Re: [gmx-users] About the removal of the center of mass
yes. you need to and can still put System for the removal group. On Feb 21, 2012 5:51 PM, xiaojing gong xnz...@gmail.com wrote: Dear all, I used the GMX 4.5.5 to run a simulation with a fixed plane and water. I wonder to know if I fix the plane, shall I use the command of the removal of the center of mass for water? I will appreciate it if you will share your opion. Many thanks XJ -- 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]Question about reduced unit for coarse grain
Hi, The unit in output is in assumed to be for the standard unit input while the value is in reduced unit. So you need to do your own calculation to figure out what's the reduced unit is. Regards, Yang Ye On Thu, Jun 23, 2011 at 5:48 AM, Ye Yang knightyang...@gmail.com wrote: Dear all: I see from the user's manual that if our input is in reduced unit, the output will also be in reduced unit(, ftp://ftp.gromacs.org/pub/manual/3.1/manual-a4-3.1.1.pdf), P25. On the contrary, if we use standard unit, the out put will be in standard unit. This brings the question up when we use coarse grain Clementi's model webtool (http://smog.ucsd.edu/sbm_faq.html), according to the author, it seems that everything is in reduced unit, so the output file should also be in reduced unit, yet I found the topology file that the energy unit is KJ/mol. What exactly is the unit of the input and out put file? When I pull the molecules, do I get the reduced unit result or the physical unit result? Since I am an experimentalist, getting the physical units is more important to me, so as to compare with the experimental results, albeit the intrinsic difference. If I get something in reduced unit, there is necessity for me to change it into physical unit, or at least clarify it in comparison. Thank you very much. Ye -- 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] add a new force field to the pdb2gmx list
Please use find to locate FF.dat in your particular installation. Regards, Yang Ye On Wed, Dec 1, 2010 at 12:17 PM, Jia Haitao jiahai...@gmail.com wrote: Dear all, I have constructed a new CG force field named polycg, and added them to direction ..$GMXLIB/polycg.ff. Can anybody tell me how to add my new force field to gromacs default force field list, in case I can use it to convert pdb files in program pdb2gmx. My gromacs version is 4.5. There is not FF.dat file in direction $GMXLIB any more. I will be very appreciate for your help. -- 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] cvs version
# source GMXRC.bash (or .csh, .sh) to set environment variables or you can refer to it to set them manually. Regards On Mon, Mar 29, 2010 at 11:38 AM, Mu Yuguang (Dr) y...@ntu.edu.sg wrote: Hi all, When I use cvs version, pdb2gmx, it shows such error Program pdb2gmx_cvs, VERSION 4.0.99-dev-20100328-954f577 Source code file: pdb2top.c, line: 137 Fatal error: No force fields found (files with name 'forcefield.itp' in subdirectories ending on '.ff') For more information and tips for trouble shooting please check the GROMACS website at http://www.gromacs.org/Documentation/Errors how to treat with? Yuguang CONFIDENTIALITY: This email is intended solely for the person(s) named. The contents may be confidential and/or privileged. If you are not the intended recipient, please delete it, notify us, and do not copy or use it, nor disclose its contents. Thank you. Towards A Sustainable Earth: Print Only When Necessary -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Regards, Yang Ye -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] [help]How to produce .top file from Material Studio
No way from MS. Check x2top. Yang YE On Mon, Mar 22, 2010 at 10:42 PM, 程迪 chengdi123...@gmail.com wrote: Hi,everyone I have build a SiO2 structure in Material Studio, And I've set the xyz coordinates and force field parameters of the structure. Is there some tool or method to produce a .top file from MS. I do not want to write .top file line by line. Thanks. Di Cheng University of Science and Technology of China Hefei, Anhui Province 230026 P. R. China E-mail: chen...@mail.ustc.edu.cn Tel.: +86-15321055911 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Regards, Yang Ye -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Is there anyone who has tip3p.gro?
You may find it in gromacs source. On Tue, Jan 19, 2010 at 2:08 PM, xiao shijun xshi...@gmail.com wrote: Hi there, Recently, I cannot add tip3p water in my system, because GMX cannot find tip3p.gro in GMXLIB. I am wondering is there anyone who has tip3p.gro, and could you please give me one copy. highly appreciate!! shijun -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Regards, Yang Ye -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] compiling problem
Just a work-around, force mpicc to point to cc. alias mpicc=cc Yang Ye On Wed, Sep 16, 2009 at 5:35 PM, Mu Yuguang (Dr) y...@ntu.edu.sg wrote: No, even I do not use mpi , the error is still there. Regards Yuguang -- *From:* gmx-users-boun...@gromacs.org [mailto: gmx-users-boun...@gromacs.org] *On Behalf Of *Yang Ye *Sent:* Wednesday, September 16, 2009 2:34 PM *To:* Discussion list for GROMACS users *Subject:* Re: [gmx-users] compiling problem Is LAM-MPI's binary in PATH? if you run mpicc from console, will it also show No such file or directory? Check LAM-MPI installation. Regards, Yang Ye On Wed, Sep 16, 2009 at 12:39 PM, Mu Yuguang (Dr) y...@ntu.edu.sg wrote: Hi, I use git clone git://git.gromacs.org/gromacs.git to get the lastest version and ./bootstrap To generate the configure file Then use ./configure successfully Howeve, after make The error appears as foloowing: mpicc -DHAVE_CONFIG_H -I. -I. -I../../../../src -I/usr/X11R6/include -I/usr/include/libxml2 -I../../../../include -DGMXLIBDIR=\/home/ygmu/software/gmx_cvs/gromacs/share/top\ -I/home/ygmu/software/fftw-3.2/float/include -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 -MT nb_kernel400_x86_64_sse.lo -MD -MP -MF .deps/nb_kernel400_x86_64_sse.Tpo -c nb_kernel400_x86_64_sse.c -o nb_kernel400_x86_64_sse.o nb_kernel400_x86_64_sse.c: In function `nb_kernel400_x86_64_sse': nb_kernel400_x86_64_sse.c:93: warning: implicit declaration of function `_mm_castsi128_ps' nb_kernel400_x86_64_sse.c:93: error: invalid initializer nb_kernel400_x86_64_sse.c:94: error: invalid initializer nb_kernel400_x86_64_sse.c:95: error: invalid initializer mpicc: No such file or directory make[5]: *** [nb_kernel400_x86_64_sse.lo] Error 1 Regards Yuguang ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Regards, Yang Ye ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Regards, Yang Ye ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] compiling problem
Is LAM-MPI's binary in PATH? if you run mpicc from console, will it also show No such file or directory? Check LAM-MPI installation. Regards, Yang Ye On Wed, Sep 16, 2009 at 12:39 PM, Mu Yuguang (Dr) y...@ntu.edu.sg wrote: Hi, I use git clone git://git.gromacs.org/gromacs.git to get the lastest version and ./bootstrap To generate the configure file Then use ./configure successfully Howeve, after make The error appears as foloowing: mpicc -DHAVE_CONFIG_H -I. -I. -I../../../../src -I/usr/X11R6/include -I/usr/include/libxml2 -I../../../../include -DGMXLIBDIR=\/home/ygmu/software/gmx_cvs/gromacs/share/top\ -I/home/ygmu/software/fftw-3.2/float/include -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 -MT nb_kernel400_x86_64_sse.lo -MD -MP -MF .deps/nb_kernel400_x86_64_sse.Tpo -c nb_kernel400_x86_64_sse.c -o nb_kernel400_x86_64_sse.o nb_kernel400_x86_64_sse.c: In function `nb_kernel400_x86_64_sse': nb_kernel400_x86_64_sse.c:93: warning: implicit declaration of function `_mm_castsi128_ps' nb_kernel400_x86_64_sse.c:93: error: invalid initializer nb_kernel400_x86_64_sse.c:94: error: invalid initializer nb_kernel400_x86_64_sse.c:95: error: invalid initializer mpicc: No such file or directory make[5]: *** [nb_kernel400_x86_64_sse.lo] Error 1 Regards Yuguang ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Regards, Yang Ye ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] how to set up a rigid system
To set up rigid system, you need to put (3n-6) constraints (in the form of bond, angle), where n is the atom/bead (in the case of coarse-grain model) number in the molecule. YY On Fri, Dec 5, 2008 at 1:03 PM, Xin Liu [EMAIL PROTECTED] wrote: Dear GMX users, I am carrying out MD simulation of acetylacetone by Gromacs. As we know, there are keto and enol two tautomers for acetylacetone. The tautomers were treated as rigid species in the literature (Y.K. Park, C. H. Turner, J. Supercrit. Fluids 37 (2006) 201–208)). The parameters of the LJ interactions and the electrostatic interactions of keto and enol models for acetylacetone and their equilibrium geometry were given. Dihedral angles are included in the models to specify the keto geometry, while the enol form is calculated to be a planar molecule. Model parameters Molecule Site q/eσ (nm) ε/kb (K) Geometry Acetylacetone (Keto) CH3−0.120.39673.02 C-C: 0.151 nm, ∠CCCH2: 116.7◦ ∠CCO: 123.1◦, ∠CCCH2C: −81.7◦ C= 0.480.37552.876C-CH2: 0.152 nm, ∠CCH2C: 111.7◦, ∠CCH2CC: −162.1◦ O= −0.340.296105.75C=O: 0.122 nm -CH2- 0.0 0.390559.42 CH2-C: 0.153 nm, ∠CH2CO: 122.0◦ ∠CH2CC: 115.4◦ C=0.52 0.375 52.876 C=O: 0.122 nm, C-CH3: 0.151 nm O= −0.320.296 105.75 CH3 −0.220.396 73.02 Acetylacetone (E) O −0.3660.30085.609 O-C: 0.133 nm, ∠OCC(H3): 113.6◦ H(-O-) 0.4110.0 0.0H-O: 0.099 nm, ∠HOC: 105◦ C(-OH) 0.3030.37552.876 C-CH3: 0.150 nm, C=CH: 0.137 nm CH3−0.1730.39180.573 ∠CH3C(-O)C: 124.2◦ CH0.197 0.380 57.912 ∠CC(H)C: 120.5◦, C C( O): 0.145nm, ∠C(H)C=O: 121.6◦, ∠CC(=O)CH3: 121.6◦ C(=O)0.360 0.37552.876 C=O: 0.125 nm, CCH3: 0.151 nm CH3−0.258 0.391 80.573 O=−0.474 0.296 105.75 But I could not know how to set up this rigid system in gromacs. If you could give me some advice or some material, I will appreciate it. Thank you! Dr. Xin Liu, School of Chemistry and Chemical Engineering Sun Yat-Sen University No.135, Xingang Xi Road, Guangzhou, 510275 P. R. China Tel.: +86-20-84115559 Fax: +86-20-84112245 E-mail: [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] 2008-12-05 ___ 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 -- Regards, Yang Ye ___ 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] About REMD specification in mdrun argument
each tpr contains only one temperature. On Tue, Dec 2, 2008 at 1:29 PM, Lee Soin [EMAIL PROTECTED] wrote: Hi, everyone! There's something that I'm not clear about REMD in gromacs. Since all the inputs are unified into a unique .tpr file, why should the REMD options -multi and -replex be sprcified as mdrun arguments instead of being integrated into the same .tpr file? -- Sun Li Department of Physics Nanjing University, China ___ 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 -- Regards, Yang Ye ___ 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] mdrun in parallel
grompp -np 16 On 11/21/08 7:06 PM, [EMAIL PROTECTED] wrote: Hi All, I'd need an help to run GROMACS 3.3.3 in parallel. I'm running mdrun in parallel using the command: mpirun -machinefile /storage1/home/rgr/machines_16 -np 16 /storage2/rgr/software/gromacs/bin/mdrun_d -s min0.tpr -g min0.log -e min0.edr -o min0.trr -x min0.xtc -c min0.gro but the following error appear: Program mdrun_d, VERSION 3.3.3 Source code file: init.c, line: 69 Fatal error: run input file min0.tpr was made for 1 nodes, while mdrun_d expected it to be for 16 nodes. Many thanks and regard Alessandro ___ 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] the Temperature in the mdp.file
Is it a real diassociation or an illusion? Visualize with PBC in mind. To put them back, use trjconv to center one chain of the DNA and output the two chains. On 11/11/08, He, Yang [EMAIL PROTECTED] wrote: Hi all users. When I change the Temperature in the madp file to try to get different result about DNA model\'s disassociation , but it is strange that result seems to be the same for different Temperature. Even I change the Temperature by 0K ,the disassociation happened. I have tried to reduce the force between some bond and non-bond, but the effect is not very good. This is part of my mdp file: ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit= 0 dt = 0.0001 nsteps =10 ; For exact run continuation or redoing part of a run init_step= 0 ; mode for center of mass motion removal comm-mode= Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 10 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = xyz ; nblist cut-off rlist= 0.686 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = User rcoulomb-switch = 0 rcoulomb = 0.9 ; Relative dielectric constant for the Cut-off or DC of the reaction field epsilon-r= 78 ; Method for doing Van der Waals vdw-type = User ; cut-off lengths rvdw-switch = 0 rvdw = 0.9 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Seperate tables between energy group pairs energygrp_table = ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; 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= 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no ; GENERALIZED BORN ELECTROSTATICS ; Algorithm for calculating Born radii gb_algorithm = Still ; Frequency of calculating the Born radii inside rlist nstgbradii = 1 ; Cutoff for Born radii calculation; the contribution from atoms ; between rlist and rgbradii is updated every nstlist steps rgbradii = 2 ; Salt concentration in M for Generalized Born models gb_saltconc = 0 ; IMPLICIT SOLVENT (for use with Generalized Born electrostatics) implicit_solvent = No ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling Tcoupl = berendsen ; Groups to couple separately tc-grps = System ; Time constant (ps) and reference temperature (K) tau_t= 0.1 ref_t= 300 ; Pressure coupling Pcoupl = no Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p= 0.5 compressibility = 4.5e-5 ref_p= 1.0 ; Random seed for Andersen thermostat andersen_seed= 815131 Can anyone of you tell me what is the reason for that? Thank you in advance. Yang ___ 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 -- Regards, Yang Ye ___ 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: High frequency output slow down the simulation?
Writing on local or remote certainly makes a difference. How about the speed with no output at all? Regards, Yang Ye From: xianghong qi [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, November 9, 2008 12:36:40 AM Subject: Re: [gmx-users] Re: High frequency output slow down the simulation? The time difference is : for simulation with every 100ps output, 160ns/day; for simulation with every 0.1ps output, It has been running for 4 days, only wrote to 2300ps . I am not sure the local hard disk since I run my simulation in some cluster. Thanks. -Xianghong Qi On Sat, Nov 8, 2008 at 11:09 AM, Yang Ye [EMAIL PROTECTED] wrote: More details please. Local hard disk? How much the time difference? YY On 11/8/08 12:41 PM, xianghong qi wrote: Hello, all: I compare the two simulations with different output frequency for .xtc file in same machine. One with low frequency runs much faster than the one with high frequency. Is that reasonable? I think the frequency shouldn't affect the simulation speed. Anyone has idea about this situation? Thanks. -Xianghong Qi -- Some people make the world more special just by being in it. ___ 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 -- Some people make the world more special just by being in it. ___ 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] mpi- gromacs
g_energy needs input to supply which energy item you would like to output. To automate this, use echo -e 1\n2\n | g_energy_mpi -f minim_ener.edr -o minim_ener.xvg However, I don't see any point to run g_energy with mpi. If you have (mis-)compiled it with MPI, build a non-MPI version for all analysis programs. Regards, Yang Ye On 10/30/08 11:40 AM, Chih-Ying Lin wrote: Hi Here is my pdb file. #!/bin/bash #PBS -l nodes=2 cat $PBS_NODEFILE echo Working directory is $PBS_O_WORKDIR cd $PBS_O_WORKDIR mpirun -np 2 g_energy_mpi -f minim_ener.edr -o minim_ener.xvg 11 0 Then, it showed Fatal error: No energy terms selected How to fix the problem Thank you Lin ___ 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] Cann't get the same result ?
This is normal. You shall get statistical identical properties between runs. Besides obvious reasons (gen_vel=yes and gen_seed=-1, or optimize_fft=yes), there might be other factors. Regards, Yang Ye On 9/22/08 8:26 AM, xuji wrote: Hi all: I run mdrun of gromacs-3.3.3 6 times of a small simulation, but I cann't get the same result every time. I run the mdrun program using ./mdrun -v -s md1.tpr -o md1.trr -c after_md1.gro -g md1.log -e md1.edr -x md1.xtc md1.job ./mdrun -v -s md1.tpr -o md1.trr -c after_md1.gro -g md1.log -e md1.edr -x md1.xtc md1.job ./mdrun -v -s md1.tpr -o md1.trr -c after_md1.gro -g md1.log -e md1.edr -x md1.xtc md1.job. Three simulations one time. And run two times. The 6 log files are in the accessory. Can someone tell me why cann't I get the same result of the 6 simulations? Appreciate any help in advance! Best wishes! Ji Xu [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] 2008-09-22 ___ 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] Dissipative Particle Dynamics (DPD)
there is dpdmacs available.. Regards, Yang Ye - Original Message From: Suman Chakrabarty [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, September 1, 2008 5:50:15 PM Subject: [gmx-users] Dissipative Particle Dynamics (DPD) Dear all, since one of my mails with multiple questions went completely unanswered ( http://www.mail-archive.com/gmx-users@gromacs.org/msg15437.html ), let me try this time with more specific question. Is there any chance of Dissipative Particle Dynamics (DPD) being incorporated in Gromacs as a companion (or even replacement) of Brownian Dynamics? According to the book Understanding Molecular Simulation by Frenkel and Smit (Second edition, 2002, page 467), Brownian Dynamics does not conserve momentum, does not obey Newton's 3rd law and hence does not recover correct hydrodynamic (Navier-Stokes) behaviour at large length and time scales, while DPD takes care of all these problems. In that case, wouldn't it be more appropriate to use this technique as a replacement of Brownian/Langevin dynamics? Regards, Suman Chakrabarty.___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to calculate van der Waals potential between a given residue and the rest of residues in the protein?
A more complete answer is that to define energy groups for this reside and rest residues respectively, generate the tpr with grompp and then use mdrun -rerun to run through the existing trajectory to obtain what you wanted. Regards, Yang Ye - Original Message From: Justin A. Lemkul [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, September 1, 2008 5:37:47 AM Subject: Re: [gmx-users] How to calculate van der Waals potential between a given residue and the rest of residues in the protein? Limei Zhang wrote: Dear all, Is it possible to use GROMACS function(s) to calculate the averaged van der Waals potential /Coulomb potential between a given residue and the rest residues in the protein during a certain time of simulation? Different contributions to the potential can be analyzed by specifying the appropriate 'energygrps' in the .mdp file. -Justin Thanks, LZhang ___ gmx-users mailing list gmx-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 jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing list gmx-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] Run test in parallel
I would guess that you have got gromacs installed correctly from the two-process tests. The failure of eight-core test may depends how you start your MPI daemon or other factors that mdrun could be not running at all. Paste your log file from eight-core test or just wait for some one has experience with OpenMPI. Regards, Yang Ye ikedaike wrote: Hi I built GROMACS-3.3.3 with GCC-3.4.6 and OpenMPI-1.2.5 on CentOS 4.5(Intel Core2 Duo). I tested with gmxtest-3.3.3 and all tests passed in non-parallel. However, when I tested in parallel, I encountered the following messages. [Use 2 Cores] % ./gmxtest.pl -np 2 all Will test on 2 processors All 16 simple tests PASSED FAILED. Check files in dec+water 1 out of 14 complex tests FAILED All 63 kernel tests PASSED Error not all 45 pdb2gmx tests have been done successfully Only 0 energies in the log file Can I ignore above messages about the pdb2gmx test? [Use 8 Cores] % ./gmxtest.pl -np 8 all Will test on 8 processors FAILED. Check files in angles1 FAILED. Check files in angles125 FAILED. Check files in bham FAILED. Check files in bonds1 FAILED. Check files in bonds125 FAILED. Check files in dih1 FAILED. Check files in dih125 FAILED. Check files in g96angles1 FAILED. Check files in g96angles125 FAILED. Check files in g96bonds1 FAILED. Check files in g96bonds125 FAILED. Check files in imp1 FAILED. Check files in imp36 FAILED. Check files in morse FAILED. Check files in rb1 FAILED. Check files in rb125 16 out of 16 simple tests FAILED FAILED. Check files in acetonitrilRF FAILED. Check files in aminoacids FAILED. Check files in argon FAILED. Check files in butane FAILED. Check files in dec+water FAILED. Check files in ethyleenglycol No topol.tpr file in fe_test. grompp failed FAILED. Check files in fe_test FAILED. Check files in field FAILED. Check files in nacl FAILED. Check files in sw FAILED. Check files in tip4p FAILED. Check files in tip4pflex FAILED. Check files in urea FAILED. Check files in water 14 out of 14 complex tests FAILED FAILED. Check files in kernel010 FAILED. Check files in kernel020 FAILED. Check files in kernel030 FAILED. Check files in kernel100 FAILED. Check files in kernel101 FAILED. Check files in kernel102 FAILED. Check files in kernel103 FAILED. Check files in kernel104 FAILED. Check files in kernel110 FAILED. Check files in kernel111 FAILED. Check files in kernel112 FAILED. Check files in kernel113 FAILED. Check files in kernel114 FAILED. Check files in kernel120 FAILED. Check files in kernel121 FAILED. Check files in kernel122 FAILED. Check files in kernel123 FAILED. Check files in kernel124 FAILED. Check files in kernel130 FAILED. Check files in kernel131 FAILED. Check files in kernel132 FAILED. Check files in kernel133 FAILED. Check files in kernel134 FAILED. Check files in kernel200 FAILED. Check files in kernel201 FAILED. Check files in kernel202 FAILED. Check files in kernel203 FAILED. Check files in kernel204 FAILED. Check files in kernel210 FAILED. Check files in kernel211 FAILED. Check files in kernel212 FAILED. Check files in kernel213 FAILED. Check files in kernel214 FAILED. Check files in kernel220 FAILED. Check files in kernel221 FAILED. Check files in kernel222 FAILED. Check files in kernel223 FAILED. Check files in kernel224 FAILED. Check files in kernel230 FAILED. Check files in kernel231 FAILED. Check files in kernel232 FAILED. Check files in kernel233 FAILED. Check files in kernel234 FAILED. Check files in kernel300 FAILED. Check files in kernel301 FAILED. Check files in kernel302 FAILED. Check files in kernel303 FAILED. Check files in kernel304 FAILED. Check files in kernel310 FAILED. Check files in kernel311 FAILED. Check files in kernel312 FAILED. Check files in kernel313 FAILED. Check files in kernel314 FAILED. Check files in kernel320 FAILED. Check files in kernel321 FAILED. Check files in kernel322 FAILED. Check files in kernel323 FAILED. Check files in kernel324 FAILED. Check files in kernel330 FAILED. Check files in kernel331 FAILED. Check files in kernel332 FAILED. Check files in kernel333 FAILED. Check files in kernel334 63 out of 63 kernel tests FAILED Error not all 45 pdb2gmx tests have been done successfully Only 0 energies in the log file I don't know why the all tests failed. Could you please give the information about test in parallel ? Thank you in advance. Teru ___ 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
Re: [gmx-users] Run test in parallel
ikedaike wrote: Dear Yang, Thank you for your quick reply. I checked the log files and then found that the mpirun command cannot find the mdrun(executable) file.. I modified to use the absolute path in the gmxtest.pl and ran it. However some tests still failed. % ./gmxtest.pl -np 8 all Will test on 8 processors FAILED. Check files in angles125 1 out of 16 simple tests FAILED FAILED. Check files in dec+water No topol.tpr file in fe_test. grompp failed FAILED. Check files in fe_test 2 out of 14 complex tests FAILED All 63 kernel tests PASSED Error not all 45 pdb2gmx tests have been done successfully Only 0 energies in the log file Can I ignore above error messages? Most likely. I checked those errors before and they are indeed not errors. gmxtest suite is not just not very up-to-date with gromacs. Thank you in advance. Regards, Teru 2008/8/7 Yang Ye [EMAIL PROTECTED]: I would guess that you have got gromacs installed correctly from the two-process tests. The failure of eight-core test may depends how you start your MPI daemon or other factors that mdrun could be not running at all. Paste your log file from eight-core test or just wait for some one has experience with OpenMPI. Regards, Yang Ye ikedaike wrote: Hi I built GROMACS-3.3.3 with GCC-3.4.6 and OpenMPI-1.2.5 on CentOS 4.5(Intel Core2 Duo). I tested with gmxtest-3.3.3 and all tests passed in non-parallel. However, when I tested in parallel, I encountered the following messages. [Use 2 Cores] % ./gmxtest.pl -np 2 all Will test on 2 processors All 16 simple tests PASSED FAILED. Check files in dec+water 1 out of 14 complex tests FAILED All 63 kernel tests PASSED Error not all 45 pdb2gmx tests have been done successfully Only 0 energies in the log file Can I ignore above messages about the pdb2gmx test? [Use 8 Cores] % ./gmxtest.pl -np 8 all Will test on 8 processors FAILED. Check files in angles1 FAILED. Check files in angles125 FAILED. Check files in bham FAILED. Check files in bonds1 FAILED. Check files in bonds125 FAILED. Check files in dih1 FAILED. Check files in dih125 FAILED. Check files in g96angles1 FAILED. Check files in g96angles125 FAILED. Check files in g96bonds1 FAILED. Check files in g96bonds125 FAILED. Check files in imp1 FAILED. Check files in imp36 FAILED. Check files in morse FAILED. Check files in rb1 FAILED. Check files in rb125 16 out of 16 simple tests FAILED FAILED. Check files in acetonitrilRF FAILED. Check files in aminoacids FAILED. Check files in argon FAILED. Check files in butane FAILED. Check files in dec+water FAILED. Check files in ethyleenglycol No topol.tpr file in fe_test. grompp failed FAILED. Check files in fe_test FAILED. Check files in field FAILED. Check files in nacl FAILED. Check files in sw FAILED. Check files in tip4p FAILED. Check files in tip4pflex FAILED. Check files in urea FAILED. Check files in water 14 out of 14 complex tests FAILED FAILED. Check files in kernel010 FAILED. Check files in kernel020 FAILED. Check files in kernel030 FAILED. Check files in kernel100 FAILED. Check files in kernel101 FAILED. Check files in kernel102 FAILED. Check files in kernel103 FAILED. Check files in kernel104 FAILED. Check files in kernel110 FAILED. Check files in kernel111 FAILED. Check files in kernel112 FAILED. Check files in kernel113 FAILED. Check files in kernel114 FAILED. Check files in kernel120 FAILED. Check files in kernel121 FAILED. Check files in kernel122 FAILED. Check files in kernel123 FAILED. Check files in kernel124 FAILED. Check files in kernel130 FAILED. Check files in kernel131 FAILED. Check files in kernel132 FAILED. Check files in kernel133 FAILED. Check files in kernel134 FAILED. Check files in kernel200 FAILED. Check files in kernel201 FAILED. Check files in kernel202 FAILED. Check files in kernel203 FAILED. Check files in kernel204 FAILED. Check files in kernel210 FAILED. Check files in kernel211 FAILED. Check files in kernel212 FAILED. Check files in kernel213 FAILED. Check files in kernel214 FAILED. Check files in kernel220 FAILED. Check files in kernel221 FAILED. Check files in kernel222 FAILED. Check files in kernel223 FAILED. Check files in kernel224 FAILED. Check files in kernel230 FAILED. Check files in kernel231 FAILED. Check files in kernel232 FAILED. Check files in kernel233 FAILED. Check files in kernel234 FAILED. Check files in kernel300 FAILED. Check files in kernel301 FAILED. Check files in kernel302 FAILED. Check files in kernel303 FAILED. Check files in kernel304 FAILED. Check files in kernel310 FAILED. Check files in kernel311 FAILED. Check files in kernel312 FAILED. Check files in kernel313 FAILED. Check files in kernel314 FAILED. Check files in kernel320 FAILED. Check files in kernel321 FAILED. Check files in kernel322 FAILED. Check files in kernel323 FAILED. Check files in kernel324 FAILED. Check files in kernel330 FAILED. Check files in kernel331 FAILED. Check files in kernel332 FAILED. Check files in kernel333 FAILED. Check files in kernel334 63
Re: [gmx-users] some questions about gmx_density.c
Hi, Perhaps gmx-devel is a better place for this mail. t_filenm does nothing with the algorithm flow. It's a struct to hold various input/output file names. The definition is found in some file under include/. Most analysis program follow a template as shown in share/template/template.c. What the template does, in simple words, is: it reads the trajectory frame by frame, for each frame, perform some calculation. If you want to write your own analysis program, start from one analysis program (for g_density, modify function calc_density shall only involve the real algorithm of calculating density) or the template. To understand some development work for Gromacs (not only analysis tools), I recommend Erik's talk in CSC2007. http://www.csc.fi/english/research/sciences/chemistry/courses/gmx2007 Thursday 1.3. Workshop day 3 *Gromacs development.* Regards, Yang Ye beibei wrote: Hi, all Maybe since I am a newer with programming in C, I felt very difficult in reading codes of GROMACS. I want to know the arithmetic flow of gmx_density.c. I read many times but have no idea about it. Could anybody tell me the arithmetic flow of gmx_density.c? And where is the definition of t_filenm? Many thanks. Beibei 雅虎邮箱，您的终生邮箱！ http://cn.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 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] settle issue
David van der Spoel wrote: Mu Yuguang (Dr) wrote: Dear All, When I try to simulate TIP4Pew water box at 298K, and found the density got from gromacs is relative low (983 g/cm3) than the amber (sander) version 994 g/cm3. I cannot find the reason. The parameters for the tip4pew model are identical. When I check some intra-molecular distances, and seem to find a hint: in gromacs simulation the intra-molecular atom-atom distance (should be fixed by settle) fluctuation is quite large! How can one increase the accuracy of settles in gromacs? Settle is analytical and there is no tolerance. However you may be using settle with the SPC parameters (unlikely though). Maybe you should turn on the Dispersion Correction to the pressure (EnerPres). That gives a similar density difference. Thanks, David. It works. With DispCorr=EnerPres, it gives 994. Regards Yuguang ___ 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] Error:Cannot determine precision of trn file
[EMAIL PROTECTED] wrote: Dear colleagues, I successfully finished a 3 ns gromacs run using 40 nodes. When, I tried to convert .trr file to .xtc using trjconv, the run stops at 560 frame giving error cannot determimine precision of trn file. I tried various options like -skip, -b and -e, -dt option as well as -ndx option . But, each time, the run stops at 560. The second run I gave for 6 ns and this time, the trjconv stops at 1180 frame. I have observed the .trr files occupying huge memory space - 18 G for 3ns and 34 G for 6 ns runs respectively. Memory is not a problem, as I have lot of disk space available. As some guidelines, 1. Try to use XTC in first place; avoid using TRR unless for some specific calculation. 2. Having a lot of disk space doesn't mean the latency is short and data integrity is guaranteed. Check network traffic status if you are using network file system like NFS. 3. Restart and continue simulation for every 1ns. My system is a pentamer with 1052 residues and 47201 water molecules.The simulation ran for 5 days. I would be extremely thankful for any kind of suggestions in this regard. Prema, Graduate student, University of Houston. ___ 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] low cpu usage
I don't think Python is to be blamed. How about lam-mpi? Regards, Yang Ye Dr. Bernd Rupp wrote: Dear all, CPU: Intel(R) Core(TM)2 Extreme CPU Q6850 @ 3.00GHz System: fedora 8 Kernel: 2.6.25.6-27.fc8 #1 SMP gromacs 3.3.3 correct compiled MPI : mpich or mpich2 We had the same problem with mpich2. single processor run CPU load 100% double processor run CPU load around 70% quad processor run CPU load around 40% With mpich we have no problem: quad processor run CPU load around 95% We think that implementation of python are the reason of the bad scaling of mpich2. Because mpiexec and mpdboot of mipch2 are python scipts. May be we are wrong, but mpich dont use python and runs well!? see you Bernd Am Samstag, 21. Juni 2008 schrieb ha salem: Dear users my gromacs is 3.3.3 my cpus are intel core2quad 2.4 GHz and my mpi is LAM 7.0.6 I can get the cpu usage of 4 cores on one node but when I run on 2 node the cpu usage of cores is low I have installed gromacs with these instructions Compile LAM 7 ./configure --prefix=/usr/local/share/lam7 --enable-static make |tee make.log make install make clean Compile fftw export MPI_HOME=/usr/local/share/lam7 export LAMHOME=/usr/local/share/lam7 export PATH=/usr/local/share/lam7/bin:$PATH ./configure --prefix=/usr/local/share/fftw3 --enable-mpi make |tee make.log make install make distclean Compile Gromacs export MPI_HOME=/usr/local/share/lam7 export LAMHOME=/usr/local/share/lam7 export PATH=/usr/local/share/lam7/bin:$PATH ./configure --prefix=/usr/local/share/gromacs_333 --exec-prefix=/usr/local/share/gromacs_333 --program-prefix= --program-suffix= --enable-static --enable-mpi --disable-float make |tee make.log make install make distclean lamboot -v lamhosts Run Gromacs on 2 machine (each machine has 1 core2quad) /usr/local/share/gromacs_333/bin/grompp -f md.mdp -po mdout.mdp -c md.gro -r md_out.gro -n md.ndx -p md.top -o topol.tpr -np 2 mpirun -np 2 /usr/local/share/gromacs_333/bin/mdrun -np 2-f topol.tpr -o md.trr -c md_out.gro -e md.edr -g md.log I also test with -np 8 but my cpu usage is low and the speed is less than single run!!! thank you in your advance -- ___ 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 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] low cpu usage
It could be system-specific. Could you try out dppc in tutor/gmxbench or download gmxbench from gromacs' website (section Benchmark)? Regards, Yang Ye Dr. Bernd Rupp wrote: same problem as mpich2. regards, Bernd Am Mittwoch, 25. Juni 2008 schrieb Yang Ye: I don't think Python is to be blamed. How about lam-mpi? Regards, Yang Ye Dr. Bernd Rupp wrote: Dear all, CPU: Intel(R) Core(TM)2 Extreme CPU Q6850 @ 3.00GHz System: fedora 8 Kernel: 2.6.25.6-27.fc8 #1 SMP gromacs 3.3.3 correct compiled MPI : mpich or mpich2 We had the same problem with mpich2. single processor run CPU load 100% double processor run CPU load around 70% quad processor run CPU load around 40% With mpich we have no problem: quad processor run CPU load around 95% We think that implementation of python are the reason of the bad scaling of mpich2. Because mpiexec and mpdboot of mipch2 are python scipts. May be we are wrong, but mpich dont use python and runs well!? see you Bernd Am Samstag, 21. Juni 2008 schrieb ha salem: Dear users my gromacs is 3.3.3 my cpus are intel core2quad 2.4 GHz and my mpi is LAM 7.0.6 I can get the cpu usage of 4 cores on one node but when I run on 2 node the cpu usage of cores is low I have installed gromacs with these instructions Compile LAM 7 ./configure --prefix=/usr/local/share/lam7 --enable-static make |tee make.log make install make clean Compile fftw export MPI_HOME=/usr/local/share/lam7 export LAMHOME=/usr/local/share/lam7 export PATH=/usr/local/share/lam7/bin:$PATH ./configure --prefix=/usr/local/share/fftw3 --enable-mpi make |tee make.log make install make distclean Compile Gromacs export MPI_HOME=/usr/local/share/lam7 export LAMHOME=/usr/local/share/lam7 export PATH=/usr/local/share/lam7/bin:$PATH ./configure --prefix=/usr/local/share/gromacs_333 --exec-prefix=/usr/local/share/gromacs_333 --program-prefix= --program-suffix= --enable-static --enable-mpi --disable-float make |tee make.log make install make distclean lamboot -v lamhosts Run Gromacs on 2 machine (each machine has 1 core2quad) /usr/local/share/gromacs_333/bin/grompp -f md.mdp -po mdout.mdp -c md.gro -r md_out.gro -n md.ndx -p md.top -o topol.tpr -np 2 mpirun -np 2 /usr/local/share/gromacs_333/bin/mdrun -np 2-f topol.tpr -o md.trr -c md_out.gro -e md.edr -g md.log I also test with -np 8 but my cpu usage is low and the speed is less than single run!!! thank you in your advance ___ 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] Does GROMACS have a multi-thread implementation?
For latest stable 3.3.3, there is no multi-thread implementation. For CVS version for coming 4.0, might be, I am not sure, but that's only for testing. Your question tricky without indicating the version. Regards, Yang Ye Lee Soin wrote: But I see that in mdrun there's an option nt--number of threads to start on each node. Does this mean multi-thread? 2008/6/24 Carsten Kutzner [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]: Lee Soin wrote: Does GROMACS have a multi-thread implementation, instead of using MPI? No, at least not yet. Carsten ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-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] mailto:[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 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: The number of PME nodes
Carsten Kutzner wrote: Hi Xuji, xuji wrote: Hi Carsten: First, thanks for your reply. Second, someone in the mailing-list said:Please cut of your email from the digest. It confuses people. And it seems that there's no other people that is interest in this topic. So I think it's maybe better we discuss this problem in private email. I think Yang Ye simply meant that you should choose a meaningful subject - not Re: [gmx-developers]. I also forward this to the users mailing list, which is the best place for this discussion. Hi, Xuji I hope you also subscribed to gmx-user. First, you shall know that mailing list is not only meant to solve your own problem but to leave an archive for other users to take as reference. Many other subscribers may not reply but they are keeping an eye on the outcome of the thread. Second, what I meant in cut is when you draft a reply, you shall tailor the original mail and your reply to make your reply relevant to one paragraph and one sentence. It is alright to remove the points that you don't reply because the archive will have all mails in one thread. What you did is to include the whole digest, a bundle of mails, which includes mails not originated from your mail together. This is not a good practice. Towards your problem, I hope that you follow what Carsten wrote. On top of it, I am aware that you used CVS version, it would be good to take latest stable versions like 3.3.3 and do scaling test. Lastly, when you reply this mail, make sure that you only write to [EMAIL PROTECTED] I am already subscribed to this list. Regards, Yang Ye ___ 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: The number of PME nodes
Carsten Kutzner wrote: Hi Xuji, xuji wrote: Hi Carsten: First, thanks for your reply. Second, someone in the mailing-list said:"Please cut of your email from the digest. It confuses people." And it seems that there's no other people that is interest in this topic. So I think it's maybe better we discuss this problem in private email. I think Yang Ye simply meant that you should choose a meaningful subject - not "Re: [gmx-developers]". I also forward this to the users mailing list, which is the best place for this discussion. Hi, Xuji I hope you also subscribed to gmx-user. First, you shall know that mailing list is not only meant to solve your own problem but to leave an archive for other users to take as reference. Many other subscribers may not reply but they are keeping an eye on the outcome of the thread. Second, what I meant in "cut" is when you draft a reply, you shall tailor the original mail and your reply to make your reply relevant to one paragraph and one sentence. It is alright to remove the points that you don't reply because the archive will have all mails in one thread. What you did is to include the whole digest, a bundle of mails, which includes mails not originated from your mail together. This is not a good practice. Towards your problem, I hope that you follow what Carsten wrote. On top of it, I am aware that you used CVS version, it would be good to take latest stable versions like 3.3.3 and do scaling test. Lastly, when you reply this mail, make sure that you only write to gmx-users@gromacs.org. I am already subscribed to this list. Regards, Yang Ye ___ 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: [Bulk] [gmx-users] RMSD graph
Quite likely, it is due to part of molecule moving out of box. Also, the molecule could be of multiple chain. So you need to find a way to put the whole molecule in one piece. Try various options from trjconv -pbc. If it is DNA, a trick is to define one chain as an index group and then center that group. Regards, Yang Ye Anamika Awasthi wrote: Dear All, Please tell, what should I predict from this graph? I can understand this is normal type of graph. Sorry for inconvenience, but I want to ask some questions, my this job crashed many time, because of power shut down and I had to restart this again and again, I used tpbconv for the same. but now when I was trying to get rmsd plot from my running job..its not reading the tpr file, which I got from tpbconv , its reading previous tpr file. Is it okey? Thanks in advance Anamika ___ 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] [Fwd: some questions about simulate a liquid-vapor interface of a solution, many thanks]
Hi, beibei The first point made by Mark is to check whether volume stabilizes when the system is subjected to NPT simulation. Regards, Yang Ye Mark Abraham wrote: Please leave GROMACS-related correspondence on the GROMACS mailing list. That way others can follow and contribute to the discussion, and it is archived for people to search later. Mark Original Message Subject: some questions about simulate a liquid-vapor interface of a solution, many thanks Date: Thu, 12 Jun 2008 22:40:05 +0800 (CST) From: beibei [EMAIL PROTECTED] To: [EMAIL PROTECTED] Hi, Mark Thank you very much to your reply. I cannot undersand some points in your reply. How to compute the volume that will lead to this pressure when the system is equilibrated? in addition, do you mean the sysytem is sandwich box or the cubic box? looking forward to your advice. Thank you very much. Best wishes. Beibei beibei wrote: Hi all, I want to simulate the liquid-vapor interface of I lithium bromide solution at 303K and 0.008bar. First I put the solution to a cubic box and used NPT ensemble to simulate. Then, I enlarged the box to form two liquid-vapor interface,and used NVT ensemble, but the pressure is not 0.008 bar. You need to determine a volume that will lead to this pressure when the system is equilibrated. Then you need to measure for long enough to get a meaningful average pressure. Trial and error might be the most effective approach. Best of luck! If I used NPT emsemble in the second step, the box becomes smaller with the run time. Of course... you won't get phase separation at equilibrium in NPT unless you happen to be at a critical point. Think about heating and cooling a closed and open beaker of real water. I want to know how to do when I want to simulate the liquid-vapor interface of a solution at a low pressure. 雅虎邮箱，您的终生邮箱！ http://cn.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 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] amber ports in gromas - bond length warning
What are the atoms involved in the Long Bond waring? For cyclic peptide, you also need to hand edit the topology file after pdb2gmx to connect the last residue to the first residue. Regards, Yang Ye David van der Spoel wrote: N-J.M. Macaluso wrote: Hello, I am using the Amber ports for Gromacs provided by the following website: http://chemistry.csulb.edu/ffamber/ I would like to use the Amber99sb force field for the simulation of a cyclic peptide, joined by a disulfide bond between terminal cysteine residues. I think I am using the appropriate Amber residue notation in the pdb file for each cysteine. The N-terminal cysteine is called NCYX and the C-terminal cysteine is CCYX. However, when I used pdb2gmx -ff amber99sb to get a .gro file, I receive several Long Bond warnings. I am working with a minimized structure, so I'm a bit confused as to why this is happening. Has anyone come up against this problem before? Have you checked the structure in Pymol or something like that? Many thanks, Max ___ 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] how to edit pdb file
Hi, Andrea As Xiupeng is on th side of using proprietory software, Xemacs would definitely be an overdose. Hi, Xiupeng All you need is to know is basic PDB file format. ATOM records in PDB file is in fixed-width column format. You need to format your line according to what said here. http://www.wwpdb.org/documentation/format23/sect9.html The same applies to GRO file, which is described in GROMACS manual. Regards, Yang Ye andrea spitaleri wrote: Hi, have look to this: http://stein.bioch.dundee.ac.uk/~charlie/software/pdb-mode/pdb-mode.html I found it very useful regards andrea Wei, Xiupeng wrote: Dear GMX users, I have a basic question. I want to put two same box in x direction. So I need increase the number of atoms and change their x coordinates,then combine it with the original one. But the file created by Excel can't be recoganized by gromacs. Is there any method in Gromacs to handle that? I also used Matlab, but it can't read pdb file correctly. Thanks. Best regards, xiupeng ___ 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] Is such hardware suitable for gromacs
Hi, Your mail looks like spam at first glance. Surely. They can be used to run Gromacs. In fact, Gromacs welcomes both Intel and AMD' modern CPU with SIMD capability. To build a small cluster, you also need some networking devices: a GB ether switch and some good cables. Rest is software installation (Linux) and configuration on network and LAM-MPI libraries. Regards, Yang Ye 之光 贾 wrote: ASUS DSBV-DX/C or Intel S5000VSA E5410 2.33 * 2 FB-DIMM 1G * 8... I could only find some body test their E5410 on Gromacs in google, but I am not sure this suit could compile and run Gromacs, I thirst somebody who is using such hardware tell me whether it is or isn't suitable. ..Or you has better suggestion, should I build a small cluster with 4 * 4 cpu computer? I am terrible confused abount how to make it, and I in fact know little about the parallel effect of gmx 雅虎邮箱，您的终生邮箱！ http://cn.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 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] NVT simulation
with pcoupl=none Arnab Senapati wrote: - Hi, can anyone tell me how to run a NVT simulation in gromacs. ___ 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] benchmark: buying a new cluster
There two CPUs differing not only in frequency but also in FSB speed. But the differences in FSB shall be ignorable for Gromacs. You have two dimensions to think. 1. power of all nodes = number of cores * frequency 2. power of a single node. If you intend to have one simulation running just on one node, more cores are better. This happens to be my case. If 32-core or more parallel running is planned, 2.8GHz helps. Regards, Yang Ye andrea spitaleri wrote: Hi all, we are going to buy a new cluster and we are in doubt about the frequency to consider. Basically, we have the possibility to buy either 18 nodes dual quad-core (18x8 cores) bearing Intel-Xeon E5430 2.66 MHz and FSB 1333 MHz or 15 nodes dual quad-core (15x8 cores) bearing Intel-Xeon E5462 2.8 MHz and FSB 1600 MHz. The latest seems to be **only** 10% faster then the first. However, thinking to the new gromacs4, we are in doubt about the best solution. Is it better to have a **nominal** 10% cpu faster or to have 24 further cores? Thanks in advance for any welcome suggestion, Regards andrea ___ 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] syntax for switching between multiple position restraint .itp in the .top file
All #endif lines have gone missing although I guess where they should be placed. Each #if needs to be matched with one #endif. Back to your question, it's a style matter but good style brings clarity and avoids mistakes. For the first, in mdp file, the defined variable list grows as the stage change. So the user needs to know which ones to be included in different stages. The second takes LIPID_ALL_POSRE as requirement for WATER_POSRE so it could prevent some degree of misuses. I would prefer first one because it gives total control and thus flexiblity in the mdp file. Regards, Yang Ye Low Soo Mei wrote: Hi gmx-users, If I use different position restraints during each stage of minimization, should I separately write all my restraints in the same .top file in this manner, #ifdef LIPID_ALL_POSRE #include lipid_all_posre.itp #ifdef WATER_POSRE #include water_posre.itp #ifdef LIPID_HEADGRP_POSRE #include lipid_headgrp_posre.itp or would it be possible for me to group all my restraints together in the same .top file as a switch, (I'm also not sure if the syntax below is correct in Gromacs), #ifdef LIPID_ALL_POSRE #include lipid_all_posre.itp #elseif WATER_POSRE #include water_posre.itp #else #include lipid_headgroup_posre.itp Thanks for your help in advance. Cheers, Soo Mei -- Ms. Low Soo Mei Research Assistant Biomolecular Modelling and Design Group Bioinformatics Institute, 30 Biopolis Street, #07-01, Matrix, Singapore 138671 Tel: +65-64788300 Fax: +65-64789047 e-mail: [EMAIL PROTECTED] Biomolecular Modelling and Design Group's homepage: http://www.bii.a-star.edu.sg/research/bmad/bmad.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 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] Choose of force fields of ethanol and B-DNA with 15 base pairs
Mark Abraham wrote: Collins Nganou wrote: Dear all. greetings. I need to know what force fields can I Choose to run: 1- ethanol vibrational mode. 2- B-DNA with 15 base pairs Start with a literature search. You'll need to do one later in order to defend your choice. Some person on a mailing list recommended it doesn't cut it... I agree with Mark. While for 2), there are ports from AMBER (ffamber) and CHARMM (from Contributed software on Gromacs website) available for Gromacs. 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 mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] how to make choices of COM in the system with freeze group?
You can opt for 3). If your system only compose of nanotube and water, why freeze it? Regards, Yang Ye tuyusong wrote: Hi, all, I have a system with one carbon Nanotube and lots of water, in which Nanotube is frozen. How do I remove the center-of-mass: 1) only remove the COM of SOL 2) remove both COM of SOL and CNT, separately 3) only remove the COM of system as a whole. 4) do not use any COM How do I make the choices? I use gromacs program 3.3.3 Thank you very much!!! Yusong. ___ 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] Simulation at different temperature
different mdp files with different ref_t. Regards, Yang Ye - Original Message From: s lal badshah [EMAIL PROTECTED] To: gromacs gmx-users@gromacs.org Sent: Monday, March 31, 2008 12:48:47 PM Subject: [gmx-users] Simulation at different temperature Dear Experts, Hi ! I want to simulate a protein at 298K, 283K, and at 323k.For all these temperature will I prepare different md.mdp files or single ? Regards, Lal badshah. Send instant messages to your online friends http://uk.messenger.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
Re: [gmx-users] Position restraint and distance restraints
jayant james wrote: hi! I am attempting to run a distance position restrained simulation in water. The distance and position restraining files are called from the *.top file as posres.itp and disres.itp. After a 200ps run I do not see the distance nor position restraining kicking in. I am not sure if I have specified every thing correctly. I have pasted essential parts of the topology file, em.mdp, pr.mdp, disres.itp and posres.itp. Awaiting your feedback Thanks Jayant James TOP FILE ; Include Position restraint file #ifdef POSRES ;include "posre.itp" #endif ;include"disres.itp" Putting semicolon in front of the line effectively turns off that line. Regards, Yang Ye ___ 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] why trjconv cannot split a file more than 1020 parts
Please supply us the output of trjconv. Alternatively, use trjconv -o foo.pdb -sep. Regards, Yang Ye 齐文鹏 wrote: I use the trjconv -split 1.0 to split my long xtc file to seperate pdb files to analysis with the Curves . But I cannot split files more than 1020. why? The gromacs version is 3.3.1 and only float precision. I have no ideas! Pleas give me some advise!! Thank you !! Best Regards. Wen-Peng Qi ___ 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 why trjconv cannot split a file more than 1020 parts Hi everyone, ___ 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] Help needed on using general amber force field (GAFF) in Gromacs
You might not use pdb2gmx for such task. Once you have generated topology in AMBER format with Antechamber in GAFF, you will need to use some tools like ambconv.pl or ambconv (one is Perl script and one is a C++ programme, check GROMACS' website) to convert those files into GROMACS format. There is ffamber, a port for AMBER force field to GROMACS, which largely similar to what ambconv.pl or ambconv produces. They will provide force field for protein and nuclei acids through pdb2gmx. With some hand-modifications to the files, you can combine ambconv and ffamber, so you have a solution for almost all molecules. Regards, Yang Ye Xiangyu Fan wrote: Hi all, I am using GAFF force field for Gromacs package to simulate MD of surfactant molecule. I know we can generate .top file using some simple command like pdb2gmx if we use gromos force field. I am just wondering whether I can do the similar thing when using GAFF force field. If you have any experience in GAFF+Gromacs, please give me some advice. thanks Xiangyu Fan UNC-Chapel Hill ___ 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] .gro files generation for a certain time-step interval in a simulation
trjconv -dump time Huey Ling Tan wrote: Hi All, I wonder if anyone knows what is the command to use in order to generate .gro files for a certain time-step interval in a simulation? For example, if I have a completed simulation of 10 ns long and I want to output (somehow) 10 .gro files each at 1st ns, 2nd ns, 3rd ns and so on out from a series of output files that I have (.tpr, .xtc, .edr, .log). Do you think it's do-able? -- Best regards, Huey Ling ___ 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] Gromacs setup on dual core machine
Ricardo Soares wrote: Hi everybody, I think this may sound rather trivial for most users, but I intend to install gromacs 3.3.1 on a dual core machine and I want to be sure what to do. Could anyone indicate me some online tutorial to do so (as well some simulation examples)? Is this considered parallelization (within one computer)? Yes. Simply compiling mdrun with MPI works? Yes. Before running mdrun, launching lamboot first if you're using LAM/MPI. Thanks in advance. ___ 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] about parallel run
i reckon that you have not built in mpi support to mdrun in GROMACS so each instance of mdrun produces one trajectory rather than running in parallel and produce only one trajectory. Mark Abraham wrote: Yunierkis Perez Castillo wrote: Hi all, I'm new to gromacs. I have setup a protein MD simulation in a cluster, I'm using 6 computers with 2 CPUs each one. After gromacs begun running I had 12 trajectory files in the folder the output is written: md.trr #md.trr.1# #md.trr.2# #md.trr.11# It seems like the trajectory is replicated by each CPU the simulation is running on. All files has the same size, and grows simultaneously as the simulation advances. Is that a normal thing?? Can I delete the #* files?? I infer from your results that you've run 12 single-processor simulations from the same working directory. GROMACS makes backups of files when you direct it to write to an existing file, and these are numbered as #filename.index#. Your 12 simulations are all there, but you can't assume that those files with number 5 are all from the same simulation, because of the possibility of filesystem asynchronicities in creating the files. If you're trying to run 12 single-processor simulations in the same working directory, then you need to rethink your strategy. If you're trying to do something else, then you also need to rethink :-) 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 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: Targeted MD
wei-xin xu wrote: 2008/1/10, Mark Abraham [EMAIL PROTECTED]: Some hints on practices that generally not a good idea to use: Do not use separate thermostats for different components of your system. Some molecular dynamics thermostats only work well in the thermodynamic limit. If you use one thermostat for, say, a small molecule, another for protein, and another for water, you are likely introducing errors and artifacts that are hard to predict. In particular, do not couple ions in aqueous solvent differently from that solvent. Sorry that I do not actually understand here. The link I copied above shows that better not to "couple ions in aqueous solvent differently from that solvent". Maybe not separately but differently (mean different temperature)? I am actually a novice in Gromacs. It's a bit off-topic. The paragraph quoted above implies that "not separately" so it is generally applies to cases where you want to make a temperature-coupling group of a small number of particles ___ 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] Question regarding compatibility of UFF and GROMACS
gromacs manual has the answer (FF terms) for you. Subhashis Biswas wrote: Hi, I know this issue has been discussed in some form before, but hough may be I resurface it again. Is it possible to transfer a UFF forcefield to a GROMACS forcefield with help of a script? UFF force-field cannot be used in GROMACS as per my understanding, and I renamed the FF types of an UFF based small peptide to GROMACS by hand, but I am afraid this will take for ever in longer systems. Also if someone can highlight upon what is the basic difference in UFF type forcefields and GROMACS (parameter or potential function-wise) that would be great. Thanks so much for your help. regards, Subhashis Subhashis Biswas Post-doctoral Research Associate Department of Energy, Environment Chemical Engineering Washington University in St Louis 1 Brookings Drive, Mail Stop 1180 St Louis, MO 63130 [EMAIL PROTECTED] ___ 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 thewww 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] deleted edr file
Use mdrun -rerun (will not be a complete recovery). pragya chohan wrote: Dear users I by mistake deleted the edr file generated from production run. Is there any way to recover or generate the edr file again? It's about getting married. Click here! Try it! http://ss1.richmedia.in/recurl.asp?pid=201 ___ 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] Ambconv running
you shall use AMBER's new2oldparm new old to get the old format file. I remember that David Mobley has another ambconv script on his website (http://www.alchemistry.org/) but it is not accessible right now. Regards, Yang Ye On 12/6/2007 3:52 AM, Shozeb Haider wrote: Hi, I am trying to use AMBCONV. However, it gives me a segmentation fault when I try to run it. I have seen that other users have posted a similar problem with the program on the mailing list. It seems to me that AMBCONV only uses older Amber formats. I have even generated that using set default oldprmtopformat on command. However I get the same segmentation fault. One user (David Evans) have mentioned that You can generate these from new format files using a utility in the amber package, but they will have an extra (7th) digit on the fouth line which will cause ambconv to crash. Does any one know what he means by the extra (7th) digit on the fourth line. Which file is he referring to ? The prmtop or the rst ? Any answers will be greatly appreciated. Best wishes Shozeb Haider The London School of Pharmacy ___ 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] different results when using different number cpus
1. how long is the simulation? 2. did you start from equilibration (with gen_vel=yes) or production md? 3. ... On 12/5/2007 8:28 PM, Dechang Li wrote: Dear all, I used Gromacs3.3.1 to do a simulation about two proteins in water(tip3p). I run two similar simulations, one for 2 cpus, while the other for 16 cpus. The two simulations have the same .gro, .top, and the same .mdp files. I found the results were not the same. In the 2 cpus simulation, the two proteins run closer and closer. But they run apart in the 16 cpus simulation. Is that normal the different results when using different number cpus? The size of my simulation box is 9*7*7. Best regards, 2007-12-5 = Dechang Li, PhD Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 PR China Tel: +86-10-62773779(O) Email: [EMAIL PROTECTED] = ___ 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] GROMACS in parallel on a multicore PC?
On 11/21/2007 7:33 PM, Vasilii Artyukhov wrote: Hi everybody, Sorry for a somewhat technical question, but I'd like to know which is the best way to run GROMACS on a SMP machine (in particular, a multicore PC). The (known) points of interest are: - Does GROMACS support multithreaded execution how efficient is it? No. - Should I rather use some kind of MPI which (LAM/Open/MPICH) is better why? Yes. This is the only way. Surely, there's always the option to run two serial jobs instead with a greater efficiency, but having some means to boost the single job performance by something like 1.9x would be very useful... Thanks in advance, Vasilii ___ 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] Re: Question about embedding a force field with no torsion term
Hi,Zhou Bo Please take some time to get to know what's 1-4 interaction, and what is torsion. In simple words, they are of two types: 1-4 belonging to non-bonded interaction; torsion is bonded interaction. So in nature, they are not conflicting each other; The reason why we isolate the definition of 1-4 interaction out of nonbonded interaction is that, non-bonded interaction exist for every pair of atoms, but for atoms inside one molecule, we will zero (or exclude) the interaction between adjacent atoms and 1-3 neighour, and also scaled down 1-4 neighbour interaction to avoid crashing because they are usually in close distance due to linkage. So leave the 1-4 interaction and if your forcefield doesn't have torsion, don't put that in. That's how simple the issue it is if you can sort things right. On 11/22/2007 8:55 AM, Mark Abraham wrote: Bo Zhou wrote: Thanks, Mark. Can you tell me any more in detail? No, because I don't know. However I know where to find out, and I pointed you there. I am really somewhat confused about it. I want to cooperate this force field with oplsaa, but it looks strange that there is not any torsion energy at all but can have 1-4 interactions. with nrexcel=2, Do I still need 1-4 interactions made by the procedure of genning pairs? Thanks very much. 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 mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to specify .mdp file for position restrained simulation?
A side note to -DPOSRES, it is actually a C preprocessor defined variable. There is a corresponding #ifdef POSRES ... #endif in the topology file you built. It is default to POSRES, but you can rename it to other name and change accordingly the define=.. line in the mdp file. Also, you can use this mechanism to do position restraint MD with different parts of the system, or gradually give freedom to the system. Regards, Yang Ye On 11/20/2007 4:18 PM, Maik Goette wrote: Hi Use the following term in your mdp: define = -DPOSRES Now, everything is true, depending on the question you ask and the point you're standing... What you may mean is the following: POSRES-Sims are mostly (not always) used for equilibrating the solvent around the protein. These simulations are in general quite short, because relaxation of water happens quite fast. In this case a Posres-Sim is much shorter (say 200ps or so) than a real run (usually in the range of ns). Please be aware, that there is also a parameter file for position-restraints (e.g. posre.itp), which, if automatically generated by pdb2gmx contains the positions of all heavy atoms with a force constant for x,y,z. And now a suggestion. Please, before starting MD inform yourself about: a. The theoretical aspects of molecular dynamics b. The program you are using (i.e. the manual) The probability of getting good results and no crap increases dramatically with following the two points above... Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Peggy Yao wrote: Hi, How to specify the .mdp file in order to run position restrained simulation? From the examples I found on the internet, it seems that the only difference between the .mdp file for position restrained simulation and the one for actual MD simulation is the simulation time -- the position restrained simulation is much shorter. Is this observation true in general? If yes, usually, how long is enough for the position restrained simulation? If not, how to specify the .mdp file for position restrained simulation then? Thanks a lot! Peggy ___ 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 mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to add calcium ions at desired position?
step 4) shall be add water, minimize energy. step 5) it's a bad idea to couple ion alone, see wiki pls. step 6,7) you shall at least have two stages, em, eq before production md. On 11/19/2007 5:23 AM, Peggy Yao wrote: Hi all, I would like to simulate a protein with calcium ions at the calcium binding sties. I cannot use genion to add calcium ions because genion put the ions randomly. Is there any conventional way to do this? The only way I could think of is the following: 1. Add the calcium ions in the protein PDB input file as HETATM with residue name CA2+. 2. pdb2gmx -f protein_ca.pdb -p protein_ca.top -o protein_ca.gro 3. In protein_ca.top, the last portions is ; Compound#mols Protein_A1 Protein_B1 Change the last line (Protien_B ...) to: CA2+ 2 4. Minimize energy, and add water. 5. In md.mdp, set: tc-grps = protein sol CA2+ tau_t = 0.1 0.1 0.1 ref_t = 300 300 300 6. grompp -f md.mdp -c protein_ca_water.gro -p protein_ca.top -o md.tpr 7. mdrun -s md.tpr -o protein.trr -x protein.xtc -c protein.gro However, after several MD steps, I got the following fatal error: --- Program mdrun, VERSION 3.3.2 Source code file: nsgrid.c, line: 220 Fatal error: Number of grid cells is zero. Probably the system and box collapsed. --- Why it is so? How should I do it? I am a new user of Gromacs, and I've been struggling on this issue for an entire day already. I will appreciate it very much if someone could help me. Thanks a lot! Peggy ___ 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] Differences in the bonded potentials in 3.3.2 vs. 3.3.1
submitting a bugzilla entry could be helpful in examining this case. On 11/17/2007 4:45 AM, Amadeu wrote: My student and I have been trying the latest Gromacs version (3.3.2) for the simulation of a CNT. We noticed that the bonded energies calculated with 3.3.2 are quite different compared to those from 3.3.1 (see resulting output below). Has anyone observed similar results? Was anything changed in 3.3.2 in how the bonded potentials were calculated? I tried another case for a system with harmonic bond and angle potentials, and the bonded energies were identical for both versions, which makes me believe that the Morse and G96Angle potentials are somehow different in 3.3.2. Could this be a bug? --Amadeu Initial set of energy obtained from the same TPR file. Both output were obtained with the single precision versions. _Output from Gromacs-3.3.2:_ Energies (kJ/mol) Morse G96AngleProper Dih.LJ (SR) Disper. corr. 5.78994e+031.44076e+045.47403e+02 -1.57601e+02 -2.46982e+01 Coulomb (SR) PotentialKinetic En. Total Energy Temperature 0.0e+002.05627e+043.32197e+012.05959e+04 1.11447e+01 Pressure (bar) -3.06280e+02 _Output from Gromacs-3.3.1:_ Energies (kJ/mol) Morse G96AngleProper Dih.LJ (SR) Disper. corr. 4.38162e+014.15264e+015.53398e+02 -1.57601e+02 -2.46982e+01 Coulomb (SR) PotentialKinetic En. Total Energy Temperature 0.0e+004.56441e+029.54848e+004.65990e+02 3.20338e+00 Pressure (bar) -5.04502e+02 ___ 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] make gives error in futil.c with mpi and ccc-6.5.6.002-1
Hi,
this post is bit misorganized. so you have passed ./configure stage? I
tackle the obvious first.
1. On Compaq platform, use export MPICC=gcc
-L/usr/lib/mpi/mpi_compaq/lib -lmpifarg -lmpi -lelan
2. it seems that the compiler doesn't receive Macro definition from
commandline, so you may go into the files to hard code the string values
(e.g. GMXLIBDIR are present in tools/futil.c and kernel/topio.c)
Regards,
Yang Ye
On 11/15/2007 6:59 AM, Chris Neale wrote:
I am having difficulty installing the mpi version of gromacs 3.3.2 on
a new computer. I have the same problems for 3.3.1. The serial
version appears to have worked fine. The cluster uses elan for MPI I
have parsed some values from config.log
configure:3291: ccc -V 5
Compaq C T6.5-002 on Linux 2.4.21-3.7qsnet alpha
Installed as ccc-6.5.6.002-1
Red Hat Linux release 7.2 (Enigma)
Using /usr/lib/gcc-lib/alpha-redhat-linux/2.96 (4).
Compiler Driver T6.5-001 (Linux) cc Driver
I believe my previous post was rejected since it was 2000 lines so I
have put the
entire config.log here:
http://www.pomeslab.com/CN_GromacsPost_111407.html
and reposted.
mpicc appears to link like this (although the script is complicated
enough
that I am not sure if this variable gets modified later):
my %mpilibs ='-L/usr/lib/mpi/mpi_compaq/lib -lmpifarg -lmpi -lelan'
I think that I must have autoconf somewhere since the Makefile was
created, however:
$automake --version
automake (GNU automake) 1.4-p5
$ autoconf --version
bash: autoconf: command not found
I have found some posts related to futil.c including the following
potential fix
http://www.gromacs.org/pipermail/gmx-users/2005-January/013806.html
but I didn't understand where the quotes were intended to go and the
next reply indicates that this is not a good idea in any event.
Another post indicates that I may be required to link it myself and
avoid the mpicc wrapper. I have tried including the following lines
in my compilation script before calling configure
export CC=gcc
export MPICC=gcc
export LIBS=-lmpi
but configure ends very quickly with the error message:
checking for C compiler default output file name... configure: error:
C compiler cannot create executables
Thanks for any assistance.
Chris.
I ran it like this:
#!/bin/bash
MD=/scratch/cneale/exe/gromacs-3.3.2
cd $MD
mkdir exec
export FFTW_LOCATION=/home/cneale/exe/fftw-3.1.2/exec
export GROMACS_LOCATION=${MD}/exec
export CPPFLAGS=-I$FFTW_LOCATION/include
export LDFLAGS=-L$FFTW_LOCATION/lib
./configure --prefix=$GROMACS_LOCATION --enable-mpi
--program-suffix=_mpi --disable-nice output.mpi_configure 21
make mdrun output.mpi_make_mdrun 21
make install-mdrun output.mpi_make_install_mdrun 21
#make distclean
The first error in the 'make mdrun' output is:
source='futil.c' object='futil.lo' libtool=yes \
DEPDIR=.deps depmode=none /bin/sh ../../config/depcomp \
/bin/sh ../../libtool --tag=CC --mode=compile mpicc -DHAVE_CONFIG_H
-I. -I../../src -I../../include
-DGMXLIBDIR=\/scratch/cneale/exe/gromacs-3.3.2/exec/share/top\
-I/home/cneale/exe/fftw-3.1.2/exec/include -std1 -fast -O4 -no_ifo
-arch ev6 -unroll 2 -fp_reorder -c -o futil.lo futil.c
mpicc -DHAVE_CONFIG_H -I. -I../../src -I../../include
-DGMXLIBDIR=\/scratch/cneale/exe/gromacs-3.3.2/exec/share/top\
-I/home/cneale/exe/fftw-3.1.2/exec/include -std1 -fast -O4 -no_ifo
-arch ev6 -unroll 2 -fp_reorder -c futil.c -o futil.o
cc: Error: futil.c, line 521: Invalid expression. (badexpr)
strcpy(libpath,GMXLIBDIR);
-^
cc: Warning: futil.c, line 521: Invalid token discarded. (invaltoken)
strcpy(libpath,GMXLIBDIR);
-^
make[2]: *** [futil.lo] Error 1
make[2]: Leaving directory
`/mnt/scratch/cneale/exe/gromacs-3.3.2/src/gmxlib'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory
`/mnt/scratch/cneale/exe/gromacs-3.3.2/src/gmxlib'
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Re: [gmx-users] make gives error in futil.c with mpi and ccc-6.5.6.002-1
Find out the c preprocessor of the Compaq C compiler and try to obtain
its output of parsed C source file.
On 11/15/2007 10:12 AM, [EMAIL PROTECTED] wrote:
I have had some success reproducing the event with a simple c program
and the issue appears to be with the in-house mpicc wrapper script.
The difference between gcc and mpicc appears limited to strings
(-D=\string\) and does not show up in numerical form (e.g. -D=4)
I'll post another update when the issue is resolved.
Chris.
In the following examples cc is the same as mpicc (they both point to
a script called 'compile') but mpicc invokes slightly different
linking options than cc
$ cat prog.c
#include stdlib.h
#include stdio.h
int main(int argn,char *args[]){
printf(The value of MYDEF is %s\n,MYDEF);
}
$ gcc prog.c -DMYDEF=\aaa\ -o prog
$ prog
The value of MYDEF is aaa
$ cc prog.c -DMYDEF=\aaa\ -o prog
cc: Error: prog.c, line 5: In this statement, aaa is not declared.
(undeclared)
printf(The value of MYDEF is %s\n,MYDEF);
--^
###
However, when the defined value is a number, the problem dissapears:
$ cat prog_num.c
#include stdlib.h
#include stdio.h
int main(int argn,char *args[]){
printf(The value of MYDEF is %d\n,MYDEF);
}
$ gcc prog_num.c -DMYDEF=4 -o prog_num
$ prog_num
The value of MYDEF is 4
$ cc prog_num.c -DMYDEF=4 -o prog_num
$ prog_num
The value of MYDEF is 4
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Re: [gmx-users] force=nan in frame 0
how do you turn off the interactions? e.g. setting rvdw=0 doesn't mean turning of vdw interactions. Regards, Yang Ye On 11/13/2007 12:55 AM, dongsheng zhang wrote: Dear Mark, The installation works for other systems. The error happens in either EM or MD. When I turn off all interaction potentials, the forces between all particles should be zero, shouldn't they? Could you please tell me why the initial forces are NaN? Thanks! All the best! Dongsheng -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Mark Abraham Sent: Sunday, November 11, 2007 9:04 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] force=nan in frame 0 dongsheng zhang wrote: Dear Mark, Thank you for your reply. I have used gromacs before. In fact, I have built this FF before, and using it successfully. My old computer was crashed, so I need to do it again. The potential energies looked fine in the md.log. Even I turn off all potentials. I still get the initial foce = nan. Could you please give me any suggest about it? Can't tell. You still haven't told us what you were trying to do when it crashed. EM, MD? Did you minimize and/or equilibrate? Does this installation run other systems? 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 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: [Bulk] Re: [gmx-users] force=nan in frame 0
You can send me the file off the list. To solve this kind of problem, start from simple case: two or a handful of atoms. Regards, Yang Ye On 11/13/2007 5:36 AM, Dongsheng Zhang wrote: Dear Yang Ye, Thank you very much for your reply. You are very helpful in my experience. I turned off the nb interaction by c6=0, c12 = 0. If you need my force field, I can give you the package for testing. All the best! Dongsheng - Original Message From: Yang Ye [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, November 12, 2007 2:33:38 PM Subject: Re: [gmx-users] force=nan in frame 0 how do you turn off the interactions? e.g. setting rvdw=0 doesn't mean turning of vdw interactions. Regards, Yang Ye On 11/13/2007 12:55 AM, dongsheng zhang wrote: Dear Mark, The installation works for other systems. The error happens in either EM or MD. When I turn off all interaction potentials, the forces between all particles should be zero, shouldn't they? Could you please tell me why the initial forces are NaN? Thanks! All the best! Dongsheng -Original Message- From: [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED]] On Behalf Of Mark Abraham Sent: Sunday, November 11, 2007 9:04 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] force=nan in frame 0 dongsheng zhang wrote: Dear Mark, Thank you for your reply. I have used gromacs before. In fact, I have built this FF before, and using it successfully. My old computer was crashed, so I need to do it again. The potential energies looked fine in the md.log. Even I turn off all potentials. I still get the initial foce = nan. Could you please give me any suggest about it? Can't tell. You still haven't told us what you were trying to do when it crashed. EM, MD? Did you minimize and/or equilibrate? Does this installation run other systems? Mark ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-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] mailto:[EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-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] mailto:[EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-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] mailto:[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 mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to set N-terminal lysine carry only +1 unit charge?
it could not be possible since amber force field doesn't parameterized NLYN. alternative, use ACE/NME to cap the peptide. On 11/9/2007 7:36 PM, Hu Zhongqiao wrote: Hi, I am using amber force field in Gromacs. The protein I simulated is the lysozyme (PDBID: 1HEL). I want to set all lysine residues to be neutral. According to rules using Amber in Gromacs, neutral lysine should be named to LYN. Everything goes smoothly except the N-terminal lysine residue. It should carry +1 unit charge due to its location. According to the rules, I should rename this residue as NLYN. But I can not find NLYN in ffamber*.rtp. In other words, error will appear if I do so. I did not get response from Dear Dr. Eric J. Sorin who establish amber port into gromacs. So anyone knows how to set N-terminal lysine residue carry +1, not +2 unit charges using Amber FF in gmx? Zhongqiao National University of Singapore ___ 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] gmx 3.3.2 explodes with libc.so.6
Hi, Please be clear that failed test: simple/rb1 and complex/acetonitrilRF are due to different reasons. So far, simple/rb1 remains unknown but complex/acetonitrilRF has been solved. Also, a segmentation fault is different from results having difference to the benchmark data. Please be exact about their failure pattern when reporting. The fix of acetonitrilRF is available in the CVS. Even you don't apply, it won't affect if you are using parallel and you are not using RF. Regards, Yang Ye On 11/9/2007 7:49 PM, Li Qiang wrote: I see. thanks for the information. but one of my friends nearby failed on this combination just few hours ago. Maybe we need more test for the conclusion. Li Qiang On Fri, 2007-11-09 at 10:47 +, Bruce Milne wrote: Dear Li Qiang, it seems another guy get the same error(cannot pass gmxtest with rb1/acetonitrilRF) as me. and it sounds like the compatible problem between GROMACS 3.3.2 and and UBUNTU 7.10. Both are rather new. Herein I just suggest and hope others may help to install 3.3.2 on new ubuntu 7.10 to confirm the problem. I have just installed 3.3.2 on my (64-bit) Ubuntu 7.10 machine (dual-core Athlon64 4000+, 2GB RAM) and run the serial tests. All the single and double precision tests passed with and without assembly loop optimizations so I guess it's not simply Ubuntu 7.10 that is to blame (unless what you are seeing is a 32-bit distribution-specific problem?). Cheers, Bruce ___ 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] gmx 3.3.2 explodes with libc.so.6
On 11/9/2007 6:47 PM, Bruce Milne wrote: Dear Li Qiang, it seems another guy get the same error(cannot pass gmxtest with rb1/acetonitrilRF) as me. and it sounds like the compatible problem between GROMACS 3.3.2 and and UBUNTU 7.10. Both are rather new. Herein I just suggest and hope others may help to install 3.3.2 on new ubuntu 7.10 to confirm the problem. I have just installed 3.3.2 on my (64-bit) Ubuntu 7.10 machine (dual-core Athlon64 4000+, 2GB RAM) and run the serial tests. All the single and double precision tests passed with and without assembly loop optimizations so I guess it's not simply Ubuntu 7.10 that is to blame (unless what you are seeing is a 32-bit distribution-specific problem?). Quite likely a 32-bit specific problem. Could anyone install dmalloc and configure gromacs to build with dmalloc and run the test with the new mdrun? I did mine and found that it was due to one line in mshift.c srenew(g-edge[0],n); mdrun output: realloc for g-edge[0] (24 bytes, file mshift.c, line 251, g-edge[0]=0x0x 1) Regards, Yang Ye Cheers, Bruce ___ 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
On 11/9/2007 9:09 PM, David van der Spoel wrote: Yang Ye wrote: On 11/9/2007 6:47 PM, Bruce Milne wrote: Dear Li Qiang, it seems another guy get the same error(cannot pass gmxtest with rb1/acetonitrilRF) as me. and it sounds like the compatible problem between GROMACS 3.3.2 and and UBUNTU 7.10. Both are rather new. Herein I just suggest and hope others may help to install 3.3.2 on new ubuntu 7.10 to confirm the problem. I have just installed 3.3.2 on my (64-bit) Ubuntu 7.10 machine (dual-core Athlon64 4000+, 2GB RAM) and run the serial tests. All the single and double precision tests passed with and without assembly loop optimizations so I guess it's not simply Ubuntu 7.10 that is to blame (unless what you are seeing is a 32-bit distribution-specific problem?). Quite likely a 32-bit specific problem. Could anyone install dmalloc and configure gromacs to build with dmalloc and run the test with the new mdrun? I did mine and found that it was due to one line in mshift.c srenew(g-edge[0],n); mdrun output: realloc for g-edge[0] (24 bytes, file mshift.c, line 251, g-edge[0]=0x0x 1) So is this in the rb1 test? I compiled the code with dmalloc on my Mac and it passed all tests (except dec+water due to very small energy differences). Yes. Try 32-bit? 64-bit on my Opteron is alright too (with and without dmalloc). Regards, Yang Ye Cheers, Bruce ___ 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] Re: How to set N-terminal lysine carry only +1 unit charge?
ACE for the N-termail and NME for the C-terminal. They are neutral. You can do so with aids from PyMol... Regards, Yang Ye On 11/9/2007 9:50 PM, Hu Zhongqiao wrote: Thanks, Yang Ye. You mean that I put an additional ACE or NME on the N-terminal lysine residue? zhongqiao Message: 3 Date: Fri, 09 Nov 2007 20:03:21 +0800 From: Yang Ye [EMAIL PROTECTED] Subject: Re: [gmx-users] How to set N-terminal lysine carry only +1 unitcharge? To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1; format=flowed it could not be possible since amber force field doesn't parameterized NLYN. alternative, use ACE/NME to cap the peptide. On 11/9/2007 7:36 PM, Hu Zhongqiao wrote: Hi, I am using amber force field in Gromacs. The protein I simulated is the lysozyme (PDBID: 1HEL). I want to set all lysine residues to be neutral. According to rules using Amber in Gromacs, neutral lysine should be named to LYN. Everything goes smoothly except the N-terminal lysine residue. It should carry +1 unit charge due to its location. According to the rules, I should rename this residue as NLYN. But I can not find NLYN in ffamber*.rtp. In other words, error will appear if I do so. I did not get response from Dear Dr. Eric J. Sorin who establish amber port into gromacs. So anyone knows how to set N-terminal lysine residue carry +1, not +2 unit charges using Amber FF in gmx? Zhongqiao National University of Singapore ___ 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] gmx 3.3.2 explodes with libc.so.6
On 11/9/2007 9:21 PM, David van der Spoel wrote: Yang Ye wrote: On 11/9/2007 9:09 PM, David van der Spoel wrote: Yang Ye wrote: On 11/9/2007 6:47 PM, Bruce Milne wrote: Dear Li Qiang, it seems another guy get the same error(cannot pass gmxtest with rb1/acetonitrilRF) as me. and it sounds like the compatible problem between GROMACS 3.3.2 and and UBUNTU 7.10. Both are rather new. Herein I just suggest and hope others may help to install 3.3.2 on new ubuntu 7.10 to confirm the problem. I have just installed 3.3.2 on my (64-bit) Ubuntu 7.10 machine (dual-core Athlon64 4000+, 2GB RAM) and run the serial tests. All the single and double precision tests passed with and without assembly loop optimizations so I guess it's not simply Ubuntu 7.10 that is to blame (unless what you are seeing is a 32-bit distribution-specific problem?). Quite likely a 32-bit specific problem. Could anyone install dmalloc and configure gromacs to build with dmalloc and run the test with the new mdrun? I did mine and found that it was due to one line in mshift.c srenew(g-edge[0],n); mdrun output: realloc for g-edge[0] (24 bytes, file mshift.c, line 251, g-edge[0]=0x0x 1) So is this in the rb1 test? I compiled the code with dmalloc on my Mac and it passed all tests (except dec+water due to very small energy differences). Yes. Try 32-bit? 64-bit on my Opteron is alright too (with and without dmalloc). This is a 32 bit OS AFAIK (Mac OS X 10.5) with gcc 4.0.1 Anyway how did you obtain the above result? What command line? My Linux is ubuntu 32-bit on P4. If mdrun is built without dmalloc, it will report realloc error from glibc. Then I built mdrun with dmalloc, and it reports the line above (realloc for g-edge[0]...,mshift.c. line 251...) Regards, Yang Ye Cheers, Bruce ___ 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 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] genernal problem in simulation
this is a too general question. please read the wiki first. On 11/9/2007 9:58 PM, Kitty Ji wrote: Dear users: After we get some data from GMX simulation, how can we validate them? I met many difficulties in parameters setting. ___ Kitty JI Groupe Matière Condensée et Matériaux UMR-CNRS 6626 Bat. 11A, Campus de Beaulieu Université de Rennes 1 35042 Rennes cedex FRANCE Tel. : +33 2 23 23 64 97 Fax. : +33 2 23 23 67 17 ___ ___ 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] How to set N-terminal lysine carry only +1 unit charge?
DIY on the admin panel http://www.gromacs.org/index.php?option=com_wrapperItemid=83 On 11/9/2007 11:04 PM, Henry O Ify wrote: Hell my friend, i dont need any of this messages from all the members of this board, please help alert the board, its bored reading them all, i want to unsubscribe from the group */Yang Ye [EMAIL PROTECTED]/* wrote: it could not be possible since amber force field doesn't parameterized NLYN. alternative, use ACE/NME to cap the peptide. On 11/9/2007 7:36 PM, Hu Zhongqiao wrote: Hi, I am using amber force field in Gromacs. The protein I simulated is the lysozyme (PDBID: 1HEL). I want to set all lysine residues to be neutral. According to rules using Amber in Gromacs, neutral lysine should be named to LYN. Everything goes smoothly except the N-terminal lysine residue. It should carry +1 unit charge due to its location. According to the rules, I should rename this residue as NLYN. But I can not find NLYN in ffamber*.rtp. In other words, error will appear if I do so. I did not get response from Dear Dr. Eric J. Sorin who establish amber port into gromacs. So anyone knows how to set N-terminal lysine residue carry +1, not +2 unit charges using Amber FF in gmx? Zhongqiao National University of Singapore ___ gmx-users mailing list gmx-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 list gmx-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 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
got solved? I am using Ubuntu 6.10 after updating its packages, gromacs still fail on the simple/rb1 test, in a symptom similar to Li Qiang's. 3.3.1 is able to pass all the tests. Another thing is that acetonitrilRF also failed in 3.3.2 (both on Opteron and P4) but not with 3.3.1 --- Program mdrun, VERSION 3.3.2 Source code file: network.c, line: 437 Routine should not have been called: gmx_sumi --- Perhaps gmx-developer is a better place for this thread. Regards, Yang Ye On 11/8/2007 5:03 AM, Dmytro Kovalskyy wrote: 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 ___ 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
Regarding the failed test for simple/rb1, I used dmalloc and the message is realloc for g-edge[0] (24 bytes, file mshift.c, line 251, g-edge[0]=0x0x 1) the line in mshift.c is srenew(g-edge[0],n); Regards,. Yang Ye On 11/9/2007 1:35 AM, David van der Spoel wrote: Yang Ye wrote: got solved? I am using Ubuntu 6.10 after updating its packages, gromacs still fail on the simple/rb1 test, in a symptom similar to Li Qiang's. 3.3.1 is able to pass all the tests. Another thing is that acetonitrilRF also failed in 3.3.2 (both on Opteron and P4) but not with 3.3.1 --- Program mdrun, VERSION 3.3.2 Source code file: network.c, line: 437 Routine should not have been called: gmx_sumi --- Perhaps gmx-developer is a better place for this thread. i've fixed this in CVS and posted a fix on the mailing lisst as well. Regards, Yang Ye On 11/8/2007 5:03 AM, Dmytro Kovalskyy wrote: 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 ___ 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] 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] 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
Re: [gmx-users] Help: A ligand covalently bond to protein
for more features like angle or dihedral, merge each section of their itp (offset all the numbers in the second itp for an offset) shall be a more elegant way. On 11/7/2007 6:00 AM, Tanping Li wrote: Dear Yang, Really thanks for the help. Distance constraint can describe the bond length between ligand and protein, how about other propery of covalent bond? Maybe I missed something of your message. Yours Tanping --- Yang Ye [EMAIL PROTECTED] wrote: you might want to try distance constraint. On 11/7/2007 5:11 AM, Tanping Li wrote: Dear all, I searched the mailling list, and still can't find a way to set up my system: a ligand covalently bond to protein. I don't know if there is a easier way to do this. What I can think of is: 1) Add a bond I like in the specbond.dat file; 2) Add a block for ligand in the rtp file; 3) run pdb2gmx, gromacs will treat protein and ligand a one chain since it can see the bond in the specbond.dat. I just wonder if there is a eaiser way to add a ligand to rtp file? When I run Dundee PRODRG2, I get a .itp file. Is there some way to change this into rtp format? It is not trival to write a rtp manually. Really appretiate your help. Yours Tanping ___ 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 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] Help: A ligand covalently bond to protein
you might want to try distance constraint. On 11/7/2007 5:11 AM, Tanping Li wrote: Dear all, I searched the mailling list, and still can't find a way to set up my system: a ligand covalently bond to protein. I don't know if there is a easier way to do this. What I can think of is: 1) Add a bond I like in the specbond.dat file; 2) Add a block for ligand in the rtp file; 3) run pdb2gmx, gromacs will treat protein and ligand a one chain since it can see the bond in the specbond.dat. I just wonder if there is a eaiser way to add a ligand to rtp file? When I run Dundee PRODRG2, I get a .itp file. Is there some way to change this into rtp format? It is not trival to write a rtp manually. Really appretiate your help. Yours Tanping ___ 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] Fatal error:Atom index (1) in settles out of bounds (1-0)
Hi, To use GROMACS' spc topology with ffamber, you may create a new spc topology, e.g. spc-amber.itp. Following is its content. If you know C preprocessor, you can merge it with original spc.itp. [ moleculetype ] ; molname nrexcl SOL 2 [ atoms ] ; nr type resnr residue atom cgnr charge mass 1 amber99_54 1 SOL OW 1 -0.82 15.99940 2 amber99_55 1 SOLHW1 1 0.41 1.00800 3 amber99_55 1 SOLHW2 1 0.41 1.00800 #ifdef FLEXIBLE [ bonds ] ; i j funct length force.c. 1 2 1 0.1 345000 0.1 345000 1 3 1 0.1 345000 0.1 345000 [ angles ] ; i j k funct angle force.c. 2 1 3 1 109.47 383 109.47 383 #else [ settles ] ; OW funct doh dhh 1 1 0.1 0.16333 [ exclusions ] 1 2 3 2 1 3 3 1 2 #endif On 11/5/2007 2:59 PM, willting wrote: Hi, I added ffamber_v3.3.1 to gromacs-3.3.1 and wanted to use the AMBER99 Wang protein/nucleic acid forcefield. Run the commands: pdb2gmx -ignh -f sev.pdb -o sev.gro -p sev.top -missing -water spc editconf -bt cubic -f sev.gro -o sev_box.gro -c -d 1 genbox -cp sev_box.gro -cs -p sev.top -o sev_water.gro grompp -v -f em.mdp -c sev.gro -p sev.top -o sev_em.tpr then it showed: --- Program grompp, VERSION 3.3.1 Source code file: toppush.c, line: 1108 Fatal error: [ file /usr/local/gromacs/share/gromacs/top/spc.itp, line 41 ]: Atom index (1) in settles out of bounds (1-0) --- what should I do ? Thanks, will * My pdb: ATOM 3072 N NPHE P 1 49.900 57.324 4.858 1.00 17.05 N ATOM 3073 CA NPHE P 1 49.015 58.449 4.532 1.00 17.68 C ATOM 3074 C NPHE P 1 48.529 58.242 3.088 1.00 17.14 C ATOM 3075 O NPHE P 1 49.336 58.259 2.133 1.00 18.44 O ATOM 3076 CB NPHE P 1 49.786 59.754 4.742 1.00 1850 C ATOM 3077 CG NPHE P 1 48.955 60.964 4.622 1.00 22.19 C ATOM 3078 CD1 NPHE P 1 48.146 61.341 5.652 1.00 28.37 C ATOM 3079 CD2 NPHE P 1 48.962 61.710 3.451 1.00 30.13 C ATOM 3080 CE1 NPHE P 1 47.364 62.498 5.562 1.00 33.16 C ATOM 3081 CE2 NPHE P 1 48.231 62.874 3.360 1.00 31.49 C ATOM 3082 CZ NPHE P 1 47.415 63.254 4.420 1.00 33.03 C ATOM 3083 N ALA P 2 47.231 57.937 3.024 1.00 17.87 N ATOM 3084 CA ALA P 2 46.514 57.524 1.824 1.00 18.82 C ATOM 3085 C ALA P 2 46.531 58.561 0.717 1.00 19.39 C ATOM 3086 O ALA P 2 46.622 59.753 0.962 1.00 18.85 O ATOM 3087 CB ALA P 2 45.082 57.093 2.184 1.00 18.07 C ATOM 3088 N PRO P 3 46.475 58.093 -0.513 1.00 20.13 N ATOM 3089 CA PRO P 3 46.273 59.006 -1.620 1.00 23.52 C ATOM 3090 C PRO P 3 44.935 59.714 -1.371 1.00 26.20 C ATOM 3091 O PRO P 3 43.968 59.104 -0.883 1.00 30.44 O ATOM 3092 CB PRO P 3 46.123 58.061 -2.834 1.00 22.88 C ATOM 3093 CG PRO P 3 46.724 56.802 -2.456 1.00 20.87 C ATOM 3094 CD PRO P 3 46.550 56.684 -0.930 1.00 18.82 C ATOM 3095 N GLY P 4 44.860 60.944 -1.765 1.00 30.11 N ATOM 3096 CA GLY P 4 43.552 61.581 -1.771 1.00 32.23 C ATOM 3097 C GLY P 4 43.266 61.997 -3.211 1.00 30.90 C ATOM 3098 O GLY P 4 44.171 62.226 -3.966 1.00 34.59 O ATOM 3099 N ASN P 5 42.016 62.091 -3.590 1.00 33.27 N ATOM 3100 CA ASN P 5 41.666 62.673 -4.864 1.00 32.62 C ATOM 3101 C ASN P 5 41.960 61.777 -6.056 1.00 31.39 C ATOM 3102 O ASN P 5 42.610 62.291 -6.989 1.00 33.62 O ATOM 3103 CB ASN P 5 42.445 63.999 -5.073 1.00 35.10 C ATOM 3104 CG ASN P 5 42.229 65.016 -3.907 1.00 40.06 C ATOM 3105 OD1 ASN P 5 41.098 65.202 -3.404 1.00 47.96 O ATOM 3106 ND2 ASN P 5 43.323 65.656 -3.468 1.00 47.14 N ATOM 3107 N TYR P 6 41.551 60.487 -6.012 1.00 24.72 N ATOM 3108 CA TYR P 6 41.616 59.590 -7.164 1.00 22.15 C ATOM 3109 C TYR P 6 40774 60.234 -8.266 1.00 21.95 C ATOM 3110 O TYR P 6 39.555 60.176 -8.207 1.00 21.25 O ATOM 3111 CB TYR P 6 41.068 58.202 -6.866 1.00 21.39 C ATOM 3112 CG TYR P 6 41.847 57.366 -5.863 1.00 19.06 C ATOM 3113 CD1 TYR P 6 41.589 57.466 -4.512 1.00 16.12 C ATOM 3114 CD2 TYR P 6 42.800 56.441 -6.274 1.00 15.31 C ATOM 3115 CE1 TYR P 6 42.257 56.717 -3.628 1.00 15.10 C ATOM 3116 CE2 TYR P 6 43.510 55.696 -5.390 1.00 13.45 C ATOM 3117 CZ TYR P 6 43.226 55.805 -4.054 1.00 15.29 C ATOM 3118 OH TYR P 6 43.914 55.071 -3.133 1.00 14.56 O ATOM 3119 N PRO P 7 41.417 60.776 -9.285 1.00 21.63 N ATOM 3120 CA PRO P 7 40.708 61.437 -10.395 1.00 21.38 C ATOM 3121 C PRO P 7 39.731 60.470 -11.044 1.00 20.08 C ATOM 3122 O PRO P 7 40.005 59.287 -11.207 1.00 18.00 O ATOM 3123 CB PRO P 7 41.824 61.799 -11.375 1.00 23.11 C ATOM 3124 CG PRO P 7 43.064 61.687 -10.604 1.00 25.67 C ATOM 3125 CD PRO P 7 42.862 60.695 -9.527 1.00 23.44 C ATOM 3126 N ALA P 8 38.590 60.992 -11.468 1.00 18.89 N ATOM 3127 CA ALA P 8 37.595 60.159 -12.075 1.00 18.81 C ATOM 3128 C ALA P 8 38.061 59.569 -13.390 1.00 17.43 C ATOM 3129 O ALA P 8 38.796 60.195 -14.168 1.00 18.08 O ATOM 3130 CB ALA P 8 36.306 60.943 -12.286 1.00 19.45 C ATOM 3131 N CLEU P 9 37.637 58.345 -13.643 1.00 16.96 N ATOM 3132 CA CLEU P 9 37.959 57.644 -14.866 1.00 18.11 C ATOM 3133 C CLEU P 9
Re: [gmx-users] Position restricted md
Doing position-restrained simulation is useful to equilibrate solvent and ions. If you would like to study the dynamics of the peptide, PRMD doesn't help. PRMD is usually performed before production run for a duration from several hundred ps to 1ns. Regards, Yang Ye - Original Message From: sarbani chattopadhyay [EMAIL PROTECTED] To: gmx-users@gromacs.org Sent: Tuesday, October 23, 2007 1:35:14 PM Subject: [gmx-users] Position restricted md Hi, I am new to the field of MD.I want to know what is the effectivity of position restricted MD ie. where is the advantage of doing Position restricted MD.I have a small peptide of 3 reidues.Is it necessary to do a Position restricted MD. What difference will it make? I may sound very unintelligent but any suggestions are welcome. THANKS in advance. Sarbani -Inline Attachment Follows- ___ 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] entropy calaculted script??
I doubt that no one could give you such script. To plot free energy surface, you can utilize Rg/Q or Rg/ContactNumber or dPCA (http://wiki.gromacs.org/index.php/Dihedral_PCA) analysis. Regards, Yang Ye - Original Message From: xi zhao [EMAIL PROTECTED] To: gmx-users@gromacs.org Sent: Tuesday, October 23, 2007 7:21:12 PM Subject: [gmx-users] entropy calaculted script?? Dear Gro-usr friends: I want to calculat the entropy during the md,but lack calculting script for the entropy. Who can provide it for me? Thank you very much! @yahoo.cn 新域名、无限量，快来抢注！ -Inline Attachment Follows- ___ 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] pdb2gmx error - version 3.3.1
submit a bug report at bugzilla.gromacs.org? On 10/17/2007 2:40 AM, Justin A. Lemkul wrote: Hello all, I am having a strange error when using pdb2gmx. I am trying to generate the topology for a simple protein, using Gromos96 43a1. I am able to create the topology with version 3.3 without issue. However, if I use pdb2gmx under version 3.3.1, I encounter this: $ pdb2gmx -f protein.pdb -o protein.gro -ignh (pdb2gmx runs through its normal routine...) - Program pdb2gmx, VERSION 3.3.1 Source code file: pgutil.c, line: 87 Fatal error: Atom N not found in residue 1 while adding improper - If I try the ffgmx force field, everything works fine. There are no broken residues in the PDB (it's one that I've worked with before, just with a different force field). I have not tried to generate the topology under version 3.3.2, because our university's cluster only has versions 3.3 and 3.3.1 available. I suppose I can just use version 3.3, but I thought I should bring up this issue in case it needs fixing in future versions (or in case I'm missing something that should be an easy fix). -Justin == Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://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 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] pbc problem
On 10/16/2007 2:31 AM, tangxuan wrote: Dear all, If pbc is full or xyz in mdp file, do i need to use the trjconv -pbc nojump to remove the jump when the protein is separate in the box after simulation and I want to calculate the rmsd of the protein? IT is not necessary to use trjconv -pbc before running most gromacs analysis tools. they have built-in support to move atom back if they appear at the other side. What is difference of use of pbc in mdp file and in trjconv -pbc nojump? they are two separate stuff: specify pbc=full or pbc=xyz in mdp indicate that the simulation is carried out with PBC so that atoms which moves out of the box will appear on the other side of the box; trjconv -pbc nojump is a post-processing step, meant for visualization or analysis tools not provided by GROMACS. Thank you!! Tang Jiaowei ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ 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] the comm_mode
Generally, linear. For simulation in vacumm, you need rotation. With big molecules, equilibration may not be done thoroughly; this may result in very obivious rotation that Linear can not prevent. So visualize your trajectory and check your molecule. If it happens, you need to apply Rotation in the beginning of your simulation for a few ns. Regards, Yang Ye - Original Message From: Dechang Li [EMAIL PROTECTED] To: gmx-users gmx-users@gromacs.org Sent: Sunday, October 14, 2007 5:34:35 PM Subject: [gmx-users] the comm_mode Dear all, There are three options of comm_mode: Linear, Angular and none. The option Angular is said that Remove center of mass translation and rotation around the center of mass. Does it mean the option Angular remove the translation and rotation BOTH ? If I want to do a simulation such as a protein in the explicit water, which option would be better? Or it will be the same? Thank you for your reply. Best regards, 2007-10-14 = Dechang Li, PhD Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 PR China Tel: +86-10-62773779(O) Email: [EMAIL PROTECTED] =___ 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: Re: [gmx-users] the comm_mode
- Original Message From: OZGE ENGIN [EMAIL PROTECTED] To: [EMAIL PROTECTED]; gmx-users@gromacs.org Cc: gmx-users@gromacs.org Sent: Sunday, October 14, 2007 8:33:28 PM Subject: Re: Re: [gmx-users] the comm_mode Hi Yang, I am performing a simulation of a peptide in vacuum, and in the mailing archieve, I read that using of linear option of comm_mode in the vacuum simulations. Is it due to the relatively rapid convergence of molecules in the vacuum environment? It is not because of this reason, it is due to PBC. Simulation in vacuum is usually done without PBC, Rotation is recommended. COM velocity removal's effect is directly visible, so if Linear works for you, you may use it. Thanks in advance Ozge -Original Message- From: Yang Ye [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Sun, 14 Oct 2007 03:42:12 -0700 (PDT) Subject: Re: [gmx-users] the comm_mode Generally, linear. For simulation in vacumm, you need rotation. With big molecules, equilibration may not be done thoroughly; this may result in very obivious rotation that Linear can not prevent. So visualize your trajectory and check your molecule. If it happens, you need to apply Rotation in the beginning of your simulation for a few ns. Regards, Yang Ye - Original Message From: Dechang Li [EMAIL PROTECTED] To: gmx-users gmx-users@gromacs.org Sent: Sunday, October 14, 2007 5:34:35 PM Subject: [gmx-users] the comm_mode Dear all, There are three options of comm_mode: Linear, Angular and none. The option Angular is said that Remove center of mass translation and rotation around the center of mass. Does it mean the option Angular remove the translation and rotation BOTH ? If I want to do a simulation such as a protein in the explicit water, which option would be better? Or it will be the same? Thank you for your reply. Best regards, 2007-10-14 = Dechang Li, PhD Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 PR China Tel: +86-10-62773779(O) Email: [EMAIL PROTECTED] =___ 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] Tool for visualizing disulphide bonds
Program like VMD can draw extra bond. You need to get its manual and code a line or two in TCL. Regards, Yang Ye On 10/14/2007 11:38 PM, van Bemmelen wrote: Hi Ozge, I'm not sure what you mean by visualization. But what about using VMD for trajectory visualization and creating a representation that contains only the sulphur atoms forming the disulphide bonds? If that doesn't answer your question, please be more specific. Cheers, Jeroen Date: Sun, 14 Oct 2007 15:45:24 +0300 From: OZGE ENGIN [EMAIL PROTECTED] Subject: [gmx-users] Tool for visualizing disulphide bonds To: gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=UTF-8 Hi all, Is there any tool for the visualization of disulphide bonds along the whole trajectory? Regards, Ozge ___ 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] the comm_mode
Hi, It's about geometry. Be pragmatic. By inspecting the trajectory, you can which one works. if Linear works for your system, use it; otherwise, use rotation. Although I prefer to use Rotation for simulations in vacuum in the first place, and for first few ns simulation for big protein with explicit solvent. Regards, Yang Ye On 10/15/2007 12:24 AM, OZGE ENGIN wrote: Sorry, but I have to ask some more questions. I have just started to perform simulations in vacuum. I can understand not using of PME in vacuum simulations; however, I can not understand the sentence you wrote : 'rotation is recomended.' COM velocity removal's effect is directly visible. Is it related to conservation of angular momentum? Thank you very much! Oz. -Original Message- From: Yang Ye [EMAIL PROTECTED] To: gmx-users@gromacs.org Date: Sun, 14 Oct 2007 07:07:18 -0700 (PDT) Subject: Re: Re: [gmx-users] the comm_mode - Original Message From: OZGE ENGIN [EMAIL PROTECTED] To: [EMAIL PROTECTED]; gmx-users@gromacs.org Cc: gmx-users@gromacs.org Sent: Sunday, October 14, 2007 8:33:28 PM Subject: Re: Re: [gmx-users] the comm_mode Hi Yang, I am performing a simulation of a peptide in vacuum, and in the mailing archieve, I read that using of linear option of comm_mode in the vacuum simulations. Is it due to the relatively rapid convergence of molecules in the vacuum environment? It is not because of this reason, it is due to PBC. Simulation in vacuum is usually done without PBC, Rotation is recommended. COM velocity removal's effect is directly visible, so if Linear works for you, you may use it. Thanks in advance Ozge -Original Message- From: Yang Ye [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Sun, 14 Oct 2007 03:42:12 -0700 (PDT) Subject: Re: [gmx-users] the comm_mode Generally, linear. For simulation in vacumm, you need rotation. With big molecules, equilibration may not be done thoroughly; this may result in very obivious rotation that Linear can not prevent. So visualize your trajectory and check your molecule. If it happens, you need to apply Rotation in the beginning of your simulation for a few ns. Regards, Yang Ye - Original Message From: Dechang Li [EMAIL PROTECTED] To: gmx-users gmx-users@gromacs.org Sent: Sunday, October 14, 2007 5:34:35 PM Subject: [gmx-users] the comm_mode Dear all, There are three options of comm_mode: Linear, Angular and none. The option Angular is said that Remove center of mass translation and rotation around the center of mass. Does it mean the option Angular remove the translation and rotation BOTH ? If I want to do a simulation such as a protein in the explicit water, which option would be better? Or it will be the same? Thank you for your reply. Best regards, 2007-10-14 = Dechang Li, PhD Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 PR China Tel: +86-10-62773779(O) Email: [EMAIL PROTECTED] = ___ 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] running gromacs in parallel, and with nice levels
On 10/4/2007 11:50 PM, maria goranovic wrote: Dear All, - So I think I succeeded in running gromacs on a 4-core node. How does one confirm this without looking at the speed. i.e, where is it mentioned in the log file what the number of processors is ? I do get 4 different log files for 4 processors, is that the final evidence ? Make sure that mdrun is compiled with mpi; other, it will result in four independent process, with four different log files (of course, in such case, log files could more or less the same.). - The nice level by default is too high (19). One can change this by compiling mdrun with a nonice option. However, does it really matter if one is running gromacs on a dedicated supercomputing node ? Also, one can change the nice level by -nice in the mdrun command. So, in principle, there is no need to recompile mdrun ? You don't need to re-compile mdrun in order to get rid of the nice effect. Setting nice to 19 for mdrun is alright, but I got a bit inefficiency with analysis tools at nice 19. This results in slow execution of the analysis tools when there is background jobs, e.g. mdrun. Thank you so very much for the inputs, -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 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to calculate the average distance or energy between two residues?
Hi, For average distance, you can gather distance v. time by g_mindist, then average them. For average energy, you are refering to interaction energy? What you can do is to define two energy groups for two residues separatedly, make a new tpr and use mdrun rerun to get it. Regards, Yang Ye - Original Message From: MoJie Duan [EMAIL PROTECTED] To: gmx-users@gromacs.org Sent: Sunday, October 7, 2007 10:49:26 PM Subject: [gmx-users] How to calculate the average distance or energy between two residues? Hi, everyone! I want to calculate the average energy (like vdw potential) and average distance between two residues (or two atoms) during a simulation process, how can i do this? Is there any exist package? best wishes!___ 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] Nucleic Acid Simulations with Gromacs
the amber port from eric j sorin. On 10/2/2007 6:44 PM, Monika Sharma wrote: Dear All, I want to start nucleic acid simulations. I am using gromacs3.3.1. But I could not find any mention of Nucleic Acids in any of the force-field provided by gromacs distro. So does it mean that one _can not_ simulate nucleic acids with gromacs. Has anyone tried? And if someone can guide me through?? Thanks in advance Regards, Monika ___ 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] Nucleic Acid Simulations with Gromacs
Please don't use the OPLS NA forcefield. It is largely based on AMBER (OPLS takes different approach in parameterization, so you know that direct migration is so correct) and not verified. I had some communications with that group on this issue. It has some teaching value on making topology of small molecules in OPLS format but except this, don't use for serious business. Regards, Yang Ye On 10/2/2007 6:58 PM, [EMAIL PROTECTED] wrote: Hi, On the gromacs webpage in user contributions-topologies you have (at least) 2 forcefields do download that allow you to simulate NA. The first is OPLS NA records from rnp-group (http://rnp-group.genebee.msu.su/3d/oplsa_ff.html). It is for gromacs 3.2.1, so minor manual adjustments for 3.3.1 are required. The second is AMBER ff variants from Stanford (http://folding.stanford.edu/ffamber/). Good Luck Grzegorz Wieczorek Department of Bioinformatics Institute of Biochemistry and Biophysics Polish Academy of Sciences ul. Pawinskiego 5a 02-106 Warszawa, Poland On Tue, 2 Oct 2007, Monika Sharma wrote: Dear All, I want to start nucleic acid simulations. I am using gromacs3.3.1. But I could not find any mention of Nucleic Acids in any of the force-field provided by gromacs distro. So does it mean that one _can not_ simulate nucleic acids with gromacs. Has anyone tried? And if someone can guide me through?? Thanks in advance Regards, Monika ___ 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 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] Gromacs for Aerosol Particle Agglomeration
On 9/29/2007 9:13 PM, Lorenzo Isella wrote: Dear All, I am 100% new on this list and to Molecular Dynamics in general. This is what I am interested into (and would like to know if Gromacs is then the right tool). I am not really into biology or chemistry, but rather in aerosol science. I am interested in studying how diesel exhaust aerosol particles, generally carried by a turbulent exhaust flow, collide and, by sticking together, give rise to complicated structures (idea of agglomeration). We now leave aside the technicalities (how they stick, what the compenetration depends upon etc.), but first of all I would like to know if Gromacs is the right tool for doing that. You may consult the gromacs manual, which is also a good introductory material on the topic of MD. You need to check especially whether the interaction existed in your system can be found in GROMACS' supported inter-particle interaction. Typically, I deal with concentrations around 10^8 particles per cm^3 and I need to follow the evolution of the system for some seconds. The particles carrier-flow is typically turbulent, but collisions are mainly due to Brownian motion (I am thinking about some Langevin dynamics). I have access to a few nodes in a cluster (if that becomes a necessity) but have no experience in running parallel codes. You can leave this question later. A last (but not least) question: I installed gromacs on my Debian Testing laptop; how do I run the examples/tutorials? GROMACS works almost with command-line tools so you need to open the terminal windows to type commands inside them. So get yourself with some basic Linux/Unix commands first if you are no so; then proceed with the tutorial. Is there any available gromacs code you recommend me to look at for my specific problem or as a good way to learn the ropes? Check literature. I guess there would be some MD work done on your topic. You may then migrate them to GROMACS by looking at them. You may raise relevant question to this list. However, if you are doing Langevin dynamics of non-atomistic models, you may get easier life with Espresso than GROMACS. www.*espresso*.mpg.de Many thanks Lorenzo ___ 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] ANTECHAMBER GAFF
The antechamber's website has a tutorial http://amber.scripps.edu/antechamber/antechamber.html For faster results, you can use AM1/BCC for partial charge determination; while keep Guassian's version running alongside. Later you will need to transform the topology from AMBER format to GROMACS. The amb2gmx.pl from E.J. Sorin shall help (http://chemistry.csulb.edu/ffamber/tools.html). Regards, Yang Ye On 9/29/2007 10:22 PM, Dechang Li wrote: Dear gmx-users， I want to use ANTECHAMBER GAFF to generate the topology of a small molecular(HIV-1 Protease inhibitor, Nelfinavir) for gromacs. But It seems to be not so simple. Is there anyone who did the similar thing before? Is there any tutorials? With best regards, 2007-9-29 = Dechang Li, PhD Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 PR China Tel: +86-10-62773779(O) Email: [EMAIL PROTECTED] = ___ 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] Pbc and Com in simulation video
shall you try -fit progress? On 9/25/2007 11:03 PM, [EMAIL PROTECTED] wrote: Hello gmx-users! I am trying to make a simulation video in which a water droplet is rolling or sliding on a surface. Due to a periodic boundary conditions a droplet is not whole all the time but it disappears from the right and appears from the left in cycles. I think that I could create more visual video by removing the lateral motion of the center of mass of a droplet so that the droplet would stay whole in the middle of simulation window and the surface would translate below the droplet. I am not exactly sure how realistic this kind of video would be and would like to know if someone has better ideas? If there are no better ideas I would need advices to be able to create a such trajectory or video. Right now I am struggling with trjconv which might be suitable for this purpose. However, if I use the droplet as a group for translational fit (-fit translation) I get trajectory in which the whole system wanders strangly (laterally (the surface moves first to the left and then back to the right) and also in perpendicular to the surface due to the lowering of the height of the center of mass of the droplet during the simulation) and the droplet wont stay whole in the middle of the box. Any ideas what I am doing wrong or how I would be able to get rid of even this lateral wandering so that I could at least see how realistic this procedure is? Thanks for your time and help in advance, Janne -- Janne Hirvi, MSc(Physical Chemistry), Researcher University of Joensuu, Department of Chemistry, P.O.Box 111 80101 Joensuu, FI Tel: +358 13 2514544 +358 50 3474223 E-mail: [EMAIL PROTECTED] [EMAIL PROTECTED] -- ___ 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 thewww 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] Using GROMACS to do colloid simulations
Perhaps you shall look Espresso (http://www.espresso.mpg.de/) for coarse-grain simulation. Espresso saved my PhD thesis after spending more than one year's time in engaging GROMACS to do what I desired. Because of the size of the colloid simulation system, the expensive PME calculation will drag GROMACS' fastest non-bonded calculation to make it not so fast. GROMACS' mission is to create a specialized and highly optimized engine. Espresso allows you to prototype the simulation system and provides more freedom without going to the source code level. On 9/26/2007 4:13 AM, Rich Hanes wrote: Hello, I recently attended a conference where some of my colleagues were talking about GROMACS and how it was really good and fast. They work with proteins, specifically, the mechanical properties of collections of proteins, eg actin filaments. I am working in Soft Matter Physics, with colloids. I generally work with 1 micrometer PMMA spheres. I can get the interaction potential, charge, radius, polydispersity etc etc to load into gromacs, but I want to know if anyone has used gromacs for colloid simulations, or if I should look elsewhere. Things which might make GROMACS unsuitable are, time and length scales, hydrodynamics. WHat do you think? Thanks for your help with this, Richie _ Get free emoticon packs and customisation from Windows Live. http://www.pimpmylive.co.uk___ 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] Re: Atomic distances problems using gmxcheck (David van der Spoel)
for cvs version, use it with care. Regards, Yang Ye On 9/20/2007 12:05 AM, yudaqi wrote: Hello, David I have download the CVS version 3.3.2. it works well. Thank you very much for your hard work in gromacs. YuDaqi 在 2007-09-19三的 11:45 [EMAIL PROTECTED] Re: Atomic distances problems using gmxcheck (David van der Spoel) ___ 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] extract coordinates of selected atoms
g_traj On 9/20/2007 11:26 PM, Qin Shanshan wrote: Dear gms-users,if I want to extract coordinates of selected atoms changing with time,what should I do? I have seen in manual 3.2 page 167 that g_coord could do this kind of job, however, I can't find this programm in gromacs.Is there any other method? Thanks in advance. ___ 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] perl scripts to convert CHARMM27 files into .tpr
There are charmm force field download from gromacs' contribution section. You need that. On 9/18/2007 9:31 PM, Rina Ghosh wrote: / // Hi Mark,// / / form gmx-usesr list one mail draws my attention, where you// inform that you are making available under GPL two perl //scripts, one of which converts// CHARMM27.prm file into //the necessary .itp files for pdb2gmx to use to// produce / /.top files, and another that massages that .top file into// something that will produce a .tpr file that will get// CHARMM energy // force evaluations. / / I have coordinates for bilayer using CHARMM27 . I want to / /convert this into gromacs structure file. I had tried //PRODRG , but it did not work as my .pdb file contain 2000 //atoms./ / Plz suggest how can I get these perl scripts to make .tpr files. Thanks. / / / Travelling to a new city? Search for ATMs in that city. Click here. http://in.rd.yahoo.com/tagline_maps_1/*http://in.maps.yahoo.com Try the revolutionary next-gen Yahoo! Mail. Click here. http://in.rd.yahoo.com/tagline_mail_10/*http://mrd.mail.yahoo.com/dc/landing ___ 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] OPLS parametes for cholesterol
Hi, Valentin Could you describe how you obtained it? So it carries more credibility as well as makes it citable for you. Regards, Yang Ye On 9/18/2007 9:00 PM, Valentin Gogonea wrote: I have one. You have to insert it in the .rtp file and use pdb2gmx. I relabeled the atoms. This may be inconvenient if you use a pdb file with coordinates for cholesterol. Valentin [ CHL ] [ atoms ] CAopls_136 -0.120 0 HA1opls_1400.060 0 HA2opls_1400.060 0 CBopls_136 -0.120 1 HB1opls_1400.060 1 HB2opls_1400.060 1 CCopls_1370.205 2 HCopls_1400.060 2 Oopls_154 -0.683 2 Hopls_1550.418 2 CDopls_136 -0.120 3 HD1opls_1400.060 3 HD2opls_1400.060 3 CEopls_1410.000 3 CFopls_142 -0.115 4 HFopls_1440.115 4 CGopls_136 -0.120 5 HG1opls_1400.060 5 HG2opls_1400.060 5 CHopls_137 -0.060 6 HHopls_1400.060 6 CIopls_137 -0.060 7 HIopls_1400.060 7 CJopls_1390.000 7 C1opls_135 -0.180 8 H11opls_1400.060 8 H12opls_1400.060 8 H13opls_1400.060 8 CKopls_136 -0.120 9 HK1opls_1400.060 9 HK2opls_1400.060 9 CLopls_136 -0.12010 HL1opls_1400.06010 HL2opls_1400.06010 CMopls_1390.00010 C2opls_135 -0.18011 H21opls_1400.06011 H22opls_1400.06011 H23opls_1400.06011 CNopls_137 -0.06012 HNopls_1400.06012 COopls_136 -0.12013 HO1opls_1400.06013 HO2opls_1400.06013 CPopls_136 -0.12014 HP1opls_1400.06014 HP2opls_1400.06014 CQopls_137 -0.06015 HQopls_1400.06015 CRopls_137 -0.06016 HRopls_1400.06016 C3opls_135 -0.18017 H31opls_1400.06017 H32opls_1400.06017 H33opls_1400.06017 CSopls_136 -0.12018 HS1opls_1400.06018 HS2opls_1400.06018 CTopls_136 -0.12019 HT1opls_1400.06019 HT2opls_1400.06019 CUopls_136 -0.12020 HU1opls_1400.06020 HU2opls_1400.06020 CVopls_137 -0.06021 HVopls_1400.06021 CZopls_135 -0.18022 HZ1opls_1400.06022 HZ2opls_1400.06022 HZ3opls_1400.06022 C4opls_135 -0.18023 H41opls_1400.06023 H42opls_1400.06023 H43opls_1400.06023 [ bonds ] CA HA1 CA HA2 CACB CACJ CB HB1 CB HB2 CBCC CCHC CC O CCCD O H CD HD1 CD HD2 CDCE CECF CECJ CFHF CFCG CG HG1 CG HG2 CGCH CHHH CHCI CHCN CIHI CICJ CICK CJC1 C1 H11 C1 H12 C1 H13 CK HK1 CK HK2 CKCL CL HL1 CL HL2 CLCM CMHM CMCN CMCQ CMC2 C2 H21 C2 H22 C2 H23 CNHN CNCO CO HO1 CO HO2 COCP CP HP1 CP HP2 CPCQ CQHQ CQCR CRHR CRC3 C3 H31 C3 H32 C3 H33 CRCS CS HS1 CS HS2 CSCT CT HT1 CT HT2 CTCU CU HU1 CU HU2 CUCV CVHV CVCZ CVC4 CZ HZ1 CZ HZ2 CZ HZ3 C4 H41 C4 H42 C4 H43 [ dihedrals ] HFCFCGCHCHL_dih_HC_CT_CT_CT [ impropers ] CDCFCECJimproper_Z_CA_X_Y CECGCFHFimproper_Z_CA_X_Y On Sep 18, 2007, at 7:24 AM, Jochen Hub wrote: Hi, does anyone know if there are is an OPLS topology for cholesterol around. Thanks a lot in advance, Jochen Plamen -- Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users
Re: [gmx-users] re: gmx-users Digest, Vol 41, Issue 56
You can just have each atom in different charge group, namely put a sequential number in the column. On 9/18/2007 8:37 PM, wangchunlei wrote: Hi, I want to add charge on all atoms of a single wall nanotube with 100 atoms. How do I define charge group? 1 atom or 2 atoms or 3 atoms in a group? Does different charge groups affect my result? Thank you! ChunLei Wang ___ 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] dynamic cross correlation map
g_traj to extract coordinates, velocities, forces into xvg files for you perform calculation. On 9/18/2007 8:20 PM, Dhananjay wrote: Well, I have done 30ns MD simulation for a protein. The protein consists of 4 loop regions. Using g_cover programme the covariance matrix have been generated and using g_anaeig programme with option -rmsf , along first 8 eigen vectors the rms fluction of c-alpha atoms were plotted. But this is giving me just the information that particular atom is fluctuating along particular direction. I want to know over a 30 ns simulation whether the motions of two atoms or group of two atoms are correlated or anti correlated. For this I want to form a dynamics cross correlation map in which I could get the precise information of group of atoms. The function used for this kind of analysis is C(i,j) = delta r(i) * delta r(j) / sqrt sqr(delta r(i) ) . sqrt sqr(delta r(j) ) the positive C(i,j) - motions are correlated the negative C(i,j) - motions are anti-correlated I want to plot a 2-D map indicated correlated and anti-correlated motions. My question is whether it is possible in GROMACS to plot this king of map or could you please suggest any other free software which could read the trajectories generated by GROMACS and plot the map. Again thanking you in advance .. -- Dhananjay On 9/18/07, *David van der Spoel* [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: Dhananjay wrote: This may be bit different question from main theme. I want to form dynamic cross correlation map as I have trajectories generated by GROMACS 3.3. Please suggest me free software which can read the .trr file for plotting DCCM (dynamic cross correlation map ) try g_covar or otherwise explain in more detail (equations) what you want to do. Thanking you in advance -- Dhananjay ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-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] mailto:[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] mailto:[EMAIL PROTECTED][EMAIL PROTECTED] mailto:[EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing list gmx-users@gromacs.org mailto:gmx-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] mailto:[EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dhananjay C Joshi Project Assistant LT LSB, C D F D ECIL Road, Nacharam Hyderabad-500 076, INDIA Tel : +91-40-27151344 Fax : +91-40-27155610 ___ 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] OPLS parametes for cholesterol
Hi, Valentin This write-up is good so people will use it with caution. Regards,. Yang Ye On 9/19/2007 12:31 AM, Valentin Gogonea wrote: Hi Yang, To describe the bonding interactions I used atom types from the OPLS force field (.atp file). I picked the atom type based on chemical environment (eg sp3/sp2 for C or being involved in a specific functional group). So I did not create new atom types. The partial charges are the default ones given in ffoplsaanb.itp (probably adjusted adhoc a bit to sum up to zero). I did not check if the geometry fits a QM geometry, but after a MM geometry optimization in gas phase it looked OK. If you need an accurate ff for cholesterol you definitely will have to refine the parameters and charges but the set I gave you should be a good start. My interest was just to have cholesterol into a POPC bilayer and I did not need to look at specific interactions of CHL with POPC or water. So this ff was ok for me but may not be satisfactory for your purpose. I hope this helps. Valentin On Sep 18, 2007, at 11:35 AM, Yang Ye wrote: Hi, Valentin Could you describe how you obtained it? So it carries more credibility as well as makes it citable for you. Regards, Yang Ye On 9/18/2007 9:00 PM, Valentin Gogonea wrote: I have one. You have to insert it in the .rtp file and use pdb2gmx. I relabeled the atoms. This may be inconvenient if you use a pdb file with coordinates for cholesterol. Valentin [ CHL ] [ atoms ] CAopls_136 -0.120 0 HA1opls_1400.060 0 HA2opls_1400.060 0 CBopls_136 -0.120 1 HB1opls_1400.060 1 HB2opls_1400.060 1 CCopls_1370.205 2 HCopls_1400.060 2 Oopls_154 -0.683 2 Hopls_1550.418 2 CDopls_136 -0.120 3 HD1opls_1400.060 3 HD2opls_1400.060 3 CEopls_1410.000 3 CFopls_142 -0.115 4 HFopls_1440.115 4 CGopls_136 -0.120 5 HG1opls_1400.060 5 HG2opls_1400.060 5 CHopls_137 -0.060 6 HHopls_1400.060 6 CIopls_137 -0.060 7 HIopls_1400.060 7 CJopls_1390.000 7 C1opls_135 -0.180 8 H11opls_1400.060 8 H12opls_1400.060 8 H13opls_1400.060 8 CKopls_136 -0.120 9 HK1opls_1400.060 9 HK2opls_1400.060 9 CLopls_136 -0.12010 HL1opls_1400.06010 HL2opls_1400.06010 CMopls_1390.00010 C2opls_135 -0.18011 H21opls_1400.06011 H22opls_1400.06011 H23opls_1400.06011 CNopls_137 -0.06012 HNopls_1400.06012 COopls_136 -0.12013 HO1opls_1400.06013 HO2opls_1400.06013 CPopls_136 -0.12014 HP1opls_1400.06014 HP2opls_1400.06014 CQopls_137 -0.06015 HQopls_1400.06015 CRopls_137 -0.06016 HRopls_1400.06016 C3opls_135 -0.18017 H31opls_1400.06017 H32opls_1400.06017 H33opls_1400.06017 CSopls_136 -0.12018 HS1opls_1400.06018 HS2opls_1400.06018 CTopls_136 -0.12019 HT1opls_1400.06019 HT2opls_1400.06019 CUopls_136 -0.12020 HU1opls_1400.06020 HU2opls_1400.06020 CVopls_137 -0.06021 HVopls_1400.06021 CZopls_135 -0.18022 HZ1opls_1400.06022 HZ2opls_1400.06022 HZ3opls_1400.06022 C4opls_135 -0.18023 H41opls_1400.06023 H42opls_1400.06023 H43opls_1400.06023 [ bonds ] CA HA1 CA HA2 CACB CACJ CB HB1 CB HB2 CBCC CCHC CC O CCCD O H CD HD1 CD HD2 CDCE CECF CECJ CFHF CFCG CG HG1 CG HG2 CGCH CHHH CHCI CHCN CIHI CICJ CICK CJC1 C1 H11 C1 H12 C1 H13 CK HK1 CK HK2 CKCL CL HL1 CL HL2 CLCM CMHM CMCN CMCQ CMC2 C2 H21 C2 H22 C2 H23 CNHN CNCO CO HO1 CO HO2 COCP CP HP1 CP HP2 CPCQ CQHQ CQCR CRHR CRC3 C3 H31 C3 H32 C3 H33 CRCS CS HS1 CS HS2 CSCT CT HT1 CT HT2 CTCU CU HU1 CU HU2 CUCV CVHV CVCZ CVC4 CZ HZ1 CZ HZ2 CZ HZ3 C4 H41
Re: [gmx-users] To deshuffle or not to deshuffle, that is a question.
Deshuffling shall be made before 2), 3) and 4). On 9/14/2007 11:36 AM, Frankie Montenegro wrote: Hi guys, A stupid question: I got myself confused with this shuffling/deshuffling thing, which I shouldn't have been doing with protein in the first place. So this are my steps, done on the same 4 nodes, please tell me whether I was supposed to do any deshuffling of .trr and .gro files, and following which steps: 1)minimization, supplied output .gro to the next step 2)equilibration, supplied output .gro to the next step 3) NVT run, supplied output .gro and .trr to the next step 4) NPT run A simple YES or NO for each step will suffice. Thanks, Frankie ___ 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] To deshuffle or not to deshuffle, that is a question.
On 9/14/2007 5:35 PM, [EMAIL PROTECTED] wrote: Selon Yang Ye [EMAIL PROTECTED]: Deshuffling shall be made before 2), 3) and 4). Furthermore, be aware that if you use the 'sort' option, you'll also need to desort ... IIRC, there is a g_desort program that does all in one (it was published on the list some time ago), and should be avaialbe in next gromacs version. Stéphane Instead, -shuffle and -sort will all disappear in the next version. I encourage Frankie to benchmark the speed-up ratio, especially it is not a membrane system. I know that people would not use -sort/shuffle so as not to mess things up for some little lost in speed. That's just alright. On 9/14/2007 11:36 AM, Frankie Montenegro wrote: Hi guys, A stupid question: I got myself confused with this shuffling/deshuffling thing, which I shouldn't have been doing with protein in the first place. So this are my steps, done on the same 4 nodes, please tell me whether I was supposed to do any deshuffling of .trr and .gro files, and following which steps: 1)minimization, supplied output .gro to the next step 2)equilibration, supplied output .gro to the next step 3) NVT run, supplied output .gro and .trr to the next step 4) NPT run A simple YES or NO for each step will suffice. Thanks, Frankie ___ 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 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] Help! A dummy atom definition problem!
you have set the mass_B to 0 as well. On 9/11/2007 10:54 PM, Wang Qin wrote: Hi there, I met the problem when I ran grompp, the errors are: ERROR 1 [file po4lig4tip3.top, line 26741]: virtual site H21 (Res LG4-173) has non-zero mass 1.008 Check your topology. ERROR 2 [file po4lig4tip3.top, line 26741]: virtual site H22 (Res LG4-173) has non-zero mass 1.008 Check your topology. Then I checked my topology file, here were the definition of LG4-173 H21 and H22: ( I want to convert the dummy atoms to H atoms) ;nr typeresnr residue atomcgnrcharge masstype_B charge_Bmass_B 21 opls_9991 LG4 H21 21 0. 1.00800 opls_1720.4650 1.00800 22 opls_9991 LG4 H22 22 0. 1.00800 opls_1720.4650 1.00800 in which opls_999 was from what I defined by myself in the force field itp file: opls_999 DUM 0 1.008000 0.000V 0.00 0.00 I changed the both of the mass_A to 0.0, but that didn't help. Does anyone have ideas on that? Thank you very much. Regards, Qin ___ 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] Help! A dummy atom definition problem!
On 9/12/2007 12:39 AM, Wang Qin wrote: Hi Yang, I was thinking to set mass_B to 0 but what I was supposed to do is converting dummy atoms to H atoms. In my opinion, it wouldn't be H atoms if I set the mass to 0. Am I thinking wrong? it's an H as long as it shares the same VDW as H and it carries the same charge as H. Thank you. Regards, Qin On 9/11/07, *Yang Ye* [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: you have set the mass_B to 0 as well. On 9/11/2007 10:54 PM, Wang Qin wrote: Hi there, I met the problem when I ran grompp, the errors are: ERROR 1 [file po4lig4tip3.top , line 26741]: virtual site H21 (Res LG4-173) has non-zero mass 1.008 Check your topology. ERROR 2 [file po4lig4tip3.top, line 26741]: virtual site H22 (Res LG4-173) has non-zero mass 1.008 Check your topology. Then I checked my topology file, here were the definition of LG4-173 H21 and H22: ( I want to convert the dummy atoms to H atoms) ;nr typeresnr residue atomcgnrcharge masstype_B charge_Bmass_B 21 opls_9991 LG4 H21 21 0. 1.00800 opls_1720.4650 1.00800 22 opls_9991 LG4 H22 22 0. 1.00800 opls_1720.4650 1.00800 in which opls_999 was from what I defined by myself in the force field itp file: opls_999 DUM 0 1.008000 0.000V 0.00 0.00 I changed the both of the mass_A to 0.0, but that didn't help. Does anyone have ideas on that? Thank you very much. Regards, Qin ___ gmx-users mailing list gmx-users@gromacs.org mailto:gmx-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] mailto:[EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing list gmx-users@gromacs.org mailto:gmx-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] mailto:[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 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
