Re: [gmx-users] can not pass gmxtest
Hi, You shall always try to build gromacs yourself. What's the error with tutorial? Regards, Yang Ye On 11/7/2007 10:14 AM, Li Qiang wrote: hi all, I newly installed GROMACS on UBUNTU 7.10 from Synaptic Package Manager(SPM). However, it can not pass the gamxtest with log as below, but Tutorials seems OK. Actually I try to compile myself at the beginning. It is weird that the self-compiled one can pass the test but failed to run Tutorials with Segmental fault at PR MD step. Does anyboby know how to solve it? and how to uninstall GROMACS clear? thanks a lot. output from gmxtest: ++ *** glibc detected *** mdrun: realloc(): invalid next size: 0x08076ec8 *** === Backtrace: = /lib/tls/i686/cmov/libc.so.6[0xb7a45b0c] /lib/tls/i686/cmov/libc.so.6(realloc+0x106)[0xb7a47a66] /usr/lib/libgmx.so.4(save_realloc+0x39)[0xb7cbe439] /usr/lib/libgmx.so.4(mk_graph+0x494)[0xb7cadde4] mdrun[0x8059f50] mdrun[0x805a72a] /lib/tls/i686/cmov/libc.so.6(__libc_start_main+0xe0)[0xb79f0050] mdrun[0x804a491] === Memory map: 08048000-08062000 r-xp 08:04 2490502/usr/bin/mdrun 08062000-08063000 rw-p 00019000 08:04 2490502/usr/bin/mdrun 08063000-08085000 rw-p 08063000 00:00 0 [heap] b780-b7821000 rw-p b780 00:00 0 b7821000-b790 ---p b7821000 00:00 0 b79cc000-b79cd000 rw-p b79cc000 00:00 0 b79cd000-b79cf000 r-xp 08:04 2747181/lib/tls/i686/cmov/libdl-2.6.1.so b79cf000-b79d1000 rw-p 1000 08:04 2747181/lib/tls/i686/cmov/libdl-2.6.1.so b79d1000-b79d5000 r-xp 08:04 2486327/usr/lib/libXdmcp.so.6.0.0 b79d5000-b79d6000 rw-p 3000 08:04 2486327/usr/lib/libXdmcp.so.6.0.0 b79d6000-b79d8000 r-xp 08:04 2485527/usr/lib/libXau.so.6.0.0 b79d8000-b79d9000 rw-p 1000 08:04 2485527/usr/lib/libXau.so.6.0.0 b79d9000-b79da000 rw-p b79d9000 00:00 0 b79da000-b7b1e000 r-xp 08:04 2747161/lib/tls/i686/cmov/libc-2.6.1.so b7b1e000-b7b1f000 r--p 00143000 08:04 2747161/lib/tls/i686/cmov/libc-2.6.1.so b7b1f000-b7b21000 rw-p 00144000 08:04 2747161/lib/tls/i686/cmov/libc-2.6.1.so b7b21000-b7b24000 rw-p b7b21000 00:00 0 b7b24000-b7c11000 r-xp 08:04 2486347/usr/lib/libX11.so.6.2.0 b7c11000-b7c15000 rw-p 000ed000 08:04 2486347/usr/lib/libX11.so.6.2.0 b7c15000-b7c2a000 r-xp 08:04 2488182/usr/lib/libICE.so.6.3.0 b7c2a000-b7c2c000 rw-p 00014000 08:04 2488182/usr/lib/libICE.so.6.3.0 b7c2c000-b7c2d000 rw-p b7c2c000 00:00 0 b7c2d000-b7c34000 r-xp 08:04 2487000/usr/lib/libSM.so.6.0.0 b7c34000-b7c35000 rw-p 6000 08:04 2487000/usr/lib/libSM.so.6.0.0 b7c35000-b7c58000 r-xp 08:04 2747187/lib/tls/i686/cmov/libm-2.6.1.so b7c58000-b7c5a000 rw-p 00023000 08:04 2747187/lib/tls/i686/cmov/libm-2.6.1.so b7c5a000-b7c6e000 r-xp 08:04 2747206/lib/tls/i686/cmov/libnsl-2.6.1.so b7c6e000-b7c7 rw-p 00013000 08:04 2747206/lib/tls/i686/cmov/libnsl-2.6.1.so b7c7-b7c73000 rw-p b7c7 00:00 0 b7c73000-b7e27000 r-xp 08:04 2491023/usr/lib/libgmx.so.4.0.0 b7e27000-b7e3 rw-p 001b3000 08:04 2491023/usr/lib/libgmx.so.4.0.0 b7e3-b7e35000 rw-p b7e3 00:00 0 b7e35000-b7f4a000 r-xp 08:04 2491025/usr/lib/libmd.so.4.0.0 b7f4a000-b7f4b000 rw-p 00114000 08:04 2491025/usr/lib/libmd.so.4.0.0 b7f4b000-b7f4c000 rw-p b7f4b000 00:00 0 b7f4e000-b7f58000 r-xp 08:04 2747267/lib/libgcc_s.so.1 b7f58000-b7f59000 rw-p a000 08:04 2747267/lib/libgcc_s.so.1 b7f59000-b7f5c000 rw-p b7f59000 00:00 0 b7f5c000-b7f76000 r-xp 08:04 2747274/lib/ld-2.6.1.so b7f76000-b7f78000 rw-p 00019000 08:04 2747274/lib/ld-2.6.1.so bfa98000-bfaad000 rwxp bfa98000 00:00 0 [stack] bfaad000-bfaae000 rw-p bfaad000 00:00 0 e000-f000 r-xp 00:00 0 [vdso] FAILED. Check files in rb1 1 out of 16 simple tests FAILED FAILED. Check files in acetonitrilRF FAILED. Check files in dec+water 2 out of 14 complex tests FAILED All 63 kernel tests PASSED All 45 pdb2gmx tests PASSED ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Installation problem:gcc-g77
Hi, I just have a fresh install FC7 (instead of FC5). Gromacs requires the lam package as a Prerequisite, but it cannot be installed successfully due to a dependency of gcc-g77. So you might need a lam that doesn't use gcc-g77. Check with their download page for what's available. You can certainly try to install lam from source using gfortran, and then gromacs from source will also be happy. I completely installed gcc and gcc-c++. According to my architecture FC, the gcc-fortran-4.1.2-27.fc7.i386 would be installed. I think that gcc-fortran should be as same as gcc-g77, but it does not. It still require gcc-g77 for the installation of lam package. If it's just a name difference, then you can just rename something, or override whatever the objection from RPM is. You'll have to know what you're doing to get the job finished, however. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] can not pass gmxtest
hi yang, thanks for the reply. Do you mean that the installation from SMP is not right? The error with self-compiled gromacs is in position restrain step with unusual distances and the mdrun stops at step0 with Segmentation fault (core dumped). but the mdrun with constraint can run, though I do not know if it is right. The possible reason is that I install from SMP of ubuntu but forget to remove the self-compiled one. Several days ago the gromacs version from SMP is 3.3.1. I though it was simpler to install GROMACS automatically from that. Could tell me how to remove GROMACS entirely so that I can reinstall from fresh? Hope we can do it. thank you very much. Li Qiang On Wed, 2007-11-07 at 16:16 +0800, Yang Ye wrote: Hi, You shall always try to build gromacs yourself. What's the error with tutorial? Regards, Yang Ye On 11/7/2007 10:14 AM, Li Qiang wrote: hi all, I newly installed GROMACS on UBUNTU 7.10 from Synaptic Package Manager(SPM). However, it can not pass the gamxtest with log as below, but Tutorials seems OK. Actually I try to compile myself at the beginning. It is weird that the self-compiled one can pass the test but failed to run Tutorials with Segmental fault at PR MD step. Does anyboby know how to solve it? and how to uninstall GROMACS clear? thanks a lot. output from gmxtest: ++ *** glibc detected *** mdrun: realloc(): invalid next size: 0x08076ec8 *** === Backtrace: = /lib/tls/i686/cmov/libc.so.6[0xb7a45b0c] /lib/tls/i686/cmov/libc.so.6(realloc+0x106)[0xb7a47a66] /usr/lib/libgmx.so.4(save_realloc+0x39)[0xb7cbe439] /usr/lib/libgmx.so.4(mk_graph+0x494)[0xb7cadde4] mdrun[0x8059f50] mdrun[0x805a72a] /lib/tls/i686/cmov/libc.so.6(__libc_start_main+0xe0)[0xb79f0050] mdrun[0x804a491] === Memory map: 08048000-08062000 r-xp 08:04 2490502/usr/bin/mdrun 08062000-08063000 rw-p 00019000 08:04 2490502/usr/bin/mdrun 08063000-08085000 rw-p 08063000 00:00 0 [heap] b780-b7821000 rw-p b780 00:00 0 b7821000-b790 ---p b7821000 00:00 0 b79cc000-b79cd000 rw-p b79cc000 00:00 0 b79cd000-b79cf000 r-xp 08:04 2747181/lib/tls/i686/cmov/libdl-2.6.1.so b79cf000-b79d1000 rw-p 1000 08:04 2747181/lib/tls/i686/cmov/libdl-2.6.1.so b79d1000-b79d5000 r-xp 08:04 2486327/usr/lib/libXdmcp.so.6.0.0 b79d5000-b79d6000 rw-p 3000 08:04 2486327/usr/lib/libXdmcp.so.6.0.0 b79d6000-b79d8000 r-xp 08:04 2485527/usr/lib/libXau.so.6.0.0 b79d8000-b79d9000 rw-p 1000 08:04 2485527/usr/lib/libXau.so.6.0.0 b79d9000-b79da000 rw-p b79d9000 00:00 0 b79da000-b7b1e000 r-xp 08:04 2747161/lib/tls/i686/cmov/libc-2.6.1.so b7b1e000-b7b1f000 r--p 00143000 08:04 2747161/lib/tls/i686/cmov/libc-2.6.1.so b7b1f000-b7b21000 rw-p 00144000 08:04 2747161/lib/tls/i686/cmov/libc-2.6.1.so b7b21000-b7b24000 rw-p b7b21000 00:00 0 b7b24000-b7c11000 r-xp 08:04 2486347/usr/lib/libX11.so.6.2.0 b7c11000-b7c15000 rw-p 000ed000 08:04 2486347/usr/lib/libX11.so.6.2.0 b7c15000-b7c2a000 r-xp 08:04 2488182/usr/lib/libICE.so.6.3.0 b7c2a000-b7c2c000 rw-p 00014000 08:04 2488182/usr/lib/libICE.so.6.3.0 b7c2c000-b7c2d000 rw-p b7c2c000 00:00 0 b7c2d000-b7c34000 r-xp 08:04 2487000/usr/lib/libSM.so.6.0.0 b7c34000-b7c35000 rw-p 6000 08:04 2487000/usr/lib/libSM.so.6.0.0 b7c35000-b7c58000 r-xp 08:04 2747187/lib/tls/i686/cmov/libm-2.6.1.so b7c58000-b7c5a000 rw-p 00023000 08:04 2747187/lib/tls/i686/cmov/libm-2.6.1.so b7c5a000-b7c6e000 r-xp 08:04 2747206/lib/tls/i686/cmov/libnsl-2.6.1.so b7c6e000-b7c7 rw-p 00013000 08:04 2747206/lib/tls/i686/cmov/libnsl-2.6.1.so b7c7-b7c73000 rw-p b7c7 00:00 0 b7c73000-b7e27000 r-xp 08:04 2491023/usr/lib/libgmx.so.4.0.0 b7e27000-b7e3 rw-p 001b3000 08:04 2491023/usr/lib/libgmx.so.4.0.0 b7e3-b7e35000 rw-p b7e3 00:00 0 b7e35000-b7f4a000 r-xp 08:04 2491025/usr/lib/libmd.so.4.0.0 b7f4a000-b7f4b000 rw-p 00114000 08:04 2491025/usr/lib/libmd.so.4.0.0 b7f4b000-b7f4c000 rw-p b7f4b000 00:00 0 b7f4e000-b7f58000 r-xp 08:04 2747267/lib/libgcc_s.so.1 b7f58000-b7f59000 rw-p a000 08:04 2747267/lib/libgcc_s.so.1 b7f59000-b7f5c000 rw-p b7f59000 00:00 0 b7f5c000-b7f76000 r-xp 08:04 2747274/lib/ld-2.6.1.so b7f76000-b7f78000 rw-p 00019000 08:04 2747274/lib/ld-2.6.1.so bfa98000-bfaad000 rwxp bfa98000 00:00 0 [stack] bfaad000-bfaae000 rw-p bfaad000 00:00 0 e000-f000 r-xp 00:00 0 [vdso] FAILED. Check files in rb1 1 out of 16 simple tests FAILED FAILED. Check files in acetonitrilRF FAILED. Check files in dec+water 2 out of 14 complex tests FAILED
Re: [gmx-users] can not pass gmxtest
To uninstall GROMACS, you can type which mdrun to get its path and try to figure out where it has been installed. For GROMACS, it may reside under /usr/local/gromacs remove the whole directory with rm -fr. To ensure that you are using the self-built GROMACS, look for a file GMXRC.bash in the locations which you can find in make install. Run it with source /path/to/GMXRC.bash Then you can make sure that you are using your own version. Put that line source ... into ~/.bashrc shall make it default for every login session. Regards, Yang Ye On 11/7/2007 4:35 PM, Li Qiang wrote: hi yang, thanks for the reply. Do you mean that the installation from SMP is not right? The error with self-compiled gromacs is in position restrain step with unusual distances and the mdrun stops at step0 with Segmentation fault (core dumped). but the mdrun with constraint can run, though I do not know if it is right. The possible reason is that I install from SMP of ubuntu but forget to remove the self-compiled one. Several days ago the gromacs version from SMP is 3.3.1. I though it was simpler to install GROMACS automatically from that. Could tell me how to remove GROMACS entirely so that I can reinstall from fresh? Hope we can do it. thank you very much. Li Qiang On Wed, 2007-11-07 at 16:16 +0800, Yang Ye wrote: Hi, You shall always try to build gromacs yourself. What's the error with tutorial? Regards, Yang Ye On 11/7/2007 10:14 AM, Li Qiang wrote: hi all, I newly installed GROMACS on UBUNTU 7.10 from Synaptic Package Manager(SPM). However, it can not pass the gamxtest with log as below, but Tutorials seems OK. Actually I try to compile myself at the beginning. It is weird that the self-compiled one can pass the test but failed to run Tutorials with Segmental fault at PR MD step. Does anyboby know how to solve it? and how to uninstall GROMACS clear? thanks a lot. output from gmxtest: ++ *** glibc detected *** mdrun: realloc(): invalid next size: 0x08076ec8 *** === Backtrace: = /lib/tls/i686/cmov/libc.so.6[0xb7a45b0c] /lib/tls/i686/cmov/libc.so.6(realloc+0x106)[0xb7a47a66] /usr/lib/libgmx.so.4(save_realloc+0x39)[0xb7cbe439] /usr/lib/libgmx.so.4(mk_graph+0x494)[0xb7cadde4] mdrun[0x8059f50] mdrun[0x805a72a] /lib/tls/i686/cmov/libc.so.6(__libc_start_main+0xe0)[0xb79f0050] mdrun[0x804a491] === Memory map: 08048000-08062000 r-xp 08:04 2490502/usr/bin/mdrun 08062000-08063000 rw-p 00019000 08:04 2490502/usr/bin/mdrun 08063000-08085000 rw-p 08063000 00:00 0 [heap] b780-b7821000 rw-p b780 00:00 0 b7821000-b790 ---p b7821000 00:00 0 b79cc000-b79cd000 rw-p b79cc000 00:00 0 b79cd000-b79cf000 r-xp 08:04 2747181/lib/tls/i686/cmov/libdl-2.6.1.so b79cf000-b79d1000 rw-p 1000 08:04 2747181/lib/tls/i686/cmov/libdl-2.6.1.so b79d1000-b79d5000 r-xp 08:04 2486327/usr/lib/libXdmcp.so.6.0.0 b79d5000-b79d6000 rw-p 3000 08:04 2486327/usr/lib/libXdmcp.so.6.0.0 b79d6000-b79d8000 r-xp 08:04 2485527/usr/lib/libXau.so.6.0.0 b79d8000-b79d9000 rw-p 1000 08:04 2485527/usr/lib/libXau.so.6.0.0 b79d9000-b79da000 rw-p b79d9000 00:00 0 b79da000-b7b1e000 r-xp 08:04 2747161/lib/tls/i686/cmov/libc-2.6.1.so b7b1e000-b7b1f000 r--p 00143000 08:04 2747161/lib/tls/i686/cmov/libc-2.6.1.so b7b1f000-b7b21000 rw-p 00144000 08:04 2747161/lib/tls/i686/cmov/libc-2.6.1.so b7b21000-b7b24000 rw-p b7b21000 00:00 0 b7b24000-b7c11000 r-xp 08:04 2486347/usr/lib/libX11.so.6.2.0 b7c11000-b7c15000 rw-p 000ed000 08:04 2486347/usr/lib/libX11.so.6.2.0 b7c15000-b7c2a000 r-xp 08:04 2488182/usr/lib/libICE.so.6.3.0 b7c2a000-b7c2c000 rw-p 00014000 08:04 2488182/usr/lib/libICE.so.6.3.0 b7c2c000-b7c2d000 rw-p b7c2c000 00:00 0 b7c2d000-b7c34000 r-xp 08:04 2487000/usr/lib/libSM.so.6.0.0 b7c34000-b7c35000 rw-p 6000 08:04 2487000/usr/lib/libSM.so.6.0.0 b7c35000-b7c58000 r-xp 08:04 2747187/lib/tls/i686/cmov/libm-2.6.1.so b7c58000-b7c5a000 rw-p 00023000 08:04 2747187/lib/tls/i686/cmov/libm-2.6.1.so b7c5a000-b7c6e000 r-xp 08:04 2747206/lib/tls/i686/cmov/libnsl-2.6.1.so b7c6e000-b7c7 rw-p 00013000 08:04 2747206/lib/tls/i686/cmov/libnsl-2.6.1.so b7c7-b7c73000 rw-p b7c7 00:00 0 b7c73000-b7e27000 r-xp 08:04 2491023/usr/lib/libgmx.so.4.0.0 b7e27000-b7e3 rw-p 001b3000 08:04 2491023/usr/lib/libgmx.so.4.0.0 b7e3-b7e35000 rw-p b7e3 00:00 0 b7e35000-b7f4a000 r-xp 08:04 2491025/usr/lib/libmd.so.4.0.0 b7f4a000-b7f4b000 rw-p 00114000 08:04 2491025/usr/lib/libmd.so.4.0.0 b7f4b000-b7f4c000 rw-p b7f4b000 00:00 0 b7f4e000-b7f58000 r-xp 08:04 2747267/lib/libgcc_s.so.1 b7f58000-b7f59000 rw-p a000 08:04 2747267/lib/libgcc_s.so.1 b7f59000-b7f5c000 rw-p b7f59000 00:00 0 b7f5c000-b7f76000 r-xp
[gmx-users] Protonate and OPLS
Dear gmx users The tool protonate also works for the OPLS force field or only for GMX? I tried and I did not obtain sucess! Bests eef -- ___ Eudes Eterno Fileti Centro de Ciência Naturais e Humanas Universidade Federal do ABC Rua Catequese, 242 - 3º Andar 09090-400 Santo André - SP Brasil Tel: +55 11 4437-1600 ramal 408 skype: eefileti http://cromo.ufabc.edu.br/~fileti/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Force tolarence
Hi Every one I was doing my model refinment or say energy minimization of it by steep decent the congugate gradient options. Each time i run the command grompp the process stop either after completing steps number or from cutoff Fmax. I anm not able to understand the variable Fmax. What i read that it is force tolerence. But this not clear my dout. If u can explain me the term or suggest any reading material it will be very helpful Another question can i use steep and cg in sequence i mean steep-cg-steep-cg like bye _ Get free e-mail at www.jkinstitute.org ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] protein/membrane simulation parameters
N-J.M. Macaluso a écrit : Hi, I have two questions that may seem quite simple, but I haven't found clear answers to them. It has to do with the md simulation parameters of a solvated protein/membrane system. The first question is about temperature. Some papers simulate at 300 K, others at 298 K, and others at physiological temperature (310 K). I decided that simulating at 310 K gives the most realistic picture of the system, as that is biological temp. Why do many studies use 300 K? Is it incorrect to use 310 K for this system? The goal of my work is solely to simulate a GPCR and perform virtual screening on it. First, as answered by Mark Abraham, look at the literature in order to see where and how the parameters were developped. most of the time parameters are not that easily transferable and you'll need to benchmark yourself with your simulation conditions (it should not be that different, but since the software is flexible, there is no 'a priori' guarantee). Second, in using membrane simulations, you need to pay attention to the lipid glass transition, since those lipids have often hight temperature glass transistion, no question why the DPPC simulations are mostly done at 323K (and why in publications where the temperature is below 317K the lipids tend to from a glass transition). I also decided to simulate the system at physiological salt concentration (.15 M [NaCl]). Will this alter the conformation of my protein significantly? Well, although my answer may not be the common one, i'm against using a physiological concentration. PME needs a neutralisation of the system in order to work so i simply add enough ioons to have an neutral one. The physiological concentration is non-sense into such a microscopic, unique solute (the protein), system. Never forget the concentration is an average over billions of molecules, transfering this rapidly to such a simplified system seems to me quite a rough approach. Furthermore i've not seen many papers mentionning the positive role of such density of ions, but more often datas about ions artifacts due to water ordering around ions. (there are exceptions, of course for example for ion-dependent channels, but since you are interested in GPCR ...). Last, do not forget that in physiological conditions, there is a big shift in concentrations from the exterior side to the interior side of the cell, for either chloride, sodium or potassium. Since there is no way to guarantee the shift would be conserved upon the simulation (an ion leaving the bottom of the box, on the intracellular side will enter the top of the box, on the extracellular side), this is another good reason to not disturb the simulations. You will probably get more input on this, but at least you have some arguments ... Cheers, Stéphane -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig INRA, Domaine de Vilvert Tél : (33) 134 652 891 78352 Jouy-en-Josas cedex, France Fax : (33) 134 652 901 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] can not pass gmxtest
hi, I just try to remove and rebuild and install GROMACS. This time the self-built one also can not pass the test. The same errors are reported: + [EMAIL PROTECTED]:~/gromacs-3.3.2$ sudo make tests (if test -d gmxtest; then cd gmxtest; ./gmxtest.pl all; cd ..; \ else echo No gmxtest directory found. Please download and unpack it here.;\ fi) *** glibc detected *** mdrun: realloc(): invalid next size: 0x08296ec8 *** === Backtrace: = /lib/tls/i686/cmov/libc.so.6[0x401b1b0c] /lib/tls/i686/cmov/libc.so.6(realloc+0x106)[0x401b3a66] mdrun[0x8137065] === Memory map: 08048000-08278000 r-xp 08:04 2567562/usr/local/gromacs/bin/mdrun 08278000-0827f000 rwxp 0023 08:04 2567562/usr/local/gromacs/bin/mdrun 0827f000-082a5000 rwxp 0827f000 00:00 0 [heap] 4000-4001a000 r-xp 08:04 2747274/lib/ld-2.6.1.so 4001a000-4001c000 rwxp 00019000 08:04 2747274/lib/ld-2.6.1.so 4001c000-4001f000 rwxp 4001c000 00:00 0 4001f000-40029000 r-xp 08:04 2747267/lib/libgcc_s.so.1 40029000-4002a000 rwxp a000 08:04 2747267/lib/libgcc_s.so.1 4002c000-4004 r-xp 08:04 2747206/lib/tls/i686/cmov/libnsl-2.6.1.so 4004-40042000 rwxp 00013000 08:04 2747206/lib/tls/i686/cmov/libnsl-2.6.1.so 40042000-40044000 rwxp 40042000 00:00 0 40044000-4011b000 r-xp 08:04 2488482/usr/lib/libfftw3f.so.3.1.2 4011b000-40121000 rwxp 000d7000 08:04 2488482/usr/lib/libfftw3f.so.3.1.2 40121000-40144000 r-xp 08:04 2747187/lib/tls/i686/cmov/libm-2.6.1.so 40144000-40146000 rwxp 00023000 08:04 2747187/lib/tls/i686/cmov/libm-2.6.1.so 40146000-4028a000 r-xp 08:04 2747161/lib/tls/i686/cmov/libc-2.6.1.so 4028a000-4028b000 r-xp 00143000 08:04 2747161/lib/tls/i686/cmov/libc-2.6.1.so 4028b000-4028d000 rwxp 00144000 08:04 2747161/lib/tls/i686/cmov/libc-2.6.1.so 4028d000-40291000 rwxp 4028d000 00:00 0 40291000-402a5000 r-xp 08:04 2747231/lib/tls/i686/cmov/libpthread-2.6.1.so 402a5000-402a7000 rwxp 00013000 08:04 2747231/lib/tls/i686/cmov/libpthread-2.6.1.so 402a7000-402aa000 rwxp 402a7000 00:00 0 4030-40321000 rwxp 4030 00:00 0 40321000-4040 ---p 40321000 00:00 0 bf808000-bf82 rwxp bf808000 00:00 0 [stack] e000-f000 r-xp 00:00 0 [vdso] FAILED. Check files in rb1 1 out of 16 simple tests FAILED FAILED. Check files in acetonitrilRF FAILED. Check files in dec+water 2 out of 14 complex tests FAILED All 63 kernel tests PASSED All 45 pdb2gmx tests PASSED + On Wed, 2007-11-07 at 16:45 +0800, Yang Ye wrote: To uninstall GROMACS, you can type which mdrun to get its path and try to figure out where it has been installed. For GROMACS, it may reside under /usr/local/gromacs remove the whole directory with rm -fr. To ensure that you are using the self-built GROMACS, look for a file GMXRC.bash in the locations which you can find in make install. Run it with source /path/to/GMXRC.bash Then you can make sure that you are using your own version. Put that line source ... into ~/.bashrc shall make it default for every login session. Regards, Yang Ye On 11/7/2007 4:35 PM, Li Qiang wrote: hi yang, thanks for the reply. Do you mean that the installation from SMP is not right? The error with self-compiled gromacs is in position restrain step with unusual distances and the mdrun stops at step0 with Segmentation fault (core dumped). but the mdrun with constraint can run, though I do not know if it is right. The possible reason is that I install from SMP of ubuntu but forget to remove the self-compiled one. Several days ago the gromacs version from SMP is 3.3.1. I though it was simpler to install GROMACS automatically from that. Could tell me how to remove GROMACS entirely so that I can reinstall from fresh? Hope we can do it. thank you very much. Li Qiang On Wed, 2007-11-07 at 16:16 +0800, Yang Ye wrote: Hi, You shall always try to build gromacs yourself. What's the error with tutorial? Regards, Yang Ye On 11/7/2007 10:14 AM, Li Qiang wrote: hi all, I newly installed GROMACS on UBUNTU 7.10 from Synaptic Package Manager(SPM). However, it can not pass the gamxtest with log as below, but Tutorials seems OK. Actually I try to compile myself at the beginning. It is weird that the self-compiled one can pass the test but failed to run Tutorials with Segmental fault at PR MD step. Does anyboby know how to solve it? and how to uninstall GROMACS clear? thanks a lot. output from gmxtest: ++ *** glibc detected *** mdrun: realloc(): invalid next size: 0x08076ec8 *** === Backtrace: = /lib/tls/i686/cmov/libc.so.6[0xb7a45b0c]
[gmx-users] Doubt Reg. Selection of force field and pdb2gmx program
Dear All, When I run the pdb2gmx (pdb2gmx -f xxx.pdb -ignh) it is asking to select a force field which is shown below. 0: GROMOS96 43a1 force field 1: GROMOS96 43b1 vacuum force field 2: GROMOS96 43a2 force field (improved alkane dihedrals) 3: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 4: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 5: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 6: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 7: [DEPRECATED] Gromacs force field (see manual) 8: [DEPRECATED] Gromacs force field with hydrogens for NMR 9: Encad all-atom force field, using scaled-down vacuum charges 10: Encad all-atom force field, using full solvent charges I wanted to select option 7 7: [DEPRECATED] Gromacs force field (see manual), but I am confused by [DEPRECATED], why this message and what dose it mean? Thanks in advance Regards Chandu ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] can not pass gmxtest
Li Qiang wrote: hi, I just try to remove and rebuild and install GROMACS. This time the self-built one also can not pass the test. The same errors are reported: + [EMAIL PROTECTED]:~/gromacs-3.3.2$ sudo make tests As a general rule, do not do installations and tests of installations as root. This makes it very easy to break your system. One symptom of a broken system is things not working any more. Sound familiar? If you have a need to install as root, then do the unpack, configure make ( make test) in your user space as yourself, and then sudo make install. This is just sensible... if someone messes up (the distributor, or more likely you) you'd much rather not be root. (if test -d gmxtest; then cd gmxtest; ./gmxtest.pl all; cd ..; \ else echo No gmxtest directory found. Please download and unpack it here.;\ fi) *** glibc detected *** mdrun: realloc(): invalid next size: 0x08296ec8 Perhaps the authors can suggest whether gmxtest.pl uses the GROMACS binary from the same source tree, or whichever is pointed to by GMXLIB. If the latter, then you probably still have something broken somewhere. On the above sudo evidence, I'd actually be tempted to scorched-earth your machine and re-install your OS rather than mess around any more. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Protonate and OPLS
Eudes Fileti wrote: Dear gmx users The tool protonate also works for the OPLS force field or only for GMX? I tried and I did not obtain sucess! Read protonate -h and you will find out whether it is force field dependent. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Doubt Reg. Selection of force field and pdb2gmx program
[EMAIL PROTECTED] wrote: Dear All, When I run the pdb2gmx (pdb2gmx -f xxx.pdb -ignh) it is asking to select a force field which is shown below. 0: GROMOS96 43a1 force field 1: GROMOS96 43b1 vacuum force field 2: GROMOS96 43a2 force field (improved alkane dihedrals) 3: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 4: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 5: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 6: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 7: [DEPRECATED] Gromacs force field (see manual) 8: [DEPRECATED] Gromacs force field with hydrogens for NMR 9: Encad all-atom force field, using scaled-down vacuum charges 10: Encad all-atom force field, using full solvent charges I wanted to select option 7 7: [DEPRECATED] Gromacs force field (see manual), but I am confused by [DEPRECATED], why this message and what dose it mean? http://en.wikipedia.org/wiki/Deprecated Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Force tolarence
ss aa wrote: Hi Every one I was doing my model refinment or say energy minimization of it by steep decent the congugate gradient options. Each time i run the command grompp the process stop either after completing steps number or from cutoff Fmax. I anm not able to understand the variable Fmax. What i read that it is force tolerence. But this not clear my dout. If u can explain me the term or suggest any reading material it will be very helpful Please write in full sentences and check your spelling. If you want free help, you should make it easy for people to read and understand you. On point, you should be reading the GROMACS manual about energy minimization. Another question can i use steep and cg in sequence i mean steep-cg-steep-cg like Yes. Whether that does you any good is another matter. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: mdrun -rerun and box size bug not fixed?
Dear all, By reactivating the barostat as mentioned below, I managed to recover LJ energies within 0.1% for my test system, which was a box of 1136 waters. So I applied the same thing to my system of interest (a 605 residue protein with around 25000 waters). The only difference is that the run was done with PME, and the rerun is done with RF, so I cannot compare electrostatics. For the other energies I get a systematic bias with respect to the original run, for example : - LJ : 70 +-50 kJ/mol higher than original (0.05% of total) - g96 bonds : 160 +-60 kJ/mol higher than original (2.44% of total) These biases are very reproducible over many trajectories with this system. The LJ bias might be considered negligible as it is a small percentage of the total LJ energy. However, the g96 bond bias is surprising (bonds are present only in the protein). We expect that the inaccuracy of the xtc coordinates generates some random noise. But I don't understand how it could generate a systematic error of that magnitude (2.44%) ... I tried to change different parameters to trace the origin of this bias : version of gmx, platform, huge compressibility, turning off the thermostats (for the g96 bond part), etc... Only turning the constraints off influenced the results, yielding an even higher bias towards higher g96 energies (210 +-60 kJ/mol). Have such inaccuracies been observed before with -rerun? Am I doing something wrong or is there no hope of recovering better energies with a rerun? Thanks, Michel Original Message Subject:Re: mdrun -rerun and box size bug not fixed? Date: Tue, 06 Nov 2007 14:12:29 +0100 From: Michel Cuendet [EMAIL PROTECTED] To: gmx-users@gromacs.org References: [EMAIL PROTECTED] Hi, I think I got it :-) Using gmx 3.3.1 with the same thermostat and barostat settings as the original run, I get the right LJ energies within 0.1%. I used tcoupl and pcoupl = no because I somehow remembered that thermostats could do weird things when rerunning (see the old thread : http://www.gromacs.org/pipermail/gmx-developers/2005-August/001290.html ) But apparently the box is not reread form the trajectory if the pcoupl option is deactivated. It would be much safer for users if the appropriate options were automatically set when -rerun in invoked: nstlist = 1 nstenergy = 1 NO rescaling of velocities NO rescaling of box size Do read the box sizes from the trajectory Cheers, Michel == Michel Cuendet, Ph.D Molecular Modeling Group Swiss Institute of Bioinformatics CH-1015 Lausanne, Switzerland www.isb-sib.ch/groups/Molecular_Modeling.htm == -- == Michel Cuendet, Ph.D Molecular Modeling Group Swiss Institute of Bioinformatics CH-1015 Lausanne, Switzerland www.isb-sib.ch/groups/Molecular_Modeling.htm == ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Where is the GROMOS87 force field when using pdb2gmx
maria goranovic wrote: Hi, I am trying to use pdb2gmx to make a topology file for my protein using gromos87 (ffgmx). However, when I run pdb2gmx, I only get the following options. Where is GROMOS87 ?? 0: GROMOS96 43a1 force field 1: GROMOS96 43b1 vacuum force field 2: GROMOS96 43a2 force field (improved alkane dihedrals) 3: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 4: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 5: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 6: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 7: [DEPRECATED] Gromacs force field (see manual) 8: [DEPRECATED] Gromacs force field with hydrogens for NMR 9: Encad all-atom force field, using scaled-down vacuum charges 10: Encad all-atom force field, using full solvent charges if you really really really need it, it is still there. You can run pdb2gmx -ff gmx -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Where is the GROMOS87 force field when using pdb2gmx
Hi, I am trying to use pdb2gmx to make a topology file for my protein using gromos87 (ffgmx). However, when I run pdb2gmx, I only get the following options. Where is GROMOS87 ?? 0: GROMOS96 43a1 force field 1: GROMOS96 43b1 vacuum force field 2: GROMOS96 43a2 force field (improved alkane dihedrals) 3: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 4: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 5: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 6: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 7: [DEPRECATED] Gromacs force field (see manual) 8: [DEPRECATED] Gromacs force field with hydrogens for NMR 9: Encad all-atom force field, using scaled-down vacuum charges 10: Encad all-atom force field, using full solvent charges -- Maria G. Technical University of Denmark Copenhagen ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] gmx 3.3.2 explodes with libc.so.6
Hi there, Gromacs explodes with new version of libc :-) G R O M A C S (-: *** buffer overflow detected ***: editconf terminated === Backtrace: = /lib/libc.so.6(__chk_fail+0x44)[0xb7a4bb34] /lib/libc.so.6[0xb7a4aff7] /usr/lib/libgmx.so.4(get_libdir+0x2bc)[0xb7c1841c] /usr/lib/libgmx.so.4(low_libfn+0x1b2)[0xb7c18652] /usr/lib/libgmx.so.4(low_libopen+0x2c)[0xb7c1870c] /usr/lib/libgmx.so.4[0xb7c0ed28] /usr/lib/libgmx.so.4(bromacs+0x33)[0xb7c0f093] /usr/lib/libgmx.so.4(CopyRight+0x63)[0xb7c0f103] /usr/lib/libgmxana.so.4(gmx_editconf+0x151)[0xb7f6c901] editconf[0x80484c2] /lib/libc.so.6(__libc_start_main+0xdc)[0xb799505c] editconf[0x8048411] === Memory map: 08048000-08049000 r-xp 03:01 549330 /usr/bin/editconf 08049000-0804a000 rwxp 03:01 549330 /usr/bin/editconf 0804a000-0806b000 rwxp 0804a000 00:00 0 [heap] b7966000-b797 r-xp 03:01 2366571/lib/libgcc_s.so.1 b797-b7971000 rwxp a000 03:01 2366571/lib/libgcc_s.so.1 b7971000-b7972000 rwxp b7971000 00:00 0 b7972000-b7974000 r-xp 03:01 2366509/lib/libdl-2.5.so b7974000-b7976000 rwxp 1000 03:01 2366509/lib/libdl-2.5.so b7976000-b7977000 rwxp b7976000 00:00 0 b7977000-b797b000 r-xp 03:01 543574 /usr/lib/libXdmcp.so.6.0.0 b797b000-b797c000 rwxp 3000 03:01 543574 /usr/lib/libXdmcp.so.6.0.0 b797c000-b797e000 r-xp 03:01 543576 /usr/lib/libXau.so.6.0.0 b797e000-b797f000 rwxp 1000 03:01 543576 /usr/lib/libXau.so.6.0.0 b797f000-b7a9f000 r-xp 03:01 2366503/lib/libc-2.5.so b7a9f000-b7aa r-xp 0011f000 03:01 2366503/lib/libc-2.5.so b7aa-b7aa2000 rwxp 0012 03:01 2366503/lib/libc-2.5.so b7aa2000-b7aa5000 rwxp b7aa2000 00:00 0 b7aa5000-b7b8f000 r-xp 03:01 543578 /usr/lib/libX11.so.6.2.0 b7b8f000-b7b93000 rwxp 000e9000 03:01 543578 /usr/lib/libX11.so.6.2.0 b7b93000-b7ba7000 r-xp 03:01 543754 /usr/lib/libICE.so.6.3.0 b7ba7000-b7ba8000 rwxp 00013000 03:01 543754 /usr/lib/libICE.so.6.3.0 b7ba8000-b7bab000 rwxp b7ba8000 00:00 0 b7bab000-b7bb2000 r-xp 03:01 543756 /usr/lib/libSM.so.6.0.0 b7bb2000-b7bb3000 rwxp 6000 03:01 543756 /usr/lib/libSM.so.6.0.0 b7bb3000-b7bd7000 r-xp 03:01 2366511/lib/libm-2.5.so b7bd7000-b7bd9000 rwxp 00023000 03:01 2366511/lib/libm-2.5.so b7bd9000-b7bea000 r-xp 03:01 2366513/lib/libnsl-2.5.so b7bea000-b7bec000 rwxp 00011000 03:01 2366513/lib/libnsl-2.5.so b7bec000-b7bee000 rwxp b7bec000 00:00 0 b7bee000-b7da2000 r-xp 03:01 549411 /usr/lib/libgmx.so.4.0.0 b7da2000-b7dab000 rwxp 001b3000 03:01 549411 /usr/lib/libgmx.so.4.0.0 b7dab000-b7db rwxp b7dab000 00:00 0 b7db-b7ec5000 r-xp 03:01 549415 /usr/lib/libmd.so.4.0.0 b7ec5000-b7ec6000 rwxp 00114000 03:01 549415 /usr/lib/libmd.so.4.0.0 b7ec6000-b7ec7000 rwxp b7ec6000 00:00 0 b7ec7000-b7fb r-xp 03:01 549413 /usr/lib/libgmxana.so.4.0.0 b7fb-b7fb7000 rwxp 000e8000 03:01 549413 /usr/lib/libgmxana.so.4.0.0 b7fb7000-b7fb9000 rwxp b7fb7000 00:00 0 b7fd2000-b7fd3000 r-xp b7fd2000 00:00 0 [vdso] b7fd3000-b7fea000 r-xp 03:01 2366497/lib/ld-2.5.so b7fea000-b7fec000 rwxp 00016000 03:01 2366497/lib/ld-2.5.so bfd84000-bfd98000 rwxp bfd84000 00:00 0 [stack] bfd98000-bfd99000 rw-p bfd98000 00:00 0 [EMAIL PROTECTED] tmp]$ rpm -qf /lib/libc.so.6 glibc-core-2.5-alt4 Any ideas? Dima ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] combining gromos96 (43a2) and berger lipid force field
I want to use the gromos96 force field for the protein, and Tieleman's Berger force field for the lipids. How do I combine force fields or construct a topology. I have different topologies for the lipids and the protein ready. However combining them would probably lead to errors as I cannot include both the ffG43a2 and the ffgmx force fields in the same topology ? Thanks for the help, -Maria -- Maria G. Technical University of Denmark Copenhagen ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Sulfate parameters anyone ?
Check the .rtp file for your force field. If present, it will likely be listed as something like SO4 or SO42-. -Justin Quoting maria goranovic [EMAIL PROTECTED]: Sulfate ions are not present in the ions.itp file in the force field in gromacs Someone must have constructed parameters for these ions before ? If so, could you please share them ? Thank you -Maria -- Maria G. Technical University of Denmark Copenhagen ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php = Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ = ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Where is the GROMOS87 force field when using pdb2gmx
Thanks for the help, David. Actually, I just realized I was trying to decide based on mailing list archives which, in some cases, are 5 years old. My mistake. I will use the 43a2 field for my protein. Is there any standard procedure to combine 43a2 with the berger force field (ffgmx) for lipids ? -- Maria G. Technical University of Denmark Copenhagen ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: Where is the GROMOS87 force field when using pdb2gmx
maria goranovic wrote: U. Something wrong with using GROMOS87 ? I thought that was the one most commonly used for proteins ? Not really, if you look in numbers I'd guess Amber is the most popular. The G87 ff is 20 years old, and the Van Gunsteren group has already published updates in 1996 and most recently in 2005. There are known problems with it and you may indeed have problems defending your choice of force field for publications. Thanks -Maria On Nov 7, 2007 4:48 PM, maria goranovic [EMAIL PROTECTED] wrote: ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] combining gromos96 (43a2) and berger lipid force field
The quick answer would be to look at the ffgmx forcefield, and the ffgmx/Berger hybrid that can be obtained (either from Tieleman or the Gromacs website, I forget) and work out how the former was incorporated into the latter. Then replicate that for ffG43a2. Not necessarily simple or even valid, but that's MD for you. - Original Message From: maria goranovic [EMAIL PROTECTED] To: gmx-users@gromacs.org Sent: Wednesday, November 7, 2007 7:24:11 PM Subject: [gmx-users] combining gromos96 (43a2) and berger lipid force field I want to use the gromos96 force field for the protein, and Tieleman's Berger force field for the lipids. How do I combine force fields or construct a topology. I have different topologies for the lipids and the protein ready. However combining them would probably lead to errors as I cannot include both the ffG43a2 and the ffgmx force fields in the same topology ? Thanks for the help, -Maria -- Maria G. Technical University of Denmark Copenhagen ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Sulfate parameters anyone ?
Sulfate ions are not present in the ions.itp file in the force field in gromacs Someone must have constructed parameters for these ions before ? If so, could you please share them ? Thank you -Maria -- Maria G. Technical University of Denmark Copenhagen ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: mdrun -rerun and box size bug not fixed?
Hi, By reactivating the barostat as mentioned below, I managed to recover LJ energies within 0.1% for my test system, which was a box of 1136 waters. So I applied the same thing to my system of interest (a 605 residue protein with around 25000 waters). The only difference is that the run was done with PME, and the rerun is done with RF, so I cannot compare electrostatics. For the other energies I get a systematic bias with respect to the original run, for example : - LJ : 70 +-50 kJ/mol higher than original (0.05% of total) - g96 bonds : 160 +-60 kJ/mol higher than original (2.44% of total) These biases are very reproducible over many trajectories with this system. The LJ bias might be considered negligible as it is a small percentage of the total LJ energy. However, the g96 bond bias is surprising (bonds are present only in the protein). We expect that the inaccuracy of the xtc coordinates generates some random noise. But I don't understand how it could generate a systematic error of that magnitude (2.44%) ... I tried to change different parameters to trace the origin of this bias : version of gmx, platform, huge compressibility, turning off the thermostats (for the g96 bond part), etc... Only turning the constraints off influenced the results, yielding an even higher bias towards higher g96 energies (210 +-60 kJ/mol). Have such inaccuracies been observed before with -rerun? Am I doing something wrong or is there no hope of recovering better energies with a rerun? We routinely do reprocessing with the *same* settings we run with (this is in the NVT ensemble, usually) and recover energies that are very close (i.e. what one would expect from the trajectory precision). Note this is using full precision trajectories, though. See for example http://dx.doi.org/10.1021/jp0735987. So I guess what I'm saying is that in principle you should be able to get good energies with rerun. Maybe you should try and narrow down the problem by doing some testing: (a) Do some reprocessing with PME rather than RF to see if that helps. (b) Do some reprocessing on full precision trajectories rather than xtcs to rule out precision issues etc. Best wishes, David Thanks, Michel Original Message Subject:Re: mdrun -rerun and box size bug not fixed? Date: Tue, 06 Nov 2007 14:12:29 +0100 From: Michel Cuendet [EMAIL PROTECTED] To: gmx-users@gromacs.org References: [EMAIL PROTECTED] Hi, I think I got it :-) Using gmx 3.3.1 with the same thermostat and barostat settings as the original run, I get the right LJ energies within 0.1%. I used tcoupl and pcoupl = no because I somehow remembered that thermostats could do weird things when rerunning (see the old thread : http://www.gromacs.org/pipermail/gmx-developers/2005-August/001290.html ) But apparently the box is not reread form the trajectory if the pcoupl option is deactivated. It would be much safer for users if the appropriate options were automatically set when -rerun in invoked: nstlist = 1 nstenergy = 1 NO rescaling of velocities NO rescaling of box size Do read the box sizes from the trajectory Cheers, Michel == Michel Cuendet, Ph.D Molecular Modeling Group Swiss Institute of Bioinformatics CH-1015 Lausanne, Switzerland www.isb-sib.ch/groups/Molecular_Modeling.htm == -- == Michel Cuendet, Ph.D Molecular Modeling Group Swiss Institute of Bioinformatics CH-1015 Lausanne, Switzerland www.isb-sib.ch/groups/Molecular_Modeling.htm == ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] installation error
hi I had installed make_hole utility earlier but when i tried to run: make_hole.pl -f box_popc.pdb -o hole_popc.pdb -r 9.0 -lipat P8 -lipid POPC -cx 51.5 -cy 51.8 I get : bash: make_hole.pl: command not found. I tried reinstalling it by ./configure which completed successfully but when i ran make command i get the following error: nonbonded.c:272: error: `esolSPC' undeclared (first use in this function) nonbonded.c:272: error: (Each undeclared identifier is reported only once nonbonded.c:272: error: for each function it appears in.) nonbonded.c:276: error: `esolTIP4P' undeclared (first use in this function) nonbonded.c:472: error: `enlistWATER' undeclared (first use in this function) nonbonded.c:476: error: `enlistWATERWATER' undeclared (first use in this function) nonbonded.c: In function `do_nonbonded14': nonbonded.c:542: error: `eelRF_NEC' undeclared (first use in this function) nonbonded.c:569: error: `epbcFULL' undeclared (first use in this function) make[5]: *** [nonbonded.lo] Error 1 make[5]: Leaving directory `/home/saivikram/Desktop/gromacs/gromacs-3.3.1/src/gmxlib/nonbonded' make[4]: *** [all-recursive] Error 1 make[4]: Leaving directory `/home/saivikram/Desktop/gromacs/gromacs-3.3.1/src/gmxlib/nonbonded' make[3]: *** [all-recursive] Error 1 make[3]: Leaving directory `/home/saivikram/Desktop/gromacs/gromacs-3.3.1/src/gmxlib' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/saivikram/Desktop/gromacs/gromacs-3.3.1/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/home/saivikram/Desktop/gromacs/gromacs-3.3.1/src' make: *** [all-recursive] Error 1 Please help me _ Check out some new online services at Windows Live Ideas—so new they haven’t even been officially released yet. http://www.msnspecials.in/windowslive/___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] gmx 3.3.2 explodes with libc.so.6
The problem was solved by updating system libraries. [EMAIL PROTECTED] exchange]# rpm -qf /lib/libc.so.6 glibc-core-2.5-alt5 Sorry, for wrong hypothesis. Dima ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] gmx 3.3.2 explodes with libc.so.6
Dmytro Kovalskyy wrote: Hi there, Gromacs explodes with new version of libc Did you compile it yourself? Could you please recompile it with CFLAGS=-g and try to debug it? Which OS and compilers did tou use? :-) G R O M A C S (-: *** buffer overflow detected ***: editconf terminated === Backtrace: = /lib/libc.so.6(__chk_fail+0x44)[0xb7a4bb34] /lib/libc.so.6[0xb7a4aff7] /usr/lib/libgmx.so.4(get_libdir+0x2bc)[0xb7c1841c] /usr/lib/libgmx.so.4(low_libfn+0x1b2)[0xb7c18652] /usr/lib/libgmx.so.4(low_libopen+0x2c)[0xb7c1870c] /usr/lib/libgmx.so.4[0xb7c0ed28] /usr/lib/libgmx.so.4(bromacs+0x33)[0xb7c0f093] /usr/lib/libgmx.so.4(CopyRight+0x63)[0xb7c0f103] /usr/lib/libgmxana.so.4(gmx_editconf+0x151)[0xb7f6c901] editconf[0x80484c2] /lib/libc.so.6(__libc_start_main+0xdc)[0xb799505c] editconf[0x8048411] === Memory map: 08048000-08049000 r-xp 03:01 549330 /usr/bin/editconf 08049000-0804a000 rwxp 03:01 549330 /usr/bin/editconf 0804a000-0806b000 rwxp 0804a000 00:00 0 [heap] b7966000-b797 r-xp 03:01 2366571/lib/libgcc_s.so.1 b797-b7971000 rwxp a000 03:01 2366571/lib/libgcc_s.so.1 b7971000-b7972000 rwxp b7971000 00:00 0 b7972000-b7974000 r-xp 03:01 2366509/lib/libdl-2.5.so b7974000-b7976000 rwxp 1000 03:01 2366509/lib/libdl-2.5.so b7976000-b7977000 rwxp b7976000 00:00 0 b7977000-b797b000 r-xp 03:01 543574 /usr/lib/libXdmcp.so.6.0.0 b797b000-b797c000 rwxp 3000 03:01 543574 /usr/lib/libXdmcp.so.6.0.0 b797c000-b797e000 r-xp 03:01 543576 /usr/lib/libXau.so.6.0.0 b797e000-b797f000 rwxp 1000 03:01 543576 /usr/lib/libXau.so.6.0.0 b797f000-b7a9f000 r-xp 03:01 2366503/lib/libc-2.5.so b7a9f000-b7aa r-xp 0011f000 03:01 2366503/lib/libc-2.5.so b7aa-b7aa2000 rwxp 0012 03:01 2366503/lib/libc-2.5.so b7aa2000-b7aa5000 rwxp b7aa2000 00:00 0 b7aa5000-b7b8f000 r-xp 03:01 543578 /usr/lib/libX11.so.6.2.0 b7b8f000-b7b93000 rwxp 000e9000 03:01 543578 /usr/lib/libX11.so.6.2.0 b7b93000-b7ba7000 r-xp 03:01 543754 /usr/lib/libICE.so.6.3.0 b7ba7000-b7ba8000 rwxp 00013000 03:01 543754 /usr/lib/libICE.so.6.3.0 b7ba8000-b7bab000 rwxp b7ba8000 00:00 0 b7bab000-b7bb2000 r-xp 03:01 543756 /usr/lib/libSM.so.6.0.0 b7bb2000-b7bb3000 rwxp 6000 03:01 543756 /usr/lib/libSM.so.6.0.0 b7bb3000-b7bd7000 r-xp 03:01 2366511/lib/libm-2.5.so b7bd7000-b7bd9000 rwxp 00023000 03:01 2366511/lib/libm-2.5.so b7bd9000-b7bea000 r-xp 03:01 2366513/lib/libnsl-2.5.so b7bea000-b7bec000 rwxp 00011000 03:01 2366513/lib/libnsl-2.5.so b7bec000-b7bee000 rwxp b7bec000 00:00 0 b7bee000-b7da2000 r-xp 03:01 549411 /usr/lib/libgmx.so.4.0.0 b7da2000-b7dab000 rwxp 001b3000 03:01 549411 /usr/lib/libgmx.so.4.0.0 b7dab000-b7db rwxp b7dab000 00:00 0 b7db-b7ec5000 r-xp 03:01 549415 /usr/lib/libmd.so.4.0.0 b7ec5000-b7ec6000 rwxp 00114000 03:01 549415 /usr/lib/libmd.so.4.0.0 b7ec6000-b7ec7000 rwxp b7ec6000 00:00 0 b7ec7000-b7fb r-xp 03:01 549413 /usr/lib/libgmxana.so.4.0.0 b7fb-b7fb7000 rwxp 000e8000 03:01 549413 /usr/lib/libgmxana.so.4.0.0 b7fb7000-b7fb9000 rwxp b7fb7000 00:00 0 b7fd2000-b7fd3000 r-xp b7fd2000 00:00 0 [vdso] b7fd3000-b7fea000 r-xp 03:01 2366497/lib/ld-2.5.so b7fea000-b7fec000 rwxp 00016000 03:01 2366497/lib/ld-2.5.so bfd84000-bfd98000 rwxp bfd84000 00:00 0 [stack] bfd98000-bfd99000 rw-p bfd98000 00:00 0 [EMAIL PROTECTED] tmp]$ rpm -qf /lib/libc.so.6 glibc-core-2.5-alt4 Any ideas? Dima ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] cannot compute sizeof (int), 77 on AIX 5.3 PPC p575 (searched the list)
Dear GMXers I got the error message cannot compute sizeof (int) when I tried to configure GMX3.3.1 on IBM PPC p575 AIX5.3, this is how I did it: for fftw2.1.5 export CC=xlc_r -q64 -qhot export CXX=xlC_r -q64 -qhot export OBJECT_MODE=64 export FFLAGS=-O3 -qarch=pwr4 -qtune=pwr4 -qmaxmem=-1 export CFLAGS=-O3 -qarch=pwr4 -qtune=pwr4 -qmaxmem=-1 ./configure --prefix=/home/usr/programs/fftw215 --enable-float --enable-mpi --enable-thread make make install for GMX3.3.1 export CPPFLAGS=-I/home/usr/programs/fftw215/include export LDFLAGS=-I/home/usr/programs/fftw215/lib ./configure --prefix=/home/usr/programs/gromacs331mpi --with-fft=fftw2 --without-x --disable-fortran --enable-mpi --enable-float then I got the following error: checking size of int... configure: error: cannot compute sizeof (int), 77 have you guys ever experienced this problem before? Any suggestions are appreciated! Yours Xin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Where is the GROMOS87 force field when using pdb2gmx
U. Something wrong with using GROMOS87 ? I thought that was the one most commonly used for proteins ? Thanks -Maria On Nov 7, 2007 4:48 PM, maria goranovic [EMAIL PROTECTED] wrote: ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] box explodes after 13ns
Dear Gromacs users, I am running a 50ns simulations of the unbinding of two peptide strands, the calculation runs smoothly but then after 13ns the box start to explode for several ps and then it returns to normal size and this goes on. The calculation doesn't crash. I am wondering if there is anything I should change in my Mdp file so that my box doesn't explode? here is my mdp file: ; RUN CONTROL PARAMETERS = integrator = md ; start time and timestep in ps = tinit= 0 dt = 0.002 nsteps = 2500 ; 50ns ; number of steps for center of mass motion removal = nstcomm = 100 ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 1000 nstvout = 1000 nstfout = 1000 ; Output frequency for energies to log file and energy file = nstlog = 1000 nstenergy= 1000 ; Output frequency and precision for xtc file = nstxtcout= 0 xtc-precision= 1000 ; This selects the subset of atoms for the xtc file. You can = ; select multiple groups. By default all atoms will be written. = ;xtc_grps = ; NEIGHBORSEARCHING PARAMETERS = ; nblist update frequency = nstlist = 10 ; ns algorithm (simple or grid) = ns_type = grid ; Periodic boundary conditions: xyz or none = pbc = xyz ; nblist cut-off = rlist= 1.0 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW = ; Method for doing electrostatics = coulombtype = pme ;rcoulomb-switch = 0 rcoulomb = 1.0 ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon-r= 1 ; Method for doing Van der Waals = vdw-type = switch ; cut-off lengths= rvdw-switch = 0.8 rvdw = 0.9 ; Apply long range dispersion corrections for Energy and Pressure = DispCorr = EnerPres ; Spacing for the PME/PPPM FFT grid = fourierspacing = 0.1 ; FFT grid size, when a value is 0 fourierspacing will be used = fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters = pme_order= 6 ewald_rtol = 1e-06 epsilon_surface = 0 optimize_fft = no ;restraints dihre=simple dihre-fc=1 nstdihreout=1000 disre=simple disre_fc=1 ;OPTIONS FOR TEMPERATURE COUPLING Tcoupl = berendsen tc_grps = Protein Non-Protein tau_t= 0.1 0.1 ref_t= 300 300 ;OPTIONS FOR PRESSURE COUPLING Pcoupl = berendsen tau_p= 0.5 compressibility = 4.5e-05 ref_p= 1.0 ; Free energy control stuff free_energy = no sc_alpha =0.5 sc-power =1.0 sc-sigma = 0.3 ; GENERATE VELOCITIES FOR STARTUP RUN = gen_vel = yes gen_temp = 300 gen_seed = -1 ; OPTIONS FOR BONDS = constraints = all-bonds ; Type of constraint algorithm = constraint-algorithm = Lincs ; Do not constrain the start configuration = unconstrained-start = no ; Relative tolerance of shake = shake-tol= 0.0001 ; Highest order in the expansion of the constraint coupling matrix = lincs-order = 12 ; Lincs will write a warning to the stderr if in one step a bond = ; rotates over more degrees than = lincs-warnangle = 30 lincs_iter =4 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] segmentation fault
vinod kumar wrote: hi a segmentation fault occurs , when i run a system in mac os, but not in fedora can some one help me with this not unless you give us more details. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] soft-core and coulomb transformation
On Mon, 5 Nov 2007, David Mobley wrote: Hi, i am extremely sorry here.. i am plotting dg/dl vs lambda of reverse transformation onto that of forward with both axes reversed. so i should expect overlap. this is consistent with whatever you are saying. i am sorry for negligence and confusion. And taking the negative? yes but when i use SC while coulomb transforamtion also, as in LJ transformation, the curves overlap. Now the question is why is it necessary to use SC during charge transformation to get overlap of the curves. It makes no sense at least to me. My experience has been that when you turn on soft core, you get a lambda-dependent shape of the dG/dlambda curve *regardless* of what transformation you're doing (i.e., even if you're doing NOTHING). i too see the dependence. I don't understand what do you mean by doing NOTHING. Do you mean that initial and final states are the same, so the net change is NOTHING? Yes, when making no change to a molecule, there's still a lambda dependence with soft core. I assume this has to do with details of the implementation. It's only the TOTAL free energy change that is zero. Since both of your transformations here are small, with soft core on, your curve shape will be dominated by that characteristic shape from soft core, and so it will *appear* that your curves overlap perfectly. i have no experience of large transformations, but, i think, even there also the characteristic shape would be observed. anyway, only difference potentials are contributing and non-bonded interactions, which are getting soft-cored, will be too many than bonded ones (if you perturb bonded-interactions also). May be i am wrong, as bonded interactions are much stronger than nonbonded which would cancel the nonbonded contributions. My point is just that if you're trying to see signal (lambda dependence that is not due to soft core) buried in noise (the characteristic soft core shape of the curve) the signal has to be significant. Now, the modified question: why is there no overlap of the graph in the absence of SC potentials for charge transformations (again when plotted on the reverse scales, both x and y)?? The overall mod(dG) is also not same for both the simulations. I am not sure whether it is because of undersampling.. i don't think so. I am clueless. What exactly do you mean by no overlap? i.e., if you compute the two DeltaG values, how different is DeltaG_forward from -DeltaG_reverse? How does the difference compare to your computed uncertainty? All I can tell you at this point is that, if you are doing enough sampling, you have everything set up properly, and there are no bugs, DeltaG_forward MUST be equal to -DeltaG_reverse (within error). The amount of help we can provide is directly related to how much information you give; when you just say they don't overlap, it's hard to do anything to help. You could try providing us with dG/dl values at each lambad, or even with your topologies and run scripts so I can reproduce what you're doing i have sent the files to you off-list.. plz have a look at. thanks bharat David bharat please help. bharat You need to provide more detail on your protocol. David i tried this for simple ala-gly and ethane-methane transformations. please give me some insight into the problem... bharat -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting!
Re: [gmx-users] cannot compute sizeof (int), 77 on AIX 5.3 PPC p575 (searched the list)
liu xin wrote: Dear GMXers I got the error message cannot compute sizeof (int) when I tried to configure GMX3.3.1 on IBM PPC p575 AIX5.3, this is how I did it: for fftw2.1.5 export CC=xlc_r -q64 -qhot export CXX=xlC_r -q64 -qhot export OBJECT_MODE=64 export FFLAGS=-O3 -qarch=pwr4 -qtune=pwr4 -qmaxmem=-1 export CFLAGS=-O3 -qarch=pwr4 -qtune=pwr4 -qmaxmem=-1 ./configure --prefix=/home/usr/programs/fftw215 --enable-float --enable-mpi --enable-thread make make install for GMX3.3.1 export CPPFLAGS=-I/home/usr/programs/fftw215/include export LDFLAGS=-I/home/usr/programs/fftw215/lib ./configure --prefix=/home/usr/programs/gromacs331mpi --with-fft=fftw2 --without-x --disable-fortran --enable-mpi --enable-float then I got the following error: checking size of int... configure: error: cannot compute sizeof (int), 77 So the program configure tries to compile and run to check the size of int didn't work. have you guys ever experienced this problem before? Any suggestions are appreciated! Look at the last several hundred lines of output in config.log and see what the problem was. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] installation error
pragya chohan wrote: hi I had installed make_hole utility earlier but when i tried to run: make_hole.pl -f box_popc.pdb -o hole_popc.pdb -r 9.0 -lipat P8 -lipid POPC -cx 51.5 -cy 51.8 I get : bash: make_hole.pl: command not found. So make-hole.pl, or something in its shebang line is probably not in your path. I tried reinstalling it by ./configure which completed successfully but when i ran make command i get the following error: This is the output from configuring GROMACS, not make_hole.pl In any case, you should do make distclean between runs of configure with different settings, and/or system configuration. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] combining gromos96 (43a2) and berger lipid force field
maria goranovic wrote: I want to use the gromos96 force field for the protein, and Tieleman's Berger force field for the lipids. How do I combine force fields or construct a topology. I have different topologies for the lipids and the protein ready. However combining them would probably lead to errors as I cannot include both the ffG43a2 and the ffgmx force fields in the same topology ? See http://wiki.gromacs.org/index.php/Force_Fields Since you've only recently chosen gromos96, how about instead choosing a forcefield for which lipid parameters have been developed in concert? See the literature for ideas on what works here. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Periodic Boundary conditions
I am running v3.3.2. I am running an RNA strand with a homemade potential. When I run a single molecule in a periodic box, the system is fine until one nucleic acid crosses the boundary. THen the entire nucleic acid gets moved to the opposite side of the box. Since there are bonds this results in an exploding system. I am running on 4 processors and am using the following mdp file. Any ideas what is going on? The system runs normally for over 20 time steps. It runs fine until the boundary issue occurs. title= Paul Template ;Preprocessor cpp = cpp ;Run control: A leap-frog algorithm for integrating Newton's equations. integrator = sd :time step in femtoseconds dt = 0.0005 ;number of stepsi nsteps = 1000 ;frequency to write coordinates to output trajectory file nstxout = 0 ;frequency to write velocities to output trajectory file nstvout = 0 ;frequency to write energies to log file nstlog = 1000 ;frequency to write energies to energy file nstenergy= 1000 ;frequency to write coordinates to xtc trajectory nstxtcout= 1000 ;group(s) to write to xtc trajectory xtc_grps = system ;group(s) to write to energy file energygrps = system ;Frequency to update the neighbor list (and the long-range forces, ;when using twin-range cut-off's). nstlist = 50 coulombtype = Cut-off ;Make a grid in the box and only check atoms in neighboring grid cells ;when constructing a new neighbor list every nstlist steps. ns_type = grid ;cut-off distance for the short-range neighbor list rlist= 2.5 ;treatment of electrostatic interactions table_extension = 150.0 rcoulomb = 2.5 epsilon_r= 0 ;treatment of van der waals interactions rvdw = 2.5 ; Periodic boudary conditions in all the directions pbc = full ;Temperature coupling tc-grps = system tau_t= 10.0 ref_t= 100 ;Pressure coupling Pcoupl = no ;Velocity generation gen_vel = yes gen_temp = 100 gen_seed = 12345 ;Constrain all bonds constraints = none ;constraint_algorithm= lincs ;lincs_iter=8 comm_mode = angular thanks -Paul ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] segmentation fault
hi a segmentation fault occurs , when i run a system in mac os, but not in fedora can some one help me with this ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
