[gmx-users] script to add water in protein
Hi I want to add water molecule in my structure. Do anyone have idea how to add water molecules in protein structure. I little aware of python. How the gromacs spc216 add the water molecule. Can i get the code for the same? pooja -- 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] script to add water in protein
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/03_solvate.html On Mon, Aug 12, 2013 at 4:09 PM, pooja_gu...@nccs.res.in wrote: Hi I want to add water molecule in my structure. Do anyone have idea how to add water molecules in protein structure. I little aware of python. How the gromacs spc216 add the water molecule. Can i get the code for the same? pooja -- 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] script to add water in protein
Thanks I am looking for code (python, C++), not gromacs command line. pooja http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/03_solvate.html On Mon, Aug 12, 2013 at 4:09 PM, pooja_gu...@nccs.res.in wrote: Hi I want to add water molecule in my structure. Do anyone have idea how to add water molecules in protein structure. I little aware of python. How the gromacs spc216 add the water molecule. Can i get the code for the same? pooja -- 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] Lateral Diffusion of Lipids
Via an index file, I would guess... Or what do you mean exactly? Dr. Vitaly V. Chaban On Mon, Aug 12, 2013 at 5:26 AM, Kieu Thu Nguyen kieuthu2...@gmail.comwrote: Dear users, I want to use g_msd to measure diffusion coefficients of lipid bilayer. But i do not know how to choose the reference atom per lipid for an any type of lipid, such as POPC, DOPC,... Where i can get these references ? Thanks so much for any help ! ~Thu -- 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] script to add water in protein
Hi Pooja, Do you mean solvating around the protein, or placing water inside? If you feel brave, you can check out the C code of genbox. Genbox copies a box of solvent to cover the box with the protein, and then removes all solvent which has overlaps with the protein. Cheers, Tsjerk On Mon, Aug 12, 2013 at 9:43 AM, pooja_gu...@nccs.res.in wrote: Thanks I am looking for code (python, C++), not gromacs command line. pooja http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/03_solvate.html On Mon, Aug 12, 2013 at 4:09 PM, pooja_gu...@nccs.res.in wrote: Hi I want to add water molecule in my structure. Do anyone have idea how to add water molecules in protein structure. I little aware of python. How the gromacs spc216 add the water molecule. Can i get the code for the same? pooja -- 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 -- Tsjerk A. Wassenaar, Ph.D. -- 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] Lateral Diffusion of Lipids
On 8/11/13 11:26 PM, Kieu Thu Nguyen wrote: Dear users, I want to use g_msd to measure diffusion coefficients of lipid bilayer. But i do not know how to choose the reference atom per lipid for an any type of lipid, such as POPC, DOPC,... Where i can get these references ? Most people choose the phosphorus atom as the reference atom. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] Lateral Diffusion of Lipids
Thanks so much ! I guessed should i choose it but i am not sure :-) So, if most people choose it, i think it is ok. On Mon, Aug 12, 2013 at 4:25 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/11/13 11:26 PM, Kieu Thu Nguyen wrote: Dear users, I want to use g_msd to measure diffusion coefficients of lipid bilayer. But i do not know how to choose the reference atom per lipid for an any type of lipid, such as POPC, DOPC,... Where i can get these references ? Most people choose the phosphorus atom as the reference atom. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- 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
Fwd: [gmx-users] Assistance needed running gromacs 4.6.3 on Blue Gene/P
Re-sending to list; original bounced when we had some issues with gmx-users over the weekend. Mark -- Forwarded message -- From: Mark Abraham mark.j.abra...@gmail.com Date: Sat, Aug 10, 2013 at 11:49 AM Subject: Re: [gmx-users] Assistance needed running gromacs 4.6.3 on Blue Gene/P To: prentice.bis...@rutgers.edu, Discussion list for GROMACS users gmx-users@gromacs.org On Fri, Aug 9, 2013 at 6:03 PM, Prentice Bisbal prentice.bis...@rutgers.edu wrote: Mark, Since I was working with 4.6.2, I built 4.6.3 to see if this was the result of a bug in 4.6.2. It isn't I get the same error with 4.6.3, but that is the version I'll be working with from now on, since it's the latest. Since the problem occurs with both versions, might as well try to fix it in the latest version, right? Yep. I compiled 4.6.3 with the following options to include debugging information: cmake .. \ -DCMAKE_TOOLCHAIN_FILE=../cmake/Platform/BlueGeneP-static-XL-C.cmake \ -DBUILD_SHARED_LIBS=OFF \ -DGMX_MPI=ON \ -DCMAKE_C_FLAGS=-O0 -g -qstrict -qarch=450 -qtune=450 \ -DCMAKE_INSTALL_PREFIX=/scratch/bgapps/gromacs-4.6.3 \ -DGMX_CPU_ACCELERATION=None \ -DGMX_THREAD_MPI=OFF \ -DGMX_OPENMP=OFF \ -DGMX_DEFAULT_SUFFIX=ON \ -DCMAKE_PREFIX_PATH=/scratch/bgapps/fftw-3.3.2 \ 21 | tee cmake.log For qarch, I removed the 'd' from the end, so that the double-FPU isn't used, which can cause problems if the data isn't aligned correctly. The -qstrict makes sure certain optimizations aren't performed. It should be superfluous with optimization levels below 3, but I through it in just to be safe, and set -O0. (of course, I think -g turns off all optizations, anyway) Mostly true, but mostly fine and immaterial :-) On the BG/P, I had to install FFTW3 separately, and that wasn't installed with debugging active, so there are no symbols for FFTW. Yeah, that won't be a problem. One of my coworkers wrote a script that converts BG/P core files to stack traces. In all the kernels I've looked at so far (9 out of 64), the stack ends at a vfprintf call. For example: Functions like vfprintf with va_list arguments use a macro that was not implemented correctly on BG/L and BG/P. This has caused problems with GROMACS before. See http://www-01.ibm.com/support/docview.wss?uid=swg1LI73769 for details. If this turns out to be the problem, then compiling just the files that use va_list with -O0 should help (starting with src/gmxlib/gmx_fatal.c). Or perhaps update the compiler if IBM really did fix this some time, and/or file a support request with IBM. However... - /bgsys/drivers/V1R4M2_200_2010-100508P/ppc/toolchain/gnu/glibc-2.4/stdio-common/vfprintf.c:1819 /bgsys/drivers/V1R4M2_200_2010-100508P/ppc/toolchain/gnu/glibc-2.4/resolv/res_init.c:414 /bgsys/drivers/V1R4M2_200_2010-100508P/ppc/toolchain/gnu/glibc-2.4/libio/wgenops.c:419 /scratch/pbisbal/build/gromacs-4.6.3/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW4P1_c.c:673 ??:0 /bghome/bgbuild/V1R4M2_200_2010-100508P/ppc/bgp/comm/sys/dcmf/../ccmi/executor/Broadcast.h:83 /bghome/bgbuild/V1R4M2_200_2010-100508P/ppc/bgp/comm/lib/dev/mpich2/src/mpid/dcmfd/src/coll/reduce/reduce_algorithms.c:69 /bghome/bgbuild/V1R4M2_200_2010-100508P/ppc/bgp/comm/lib/dev/mpich2/src/mpid/dcmfd/src/coll/bcast/bcast_algorithms.c:227 /scratch/pbisbal/build/gromacs-4.6.3/src/mdlib/nbnxn_atomdata.c:779 /scratch/pbisbal/build/gromacs-4.6.3/src/mdlib/nbnxn_atomdata.c:762 /scratch/pbisbal/build/gromacs-4.6.3/src/mdlib/nbnxn_atomdata.c:374 /scratch/pbisbal/build/gromacs-4.6.3/src/mdlib/calcmu.c:88 /scratch/pbisbal/build/gromacs-4.6.3/src/kernel/mdrun.c:113 /scratch/pbisbal/build/gromacs-4.6.3/src/kernel/runner.c:1492 /scratch/pbisbal/build/gromacs-4.6.3/src/kernel/genalg.c:467 /scratch/pbisbal/build/gromacs-4.6.3/src/kernel/calc_verletbuf.c:266 ../stdio-common/printf_fphex.c:335 ../stdio-common/printf_fphex.c:452 ??:0 /bgsys/drivers/V1R4M2_200_2010-100508P/ppc/toolchain/gnu/glibc-2.4/stdio-common/vfprintf.c:1819 /bgsys/drivers/V1R4M2_200_2010-100508P/ppc/toolchain/gnu/glibc-2.4/stdio-common/vfprintf.c:1819 /bgsys/drivers/V1R4M2_200_2010-100508P/ppc/toolchain/gnu/glibc-2.4/stdio-common/vfprintf.c:1819 - This is the kind of thing I wanted to see, but it looks like you are analysing a core file using an executable that was not the one that generated the core file. The above does not make sense as a stack trace. You will need to run the debug-enabled code and look at the stack trace with the same executable. If the problem is a va_list one, you might see the last function is gmx_fatal, as mdrun was trying to exit gracefully from some other normal error condition, it ran until the above implementation error while trying to issue the error message. Another node with a different stack looks like this:
Re: [gmx-users] g_wham -sym
Hi, I think g_wham cannot symmetrize around a non-zero point. You'll have to write a little awk script or so and this yourself. Or edit the g_wham code. -zprof0 is not what you need. It sets the PMF to zero at a reference point, where the free energy is defined to zero. Best, Jochen Am 8/10/13 8:59 AM, schrieb Shima Arasteh: Thanks, I defined a new 0.0 position by -zprof0, and shifted the profile energy to a new 0.0. # g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kca -zprof0 -1.081898 -sym But -sym gets me an error: Fatal error: Cannot symmetrize profile around z=0 with min=-1.312664 and max=-1.081898 Why does the g_wham tries to still symmetrize the profile around z=0? Would you please give me any suggestion? Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Friday, August 9, 2013 2:40 PM Subject: Re: [gmx-users] g_wham -sym On 8/9/13 5:48 AM, Shima Arasteh wrote: Hi, I use the g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kca -sym I' d like to know if it is possible to symmetrize the profile around a non-zero point? forexample z=60? Use -zprof0. -Justin -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de/ --- -- 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] g_wham error analysis hangs
Hi Magnus, I just read your mail. Sound very much like a bug, which never occurred to me though. But I did not use -bs-method traj-gauss a lot. Does the error also occur with -bs-method traj? Btw: with -bs-method traj-gauss or traj, you need realistic estimates of the autocorrelation times (ACTs). If you underestimate the ACTs, you will underestimate your errors. If this error still occurs with the latest version, could you make a tar-ball of your tpr and pullf files, put them online, and send me the link? Then I will try to fix the bug. Best, Jochen Am 8/5/13 8:29 AM, schrieb Magnus Andersson: Hi, I have a problem with the error analysis of g_wham. The PMF profile and sampling windows looks good, but when I try to generate error bars g_wham hangs. This is what I do: g_wham_mpi -if pullf-files.dat -it tpr-files.dat -o -hist -nBootstrap 50 -bins 50 -bs-method traj-gauss -bsres -ac yes -bsprof -vbs This is the output after which it just hangs: Estimating integrated autocorreltion times ... [100%] ... done Back Off! I just backed up iact.xvg to ./#iact.xvg.4# Wrote iact.xvg win 0, aver = 3.413503 sig = 0.091051 win 1, aver = 3.440995 sig = 0.060213 win 2, aver = 3.536864 sig = 0.069048 win 3, aver = 3.462364 sig = 0.041276 win 4, aver = 3.508488 sig = 0.041967 win 5, aver = 3.474703 sig = 0.038848 win 6, aver = 3.546181 sig = 0.042018 win 7, aver = 3.558158 sig = 0.047886 win 8, aver = 3.870348 sig = 0.053350 win 9, aver = 3.895024 sig = 0.047226 win 10, aver = 3.905363 sig = 0.039718 win 11, aver = 3.989860 sig = 0.048854 win 12, aver = 4.033406 sig = 0.045494 win 13, aver = 4.077549 sig = 0.042215 win 14, aver = 4.096139 sig = 0.036315 win 15, aver = 4.174044 sig = 0.040574 win 16, aver = 4.119622 sig = 0.052487 win 17, aver = 4.177672 sig = 0.036798 win 18, aver = 4.148724 sig = 0.033967 win 19, aver = 4.228320 sig = 0.039398 win 20, aver = 4.161365 sig = 0.039424 win 21, aver = 4.176532 sig = 0.041844 win 22, aver = 4.224519 sig = 0.030001 win 23, aver = 4.468429 sig = 0.046136 win 24, aver = 4.536401 sig = 0.049635 win 25, aver = 4.666026 sig = 0.054179 win 26, aver = 4.670022 sig = 0.045487 win 27, aver = 4.866098 sig = 0.046887 win 28, aver = 4.935376 sig = 0.050013 win 29, aver = 4.891905 sig = 0.042927 Getting initial potential by integration. Initialized rapid wham stuff (contrib tolerance 3.3e-08) Evaluating only 474 of 1500 expressions. 1) Maximum change 2.849816e-01 100) Maximum change 2.216439e-03 200) Maximum change 1.866839e-03 300) Maximum change 1.612522e-03 400) Maximum change 1.419577e-03 500) Maximum change 1.266497e-03 600) Maximum change 1.140793e-03 700) Maximum change 1.034780e-03 800) Maximum change 9.434951e-04 900) Maximum change 8.635977e-04 1000) Maximum change 7.927633e-04 1100) Maximum change 7.293254e-04 1200) Maximum change 6.720574e-04 1300) Maximum change 6.200347e-04 1400) Maximum change 5.725450e-04 1500) Maximum change 5.290277e-04 1600) Maximum change 4.890329e-04 1700) Maximum change 4.521924e-04 1800) Maximum change 4.181996e-04 1900) Maximum change 3.867947e-04 2000) Maximum change 3.577540e-04 2100) Maximum change 3.308822e-04 2200) Maximum change 3.060068e-04 2300) Maximum change 2.829734e-04 2400) Maximum change 2.616429e-04 2500) Maximum change 2.418887e-04 2600) Maximum change 2.235951e-04 2700) Maximum change 2.066558e-04 2800) Maximum change 1.909727e-04 2900) Maximum change 1.764550e-04 3000) Maximum change 1.630186e-04 3100) Maximum change 1.505854e-04 3200) Maximum change 1.390827e-04 3300) Maximum change 1.284431e-04 3400) Maximum change 1.186038e-04 3500) Maximum change 1.095063e-04 3600) Maximum change 1.010962e-04 3700) Maximum change 9.332302e-05 3800) Maximum change 8.613974e-05 3900) Maximum change 7.950267e-05 4000) Maximum change 7.337121e-05 4100) Maximum change 6.770765e-05 4200) Maximum change 6.247700e-05 4300) Maximum change 5.764678e-05 4400) Maximum change 5.318686e-05 4500) Maximum change 4.906931e-05 4600) Maximum change 4.526823e-05 4700) Maximum change 4.175964e-05 4800) Maximum change 3.852131e-05 4900) Maximum change 3.553267e-05 5000) Maximum change 3.277469e-05 5100) Maximum change 3.022973e-05 5200) Maximum change 2.788151e-05 5300) Maximum change 2.571494e-05 5400) Maximum change 2.371608e-05 5500) Maximum change 2.187205e-05 5600) Maximum change 2.017093e-05 5700) Maximum change 1.860172e-05 5800) Maximum change 1.715425e-05 5900) Maximum change 1.581912e-05 6000) Maximum change 1.458767e-05
Re: [gmx-users] g_wham error analysis hangs
Hi Jochen, Seems as if this error was associated with the mpi version. Everything worked ok when running it locally. Best regards / Magnus On Aug 12, 2013, at 1:50 PM, Jochen Hub j...@gwdg.de wrote: Hi Magnus, I just read your mail. Sound very much like a bug, which never occurred to me though. But I did not use -bs-method traj-gauss a lot. Does the error also occur with -bs-method traj? Btw: with -bs-method traj-gauss or traj, you need realistic estimates of the autocorrelation times (ACTs). If you underestimate the ACTs, you will underestimate your errors. If this error still occurs with the latest version, could you make a tar-ball of your tpr and pullf files, put them online, and send me the link? Then I will try to fix the bug. Best, Jochen Am 8/5/13 8:29 AM, schrieb Magnus Andersson: Hi, I have a problem with the error analysis of g_wham. The PMF profile and sampling windows looks good, but when I try to generate error bars g_wham hangs. This is what I do: g_wham_mpi -if pullf-files.dat -it tpr-files.dat -o -hist -nBootstrap 50 -bins 50 -bs-method traj-gauss -bsres -ac yes -bsprof -vbs This is the output after which it just hangs: Estimating integrated autocorreltion times ... [100%] ... done Back Off! I just backed up iact.xvg to ./#iact.xvg.4# Wrote iact.xvg win 0, aver = 3.413503 sig = 0.091051 win 1, aver = 3.440995 sig = 0.060213 win 2, aver = 3.536864 sig = 0.069048 win 3, aver = 3.462364 sig = 0.041276 win 4, aver = 3.508488 sig = 0.041967 win 5, aver = 3.474703 sig = 0.038848 win 6, aver = 3.546181 sig = 0.042018 win 7, aver = 3.558158 sig = 0.047886 win 8, aver = 3.870348 sig = 0.053350 win 9, aver = 3.895024 sig = 0.047226 win 10, aver = 3.905363 sig = 0.039718 win 11, aver = 3.989860 sig = 0.048854 win 12, aver = 4.033406 sig = 0.045494 win 13, aver = 4.077549 sig = 0.042215 win 14, aver = 4.096139 sig = 0.036315 win 15, aver = 4.174044 sig = 0.040574 win 16, aver = 4.119622 sig = 0.052487 win 17, aver = 4.177672 sig = 0.036798 win 18, aver = 4.148724 sig = 0.033967 win 19, aver = 4.228320 sig = 0.039398 win 20, aver = 4.161365 sig = 0.039424 win 21, aver = 4.176532 sig = 0.041844 win 22, aver = 4.224519 sig = 0.030001 win 23, aver = 4.468429 sig = 0.046136 win 24, aver = 4.536401 sig = 0.049635 win 25, aver = 4.666026 sig = 0.054179 win 26, aver = 4.670022 sig = 0.045487 win 27, aver = 4.866098 sig = 0.046887 win 28, aver = 4.935376 sig = 0.050013 win 29, aver = 4.891905 sig = 0.042927 Getting initial potential by integration. Initialized rapid wham stuff (contrib tolerance 3.3e-08) Evaluating only 474 of 1500 expressions. 1) Maximum change 2.849816e-01 100) Maximum change 2.216439e-03 200) Maximum change 1.866839e-03 300) Maximum change 1.612522e-03 400) Maximum change 1.419577e-03 500) Maximum change 1.266497e-03 600) Maximum change 1.140793e-03 700) Maximum change 1.034780e-03 800) Maximum change 9.434951e-04 900) Maximum change 8.635977e-04 1000) Maximum change 7.927633e-04 1100) Maximum change 7.293254e-04 1200) Maximum change 6.720574e-04 1300) Maximum change 6.200347e-04 1400) Maximum change 5.725450e-04 1500) Maximum change 5.290277e-04 1600) Maximum change 4.890329e-04 1700) Maximum change 4.521924e-04 1800) Maximum change 4.181996e-04 1900) Maximum change 3.867947e-04 2000) Maximum change 3.577540e-04 2100) Maximum change 3.308822e-04 2200) Maximum change 3.060068e-04 2300) Maximum change 2.829734e-04 2400) Maximum change 2.616429e-04 2500) Maximum change 2.418887e-04 2600) Maximum change 2.235951e-04 2700) Maximum change 2.066558e-04 2800) Maximum change 1.909727e-04 2900) Maximum change 1.764550e-04 3000) Maximum change 1.630186e-04 3100) Maximum change 1.505854e-04 3200) Maximum change 1.390827e-04 3300) Maximum change 1.284431e-04 3400) Maximum change 1.186038e-04 3500) Maximum change 1.095063e-04 3600) Maximum change 1.010962e-04 3700) Maximum change 9.332302e-05 3800) Maximum change 8.613974e-05 3900) Maximum change 7.950267e-05 4000) Maximum change 7.337121e-05 4100) Maximum change 6.770765e-05 4200) Maximum change 6.247700e-05 4300) Maximum change 5.764678e-05 4400) Maximum change 5.318686e-05 4500) Maximum change 4.906931e-05 4600) Maximum change 4.526823e-05 4700) Maximum change 4.175964e-05 4800) Maximum change 3.852131e-05 4900) Maximum change 3.553267e-05 5000) Maximum change 3.277469e-05 5100) Maximum change 3.022973e-05 5200) Maximum change 2.788151e-05 5300) Maximum change 2.571494e-05 5400) Maximum change 2.371608e-05 5500) Maximum change 2.187205e-05 5600) Maximum change 2.017093e-05
[gmx-users] Force Field for peptides and proteins
Dear Gromacs users, We would like to know which is the Force Field which is customarily preferred for simulations of peptides and proteins. Thank you very much. Best regards, Maria -- 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] Force Field for peptides and proteins
It depends on what properties of peptides and proteins that you want to explore. ~Thu On Mon, Aug 12, 2013 at 7:19 PM, Maria Astón Serrano m.aston.serr...@gmail.com wrote: Dear Gromacs users, We would like to know which is the Force Field which is customarily preferred for simulations of peptides and proteins. Thank you very much. Best regards, Maria -- 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] Force Field for peptides and proteins
I like CHARMM. Dr. Vitaly V. Chaban On Mon, Aug 12, 2013 at 2:19 PM, Maria Astón Serrano m.aston.serr...@gmail.com wrote: Dear Gromacs users, We would like to know which is the Force Field which is customarily preferred for simulations of peptides and proteins. Thank you very much. Best regards, Maria -- 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] Force Field for peptides and proteins
On 8/12/13 8:19 AM, Maria Astón Serrano wrote: Dear Gromacs users, We would like to know which is the Force Field which is customarily preferred for simulations of peptides and proteins. Interestingly, this same question was just asked on the development list, although the discussion indeed belongs here. http://lists.gromacs.org/pipermail/gmx-developers/2013-August/007016.html There is a wide body of literature on this topic, and it is very educational to read through as much of it as you can. Some force fields, like AMBER94 and CHARMM22+CMAP are decidedly too helical, while others (Gromos96 53A6 being a good example) tend to understate helices and overstate extended configurations. New parameter sets like AMBER99SB-ILDN and CHARMM22* are often used in protein folding studies and seem to do quite well. I think, in the end, it depends to some extent about the scope of what you are doing and the protein(s) to be studied. Even high quality force fields that perform well for folded proteins do not necessarily perform well on intrinsically disordered proteins or model peptides. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] Force Field for peptides and proteins
On this note, I wanted to ask about simulated unfolding of proteins. I have a primarily alpha-helical-protein ( about 300 amino acids, 5 alpha helices, no beta strands) and 3 of its single point mutants. Now, to answer the question of relative stability, I want to place them in a water bath and heat them until they unfold. The temperature at which they unfold should qualitatively tell me which is more stable (the most stable unfolding at the highest temperature). I have been wondering which forcefield would be more suitable. I intend to use simulated heating at a constant rate (simulated annealing option in .mdp file). Any answers will be greatly appreciated. Thank you. On Mon, Aug 12, 2013 at 6:29 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/12/13 8:19 AM, Maria Astón Serrano wrote: Dear Gromacs users, We would like to know which is the Force Field which is customarily preferred for simulations of peptides and proteins. Interestingly, this same question was just asked on the development list, although the discussion indeed belongs here. http://lists.gromacs.org/**pipermail/gmx-developers/2013-** August/007016.htmlhttp://lists.gromacs.org/pipermail/gmx-developers/2013-August/007016.html There is a wide body of literature on this topic, and it is very educational to read through as much of it as you can. Some force fields, like AMBER94 and CHARMM22+CMAP are decidedly too helical, while others (Gromos96 53A6 being a good example) tend to understate helices and overstate extended configurations. New parameter sets like AMBER99SB-ILDN and CHARMM22* are often used in protein folding studies and seem to do quite well. I think, in the end, it depends to some extent about the scope of what you are doing and the protein(s) to be studied. Even high quality force fields that perform well for folded proteins do not necessarily perform well on intrinsically disordered proteins or model peptides. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- 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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] hessian calculation with periodic boundary condition
thanks. One more question, is there an easy way to ask gromacs to output the forces and the 2nd derivative? Or one has to modify the source code to do this? Best, JT From: David van der Spoel sp...@xray.bmc.uu.se To: gmx-users@gromacs.org Sent: Sunday, August 11, 2013 12:17 PM Subject: Re: [gmx-users] hessian calculation with periodic boundary condition On 2013-08-11 17:00, John Travers wrote: Hi, I am trying to use gromacs to do hessian calculations for some of the structures along a trajectory. Do you know whether the normal mode analysis in gromacs takes into account the periodic boundary condition when computing the 2nd derivative? Thanks! Best JT Yes it does. The parallel version is broken, by the way, a fix is underway. -- 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.se http://folding.bmc.uu.se -- 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
[gmx-users] Implement a modified pull module to mdrun
Hi all, I found one paper talking about they implement a wall potential in the pull module of the mdrun program. Does anybody know how they do it please? Is it the similar method introduced in User-specified potential functions by using following in mdp: rilst = 1.0 coulombtype =user rcoulomb= 1.0 vdwtype= user rvdw = 1.0 Thanks in advance. --H.L-- 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] Implement a modified pull module to mdrun
On 8/12/13 12:52 PM, Li, Hualin wrote: Hi all, I found one paper talking about they implement a wall potential in the pull module of the mdrun program. Does anybody know how they do it please? Is it the similar method introduced in User-specified potential functions by using following in mdp: rilst = 1.0 coulombtype =user rcoulomb= 1.0 vdwtype= user rvdw = 1.0 I wouldn't think so. The tabulated nonbonded potentials and the pull code are separate entities. If they say they modified the pull function, then that's what the did. I would suggest contacting the corresponding author directly. This is the kind of question that needs to be asked directly to the people who did the work. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] Implement a modified pull module to mdrun
Hi Justin, Thank you for your reply. I also suspect that they may use like change pull source code --recomplie GROMACS --run modified mdrun . Do you know where the source code of the pull code is located please? Thanks, --H L From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin Lemkul [jalem...@vt.edu] Sent: Monday, August 12, 2013 12:02 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Implement a modified pull module to mdrun Hi all, I found one paper talking about they implement a wall potential in the pull module of the mdrun program. Does anybody know how they do it please? Is it the similar method introduced in User-specified potential functions by using following in mdp: rilst = 1.0 coulombtype =user rcoulomb= 1.0 vdwtype= user rvdw = 1.0 I wouldn't think so. The tabulated nonbonded potentials and the pull code are separate entities. If they say they modified the pull function, then that's what the did. I would suggest contacting the corresponding author directly. This is the kind of question that needs to be asked directly to the people who did the work. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] Implement a modified pull module to mdrun
On 8/12/13 1:29 PM, Li, Hualin wrote: Hi Justin, Thank you for your reply. I also suspect that they may use like change pull source code --recomplie GROMACS --run modified mdrun . Do you know where the source code of the pull code is located please? It's in src/mdlib - pull.c and pullutil.c should have everything, if memory serves. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] Implement a modified pull module to mdrun
Hi Justin, Thanks a lot. I found them. Other than changing the source code, is it possible to write a script-like code to run with mdrun in order to apply this wall potential please? Thanks, --H L From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin Lemkul [jalem...@vt.edu] Sent: Monday, August 12, 2013 12:55 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Implement a modified pull module to mdrun On 8/12/13 1:29 PM, Li, Hualin wrote: Hi Justin, Thank you for your reply. I also suspect that they may use like change pull source code --recomplie GROMACS --run modified mdrun . Do you know where the source code of the pull code is located please? It's in src/mdlib - pull.c and pullutil.c should have everything, if memory serves. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] Implement a modified pull module to mdrun
On 8/12/13 2:13 PM, Li, Hualin wrote: Hi Justin, Thanks a lot. I found them. Other than changing the source code, is it possible to write a script-like code to run with mdrun in order to apply this wall potential please? Doubtful. Again, I would try to get in contact with the authors of whatever study you read and see what they did. They will probably even give you their code so you don't have to do any new modifications. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] charmm2gromacs.py error
Dear all, I am using your script charmm2gromacs for the conversion and I am facing certain difficulties in the same. My doubts are: 1. In NAMD is was using CHARMM36 parameters as the parameters dor DOPC (dioleyl phopshotidyl choline). were available in only in that. 2. For cholesteryl ester, I have used the parameters of cholesterol from the updated version of chamm36 and added the oleate paramters from DOPC. When I imported this folder into the gromacs directory, a . gro file corresponding to the protein and DOPC were created successfully. 3. But for the cholesteryl ester, I wanted to convert the *.rtf file and *.prm file using your script which I am unable to : command used: python charmm2gromacs-pvm.py par_all36_lipid.prm top_chol_ester.rtf It created a directory called cgenff-2b7 which I am attaching for your kind perusal. In this directory: aminoacids.rtp -is incomplete atomtypes.atp,ffbonded.itp ,forcefield.doc -is empty I also see that these correspond to charmm27 parameters. I am newbie to simulations and gromacs and nobody else in my lab is working in this. I will be really grateful for your support in this regard. Thank you in advance. Yours sincerely, Revathi.S M.S. Research Scholar Computational Biophysics Lab, Department of Biotechnology, Indian Institute Of Technology, Madras India-- 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] converting Charmm36 lipidds to gromacs
Dear all , With reference to the thread on converting charmm36 lipid parameters to gromacs: http://lists.gromacs.org/pipermail/gmx-users/2010-October/054515.html The link mentioned :http://www.dbb.su.se/User:Bjelkmar/Ffcharmm no longer works. It says page not found. Kindly suggest me how to convert charmm36 lipid parameters to the gromacs format. The python script found in the use contributions also seems to have some bugs. Kindly provide your valuable suggestions. Thanks for your help in advance. Yours sincerely, Revathi.S -- 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] perl scripts to convert CHARMM ff in GROMACS
Dear all, The thread on perl,scripts for converting charmm to gromacs states that the package is deprecated and emailed off-list. http://lists.gromacs.org/pipermail/gmx-users/2010-February/048506.html How could I convert charmm to gromacs otherwise? Could anyone help me with their scripts in this regard? Thank you for your help in advance. Regards, Revathi -- 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] perl scripts to convert CHARMM ff in GROMACS
On 2013-08-12 21:33, Revthi Sanker wrote: Dear all, The thread on perl,scripts for converting charmm to gromacs states that the package is deprecated and emailed off-list. http://lists.gromacs.org/pipermail/gmx-users/2010-February/048506.html How could I convert charmm to gromacs otherwise? Could anyone help me with their scripts in this regard? http://www.gromacs.org/Downloads/User_contributions/Other_software Thank you for your help in advance. Regards, Revathi -- 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] Problem running do_dssp
Hi, I am trying to use do_dssp to generate a secondary structure map over time for a 10-ns simulation. I have installed dssp_2.2.0 at the usual /usr/local/bin I tried running it with the following command line do_dssp -f md.xtc -s md.tpr -o ss.xpm -sc ss.xvg -dt 100 -tu ps; but ended up with the following error. Thanks in advance for your help. Selected 4: 'Backbone' There are 424 residues in your selected group dssp cmd='/usr/local/bin/dssp -i dd5Yvoh4 -o ddazDUUO /dev/null 2 /dev/null' Reading frame 0 time0.000 Back Off! I just backed up dd5Yvoh4 to ./#dd5Yvoh4.1# --- Program do_dssp, VERSION 4.6.3 Source code file: /home/rsd/gromacs-4.6.3/src/tools/gmx_do_dssp.c, line: 669 Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- God is a DJ (Faithless) -Dipankar-- 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] Problem running do_dssp
On 8/12/13 4:29 PM, Dipankar Roy wrote: Hi, I am trying to use do_dssp to generate a secondary structure map over time for a 10-ns simulation. I have installed dssp_2.2.0 at the usual /usr/local/bin I tried running it with the following command line do_dssp -f md.xtc -s md.tpr -o ss.xpm -sc ss.xvg -dt 100 -tu ps; but ended up with the following error. Thanks in advance for your help. Selected 4: 'Backbone' There are 424 residues in your selected group dssp cmd='/usr/local/bin/dssp -i dd5Yvoh4 -o ddazDUUO /dev/null 2 /dev/null' Reading frame 0 time0.000 Back Off! I just backed up dd5Yvoh4 to ./#dd5Yvoh4.1# --- Program do_dssp, VERSION 4.6.3 Source code file: /home/rsd/gromacs-4.6.3/src/tools/gmx_do_dssp.c, line: 669 Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- God is a DJ (Faithless) This issue has been discussed numerous times (hint: check the archive, it will save you time!) and the solution is shown in the fatal error. DSSP has different syntax in different versions. If you have dssp-2.2.0, use -ver 2 in the do_dssp command. Also note that Backbone will not work because DSSP requires carbonyl oxygen atoms to determine hydrogen bonding patterns. You need to choose, at minimum, MainChain. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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: restraint-lambdas for position restraints in hamiltonian exchange
Hi Michael, After looking at the codes, it seems to me that the exchange scheme I posted previously incurs violation of detailed balance, which seems to be a bug. I'll really appreciate it if you can clarify this. Let me re-state what I was trying to do. I have the following 7-component restraint-lambdas: 0 0.1 0.2 0.3 0.09 0.19 0.29 The restraints are position restraints defined in top file of molecule I: #define posA0 0 0 #define posB0 0 3 [ position_restraints ] ; ai funct parA parB 1 1 posA posB 2 1 posA posB 3 1 posA posB 4 1 posAposB I initialized replicas 0 to 3 in structure C and 4 to 6 in structure D and hoped that replica 0 would sample structure C and D according to the correct thermodynamics. Now suppose an exchange is attempt between replica i and j, which are running in Hamiltonian Ui and Uj respectively. Then dE should be Ui(xj) - Uj(xj) + Uj(xi) - Ui(xi), where Ui(xj) = (1-lambda_i)*POSRES_A_i(xj) + lambda_i*POSRES_B_i(xj) = lambda_i*POSRES_B_i(xj) (last equality holds since the force constants are all 0 in state A as shown above) for any pair of i and j, where POSRES_B_i is the state-B restraint potential energy function with reference position defined in replica i. So dE = lambda_i*POSRES_B_i(xj) - lambda_j*POSRES_B_j(xj) + lambda_j*POSRES_B_j(xi) - lambda_i*POSRES_B_i(xi) But the respective terms Ui(xj) - Uj(xj) and Uj(xi) - Ui(xi) are actually calculated in the 2 simulations indepedently (function test_for_replica_exchange() in kernel/repl_ex.c around line 954) and POSRES_B_i(xj) is actually POSRES_B_j(xj) in simulation j while POSRES_B_j(xi) is actually POSRES_B_i(xi) in simulation i because simulation i and j don't communicate for reference position in this case as far as I can tell from the function real posres() as defined in include/bondf.h. The codes was able to run but I think this will give wrong detail balance and it would be nice for the program to issue a warning/error in this case. Again, thanks a lot for your help! -Dejun 2013/8/7 Dejun Lin dejun@gmail.com Hi Micheal, Sorry for keep bugging you about this but I want to make sure I'm doing what I think I'm doing :) I did some test on the following setup. restraint-lambdas = 0.3 0.29 (essentially no difference) on position restraints. replica 0 starts in structure A and replica 1 in structure B. The 2 position restraints have exactly the same set of force constants, i.e., the 2 replica used the same top/itp file. But each of this 2 replicas should have one distinct set of restraints because the difference in initial structure (gro file) are huge. Replica 0: structure *A*, restraints A (ref. position A, force constant C) Replica 1: structure *B*, restraints B (ref. position B, force constant C) Swapped between the 2 replica were observed and I looked at the trajectory from *replica 0* in VMD and noticed that there were *structure B* in it. Can assume that swap resulted in the following states ? Replica 0: structure *B*, restraints A (ref. position A, force constant C) Replica 1: structure *A*, restraints B (ref. position B, force constant C) i.e. It was the coordinates instead of lambda values were swapped between replicas, which is essentially the same as if the reference positions were swapped. Thanks again for your help! -Dejun 2013/8/3 Michael Shirts-2 [via GROMACS] ml-node+s5086n501032...@n6.nabble.com That is correct. Such a functionality wouldn't be that hard to implement - but there are a long list of easy functionalities to be implemented. You can submit a request to redmine.gromacs.org so that the request is archived. On Sat, Aug 3, 2013 at 6:12 PM, Dejun Lin [hidden email]http://user/SendEmail.jtp?type=nodenode=5010326i=0 wrote: So I take it that in the position restraint case (not COM-pulling), where the reference positions are determined by the starting structure instead of a B-state topology, the reference positions won't be swapped ? 2013/8/3 Michael Shirts-2 [via GROMACS] [hidden email] http://user/SendEmail.jtp?type=nodenode=5010326i=1 Short answer is anything that has a B state parameter can be included in in Hamiltonian exchange. If it's pull code or explicit restraints, it's controlled by restraint lambda. I went through the manual and couldn't find any definite answers to the following questions. First, I wonder if the reference positions of position restraints, not just the force constants, of different replicas are exchanged in hamiltonian exchange based on restraint-lambdas? For example, if I have 1 molecule that has 2 structures, say, A and B and the following 2-component restraint-lambdas: 1.0 1.0 with replica 0 starting in A and replica 1 in B, would the exchange between replica 0 and 1 yield anything meaningful ? Right now, the pull
