamics with gromacs
Dear friends Can someone help me with tutorial on replica exchange dynamics Thanks in advance Raghuvir -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] help on replica exchange dynamics with gromacs
On 13/03/2012 3:17 PM, Raghuvir Pissurlenkar wrote: Dear friends Can someone help me with tutorial on replica exchange dynamics Thanks in advance Raghuvir Search the GROMACS webpage, please. You will want to do some normal tutorials to understand normal workflows first. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Ques
Hi Xianwei Wang, According to the information in your mail (the comments from the mdp file), it's just the other way around: phi is the amplitude and a is the phase. Cheers, Tsjerk On Mar 13, 2012 3:11 AM, Xianwei Wang wangxianwei1...@163.com wrote: *Dear gmx users: **I would like to apply electric field to my ** simulation box.**I have already read the manual and I added this into mpd file as manual told: ; Electric fields = **7.1e-10V/nm* *; Format is number of terms (int) and for all terms an amplitude (real) = ; and a phase angle (real) = E_x = 1.0 7.1e-10 0 ;E_xt= ;E_y = ;E_yt= ;E_z = ;E_zt= as I know, this line **E_x = 1.0 7.1e-10 0** would add *x direct ion *7.1e-10V/nm electric field, but in the MD simulation log file the three number is efield-x: n = 1 a = 0.00e+00 phi = 7.10e-10 efield-xt: n = 0 efield-y: n = 0 efield-yt: n = 0 efield-z: n = 0 efield-zt: n = 0 why ** phi = 7.10e-10 and a=0? Are a and phi the strength of the electric field and phase of the cosine? * * * -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] RMSD sudden jump
Dear gromacs users, I have performed ~30ns MD on a protein in TIP4P water using the OPLS forcefield. I have concatenated the trajectories for each step using trjcat and removed pbc effects using pbc nojump. All the particles of the system now don't jump anymore and the molecule doesn't appear as broken. However, at some point from the beginning of the simulation the RMSD jumps up as in the graphs attached. Visualizing the trajectories from that point the protein just suddenly change conformation and its motions become faster (as testified by the RMSD). Can you please let me understand why this happens? If I have screwed something up with the calculation or if something due to the pbc effects not removed properly? The same thing is also happening on a different simulations involving a mutant of this protein... Any help will be very much highly appreciated! Thank you! Davide -- Davide Mercadante - PhD student - School of Chemical Sciences The University of Auckland 1142 Auckland, New Zealand attachment: rmsd_calpha.png-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
