Re: [gmx-users] freeze water
What procedure will be better? Freeze or position restrain? Anthony On Monday 01 May 2006 7:17 am, Anthony Cruz wrote: On Friday 28 April 2006 12:02 pm, David van der Spoel wrote: Anthony Cruz wrote: Hi: I want to make a simulation of a small pepetide in a box of water but I want to freeze or restrain the movement of all water molecules that have a distance grater that 3 A from the protein surface. Right know the water that are within 3 A of the protein, have a different residue name (SHL) and the other water molecules have the normal resname (SOL) How I could do the restrain??? use make_ndx to make an index file and freeze all SOL I have the index but how I used to freeze all SOL?? Thanks. Anthony ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] top file popc
hi i run pdbgmx2 for popc but errore message is here: wrong format is in ffg43a2.h line 2 7 ow whould you please help me? thanks mahboobeh __ 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 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 in mdrun when using PME
-Original Message- From: [EMAIL PROTECTED] on behalf of David van der Spoel Sent: Sat 4/29/2006 2:25 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] segmentation fault in mdrun when using PME Diane Fournier wrote: Hi, I'm new to Gromacs and I'm trying to run a enzyme-ligand complex molecular dynamics simulation. I have tried doing John Kerrigan's Drug-Enzyme tutorial and mdrun crashes with segmentation fault and core dump at the steepest descents minimization step. However, mdrun works fine when using cutoff instead of PME. I'm working with Gromacs v. 3.3.1 on a SGI altix 3700 with 32 Intel Itanium 2 processors (but I'm currently using a single node, so it's not a MPI problem) under Red Hat Enterprise Linux AS release 3 with Intel Math Kernel Librarary (MKL) v. 8.0.1 as FFT library (which is optimized for Itanium 2). the em.mdp file looks like: title = drg_trp cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = none integrator = steep dt = 0.002; ps ! nsteps = 500 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb= 0.9 rvdw= 0.9 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; ; Energy minimizing stuff ; emtol = 1000.0 emstep = 0.01 Is it possible this could be related to insufficient memory allocation ? How demanding is this PME calculation ? Not likely a memory problem. It could be a compiler issue but we need more info! Where does it crash? Is it reproducible? DOes the same tpr file cause a crash on another architecture (e.g. your desktop)? I installed gromacs 3.3.1 on my desktop (Pentium 4 under linux fedora core 4 and using the fftw3 fourier transform library). I used the .tpr file generated on the altix in mdrun and it worked fine. When I run that same file on the altix, it crashes every time without any iteration in the .log file: Removing pbc first time Done rmpbc Initiating Steepest Descents Center of mass motion removal mode is Linear We have the following groups for center of mass motion removal: 0: rest, initial mass: 14580 Started Steepest Descents on node 0 Mon May 1 11:47:39 2006 PLEASE READ AND CITE THE FOLLOWING REFERENCE S. Miyamoto and P. A. Kollman SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid Water Models J. Comp. Chem. 13 (1992) pp. 952-962 --- Thank You --- After that the file ends. There is no other error message than segmentation fault with core dump. The compilers that are used on the altix are: C++ Version 99.0-023 - 9.0-031 C++ Version 88.1-033 - 8.1-036 Fortran 99.0-021 - 9.0-032 Fortran 88.1-029 - 8.1-033 IPP 4.1 - 5.0 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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 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 winmail.dat___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] segmentation fault in mdrun when using PME
Diane Fournier wrote: -Original Message- From: [EMAIL PROTECTED] on behalf of David van der Spoel Sent: Sat 4/29/2006 2:25 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] segmentation fault in mdrun when using PME Diane Fournier wrote: Hi, I'm new to Gromacs and I'm trying to run a enzyme-ligand complex molecular dynamics simulation. I have tried doing John Kerrigan's Drug-Enzyme tutorial and mdrun crashes with segmentation fault and core dump at the steepest descents minimization step. However, mdrun works fine when using cutoff instead of PME. I'm working with Gromacs v. 3.3.1 on a SGI altix 3700 with 32 Intel Itanium 2 processors (but I'm currently using a single node, so it's not a MPI problem) under Red Hat Enterprise Linux AS release 3 with Intel Math Kernel Librarary (MKL) v. 8.0.1 as FFT library (which is optimized for Itanium 2). the em.mdp file looks like: title = drg_trp cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = none integrator = steep dt = 0.002; ps ! nsteps = 500 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb= 0.9 rvdw= 0.9 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; ; Energy minimizing stuff ; emtol = 1000.0 emstep = 0.01 Is it possible this could be related to insufficient memory allocation ? How demanding is this PME calculation ? Not likely a memory problem. It could be a compiler issue but we need more info! Where does it crash? Is it reproducible? DOes the same tpr file cause a crash on another architecture (e.g. your desktop)? I installed gromacs 3.3.1 on my desktop (Pentium 4 under linux fedora core 4 and using the fftw3 fourier transform library). I used the .tpr file generated on the altix in mdrun and it worked fine. When I run that same file on the altix, it crashes every time without any iteration in the .log file: Removing pbc first time Done rmpbc Initiating Steepest Descents Center of mass motion removal mode is Linear We have the following groups for center of mass motion removal: 0: rest, initial mass: 14580 Started Steepest Descents on node 0 Mon May 1 11:47:39 2006 PLEASE READ AND CITE THE FOLLOWING REFERENCE S. Miyamoto and P. A. Kollman SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid Water Models J. Comp. Chem. 13 (1992) pp. 952-962 --- Thank You --- After that the file ends. There is no other error message than segmentation fault with core dump. The compilers that are used on the altix are: C++ Version 99.0-023 - 9.0-031 C++ Version 88.1-033 - 8.1-036 Fortran 99.0-021 - 9.0-032 Fortran 88.1-029 - 8.1-033 IPP 4.1 - 5.0 Have you enabled fortran at the compilation stage? In that case try it without, otherwise please file a bugzilla, such that we can document this problem (and try to fix it of course). ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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 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] fudgeLJ / fudgeQQ are multiplicative factors
Perhaps someone can add this to the next update of the manual (on page 101?) Without going to Jorgensen's 1988 JACS paper it is difficult to be sure that fudge means multiply and not divide, especially given the most common usage of the word factor and that e.g. Berger Biophys. J. 1997 indicates the LJ contribution was reduced by a factor of 8 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] top file popc
Send more information. what .itp and .top files are you using? what was your pdb2gmx command? what were the 3 or 4 lines on either side of the error message (cut and paste them)? hi i run pdbgmx2 for popc but errore message is here: wrong format is in ffg43a2.h line 2 7 ow whould you please help me? thanks mahboobeh ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] GMX on 2xopteron Dual core
Hello friends! After reviewing the chart for GMX performance I purchased this 2x dual core opteron ,2.6GHz procesors and installed Fedora Core 4 (K8N-DL mother board). On booting up, the OS gives the message 'MP system not assigned by PSB bios structure. how do I overcome this problem? Would installation of another OS overcome the proble, like say example would installing SuSe 10.0 solve the problem. Your suggestions/response will be greatly appreciated. processor specifications: -- 1. AMD opteron Model 285, 2.6 GHz, Dual core 2mb Cache Qty-2 2. Motherboard Asus K8N-DL supports Dual opteron , 8-channel sound, Serial ATA, USB2.0 3. Memory, PC 3200, 1024, ECC resistered, total : 4 GB. 4. Sea gate Hard drive SATA,3.5, 300GB, 8MB cache,Native command Queing, model ST3300831AS During Installation I give - /boot- 10 GB /home-10GB /swap- 8GB Thanks Jayant ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Hydrogen bonds with version 3.3.1
Dear gmx-users, I am trying to calculate hydrogen bonds with gromacs version 3.3.1 I would like to have a cutoff of 2.7 A between hydrogen and acceptor and an angle cutoff of 60 degrees. For that I'm using the following command: g_hbond -f simulation.trr -s topol.tpr -r 0.27 -a 60 -noda -nonitacc -hbm -hbn -nomerge It seems that the cutoff -a 60 is used on the angle Donor-Hydrogen-Acceptor instead of Hydrogen-Donor-Acceptor. As a result it selects hydrogen bonds which are extremely bent and disregards hydrogen bonds which are almost planar. This is exaclty the contrary of what it should do. Does anyone have experience in calculating hydrogen bonds with version 3.3.1? Thanks a lot, Gianluca - Dr. Gianluca Interlandi [EMAIL PROTECTED] +1 (206) 685 4432 +1 (206) 714 4303 http://biocroma.unizh.ch/gianluca/ Postdoc at the Department of Bioengineering at the University of Washington, Seattle WA U.S.A. - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] cis-trans isomerization in Ryckaert Bellemans dihedrals
Hi all, I am trying to perform FEP on a double ring structure such that I want to see cis-trans isomerization of the molecule by shifting the reference angle by 180 degrees. How can I apply this shift on RB parameters of my dihedral? I read the manual, but transformation of parameters into RB form is not clear enough for me. thanks in advance. Murat CETINKAYA, M.Sc. BioNanoMaterials Group, Dept. of Engr. Science and Mechanics, The Pennsylvania State University, University Park, PA 16802 office: (814) 863 9967 web: www.personal.psu.edu/muc176 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
