[gmx-users] Re: gmx-users Digest, Vol 92, Issue 66
On 13/12/2011 11:46, gmx-users-requ...@gromacs.org wrote: Message: 1 Date: Tue, 13 Dec 2011 17:10:01 +1100 From: Mark Abrahammark.abra...@anu.edu.au Subject: Re: [gmx-users] Force field for polymer molecule - tips To: Discussion list for GROMACS usersgmx-users@gromacs.org Message-ID:4ee6ec39.2090...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 13/12/2011 5:06 PM, Jernej Zidar wrote: Hi. I would like to use a CHARMM (CGennFF based) of polymer molecule in Gromacs. The polymer is composed of three different monomer and two different terminal residues (one for each of the the two terminals) - five residues in total. The CHARMM generalized FF has already been ported to Gromacs so judging from the documentation (http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field) I should create a monomeres.rtp (arbitrary name?) file containing the information about the monomeres. Any tips on doing that? The general workflow will be: Generate the initial structure of the polymer of a given composition using Charmm* and save the coordinates as a PDB (plus two other files). Then supply the generated PDB to pdb2gmx to generate the initial GRO file. Second question: How will pdb2gmx know it has to parse the monomeres.rtp file? It can't. You must add to an existing .rtp file. Mark I will add that you will also have to add the residue to aminoacids.dat file, so that the polymer repeat unit is recognized. for your small polymer molecule you can just generate from the swissparam website -- 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] mdrun stuck with PME on BlueGene/P
Dear all, I have compiled the gromacs 4.5.5 version on BlueGene/P both on the front end and bgp using the following script : with the front end as an example -- version=$1 PREFIX=/home/users/wurl/software/gromacs$version export ac_cv_sizeof_int=4 export ac_cv_sizeof_long_int=4 export ac_cv_sizeof_long_long_int=8 export CC=xlc_r export CFLAGS=-O3 -I/.../fftw3.3/include -qarch=auto -qtune=auto export CPPFLAGS=-I/.../fftw3.3/include export CXX=xlc_r export CXXFLAGS=-O3 -qarch=auto -qtune=auto export F77=xlf_r export FFLAGS=-O3 -qnoprefetch -qarch=auto -qtune=auto export LDFLAGS= -L/.../fftw3.3/lib export LIBS=-lmass echo make distclean make distclean ../configure --prefix=$PREFIX \ --with-fft=fftw3 \ --disable-ppc-altivec \ --without-x \ --disable-software-sqrt \ --enable-ppc-sqrt \ --disable-float \ --disable-shared -- in both ways, the program gets stuck and doing nothing when using PME: --- Back Off! I just backed up md.log to ./#md.log.10# Getting Loaded... Reading file topol.tpr, VERSION 4.5.5 (double precision) Loaded with Money --- I compiled the debug version of mdrun and it told me the problem of fftw --- Program received signal SIGINT, Interrupt. [Switching to Thread -134504448 (LWP 31644)] 0x1010dd1c in fftwf_cpy2d () -- my compilation of fftw is : -- version=$1 PREFIX=/home/users/wurl/software/fftw$version export ac_cv_sizeof_int=4 export ac_cv_sizeof_long_int=4 export ac_cv_sizeof_long_long_int=8 export CC=xlc_r export CFLAGS=-O5 -qarch=auto -qtune=auto export CXX=xlc_r export CXXFLAGS=-O5 -qarch=auto -qtune=auto export F77=xlf_r export FFLAGS=-O5 -qnoprefetch -qarch=auto -qtune=auto export LIBS=-lmass echo make distclean make distclean ../configure --prefix=$PREFIX \ --disable-fortran \ # --enable-float \ -- When not using PME, the program went well. I also found the same problems on the mailing list, but it did not seem to solve the problem exactly. Does anyone know how to have this problem solved? I cannot do without PME for accurate MD simulations :) Sincerely, Liang -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Gromacs 4.0.7 on Blue Gene/P
Dear all, I have installed the gromacs 4.0.7 on the Blue Gene/P according to the instructions on the gromacs webpage, but after submitting my testing system of water box around 10 nm, I found the simulation went really slow, or not running at all, output files are always 0 bytes. the md.log file gets stuck at: -- Linking all bonded interactions to atoms The maximum number of communication pulses is: X 1 Y 1 Z 1 The minimum size for domain decomposition cells is 1.200 nm The requested allowed shrink of DD cells (option -dds) is: 0.80 The allowed shrink of domain decomposition cells is: X 0.48 Y 0.60 Z 0.60 I have used the double precision and fftw 3.2.2, the configure scripts are like this for mdrun ../configure --prefix=/home/users/wurl/software/gromacs4.0.7 --host=ppc --build=ppc64 --enable-ppc-sqrt=1 --enable-bluegene --enable-mpi --with-fft=fftw3 --without-x --program-suffix=-mpi-bgp CC=mpixlc_r CFLAGS=-O3 -qarch=450d -qtune=450 MPICC=mpixlc_r CXX=mpixlc_r CXXFLAGS=-O3 -qarch=450d -qtune=450 F77=mpixlf_r FFLAGS=-O3 -qarch=auto -qtune=auto LIBS=-lmass CPPFLAGS=-I/opt/fftw/3.2.2/include LDFLAGS=-L/opt/fftw/3.2.2/lib --disable-float I also asked the administrator to install for me, the results were the same. Does anyone have similar experience? -- Yours Sincerely, Rongliang Wu Postdoc in K.U.Leuven -- Molecular and Nanomaterials Division Department of Chemistry Katholieke Universiteit Leuven Celestijnenlaan 200f - bus 2404 3001 Heverlee, Belgium +3216327456 +32488146330 rongliang...@chem.kuleuven.be http://wurongliang.linkka.com/ -- -- 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] center of masses inappropriate
Hello, gmx-users， I report here that the center of mass calculated in g_traj, g_rdf, g_clustsize etc does not take into account the pbc conditions, for example the center of mass of cluster cutted by the box vector has position near the box center while it should be close to the box boundary. i wonder how to tackle this problem? Regards! Rongliang Wu wur...@iccas.ac.cn 2008-12-24 ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] The g_sdf in gromacs 3.3.3
Hello, gmx-users， when calculaing the spatial distribution functions using gromacs3.3.3, i always get distorted reference molecule and it is far away from the isosurface when my reference molecule has more than 3 atoms, and none of the atoms are at the oringin. the g_sdf program in gromacs3.3.3 seems problematic, and how shall i change the code? Regards! Rongliang Wu [EMAIL PROTECTED] 2008-07-30 ___ 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] BHIS for HIS?
hello,gmx-users， i am trying to simulate a peptide with residue HIS, the default in pdb2gmx used HISB for HIS in both oplsaa and gromos96 force field, but i found there are HIS1,HISH,HISB etc in the rtp files, i am not sure whether HISB will suffice for my system, i intend to simulate the binding of surfactants with the peptide. what are the difference? is there anywhere i can find the detailed description for these residues? Rongliang Wu [EMAIL PROTECTED] 2007-04-11 ___ 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] slight mistake in data angdist.xvg file
hello, gmx-users i'd here report everyone that when calculating the R_B dihedral distribution using g_angle command, the resulting sum of the proportions listed in angdist.xvg has a value of 2, which should be 1 for a normalized distribution. Rongliang Wu [EMAIL PROTECTED] 2007-04-09 ___ 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 RE:fugeQQ in buckingham
i have a polymer force field with the buckingham potential, and i still need a solvent(acetone and DMA) potenital with buckingham potential since Gromacs cannot use both buckingham and L-J for one system. i did not find such foce fields for acetone and DMA. and i have chosen to change the parameters in oplsaa into buckingham, the 1-4 L-J parameters are listed explicitly in the [ pairtypes ] section. i tried, and it could be calculated successfully, but the derived LJ1-4 energy do not have the same energy as calculated with standard oplsaa force field. i have also tried to convert my polymer force field into LJ, but it was not as accurate. does anyone know where are solvent force fields with the buckingham potential? or how to combine the buckingham with L-J in gromacs? wurl wrote: hello gmx-users since the 1-4 interaction is always scaled by the fugeQQ no matter genpairs is set to yes or no, then whether this applies for the buckingham potential? i was told both from literature and the mailling list, that the buckingham potential will not include the 1-4 scaling. this is up to the developers of the potential. but you can set it ton 1 if you wish, so what's the problem? ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] simulations of crystal cell possible?
hello everyone, does anybody know how to simulate crystal cells in gromacs? since the cell size has to be no smaller than twice the cutoff. and if cutoff is too small, the program terminates because of the thus caused too high energy. my cell is very small about 0.7 nm. regards! Rongliang Wu ICCAS,CHINA ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] the gmxdump reveals less parameters than i expect
hello,gmx-users i used grompp to get an tpr and used the gmxdump command to see if the parameters are right, but i found there are less parameters than i expect: functype[12]=ANGLES, thA= 1.09270e+02, ctA= 3.22384e+02, thB= 1.0927 0e+02, ctB= 3.22384e+02 functype[13]=ANGLES, thA= 1.08450e+02, ctA= 3.59227e+02, thB= 1.0845 0e+02, ctB= 3.59227e+02 functype[14]=ANGLES, thA= 1.07740e+02, ctA= 7.53624e+02, thB= 1.0774 0e+02, ctB= 7.53624e+02 functype[15]=ANGLES, thA= 1.18240e+02, ctA= 6.72400e+02, thB= 1.1824 0e+02, ctB= 6.72400e+02 functype[16]=ANGLES, thA= 1.05270e+02, ctA= 1.00483e+03, thB= 1.0527 0e+02, ctB= 1.00483e+03 here, i have 6 types of angles while it told me there are only 5 angle typeps in, and the parameters in the ff*bon.itp are right, the [ angles ] part in the top are also right? why? and i added the parameters in ff*bon.itp to topol.top file and grompp again, the same results are shown. what does this part mean, which is from the gmxdump commmand? regards! thanks! Rongliang Wu [EMAIL PROTECTED] 2006-09-13 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] changing the parameter numbers for torsion
hello,gmx-users i have a force field that contain 7 rychaert-bellemans dihedral coefficients, but in gromacs there are only 6, how can i manage it ? and where i should change the source code? regards! thanks! Rongliang Wu [EMAIL PROTECTED] 2006-09-12 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_h2order problem
3949 waters in slice 70 11786 waters in slice 71 25972 waters in slice 72 43494 waters in slice 73 58953 waters in slice 74 67984 waters in slice 75 75606 waters in slice 76 82786 waters in slice 77 88528 waters in slice 78 91561 waters in slice 79 92741 waters in slice 80 92275 waters in slice 81 92023 waters in slice 82 91709 waters in slice 83 91688 waters in slice 84 91710 waters in slice 85 91667 waters in slice 86 91272 waters in slice 87 91625 waters in slice 88 91645 waters in slice 89 91193 waters in slice 90 91293 waters in slice 91 91875 waters in slice 92 91003 waters in slice 93 91650 waters in slice 94 91379 waters in slice 95 91366 waters in slice 96 91429 waters in slice 97 91357 waters in slice 98 91222 waters in slice 99 100 slices Back Off! I just backed up order.xvg to ./#order.xvg.6# gcq#215: I've Got Two Turntables and a Microphone (B. Hansen) Regards Thanks Rongliang Wu [EMAIL PROTECTED] 2006-05-24 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] simulation of long chains in vacuum
Hello, gmx-users， i generated a chain of 1000 units and intended to simulate in vacuum, but the system exploded and the mdp file is as follows: title= PE cpp = /usr/bin/cpp include = define = integrator = md dt = 0.002 nsteps = 10 nstxout = 5000 nstvout = 5000 nstlog = 5000 nstenergy= 500 nstxtcout= 2000 xtc_grps = energygrps = comm_mode= angular nstlist = 0 ns_type = simple rlist= 0 rvdw = 0 rcoulomb = 0 pbc = no tcoupl = Berendsen tc-grps = system tau_t= 0.1 ref_t= 300 Pcoupl = no ;Pcoupltype = isotropic ;tau_p= 1.0 ;compressibility = 4.5e-4 ;ref_p= 1.0 ;annealing = single ;annealing_npoints = 15 ;annealing_time = 0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 ;annealing_temp = 370 365 360 355 350 345 340 335 330 325 320 315 310 305 300 gen_vel = yes gen_temp = 300 gen_seed = 173529 constraints = all-bonds optimize_fft = yes are there any obvious errors? and my system is quite large, about 49.90900 70.12100 231.85800 ns is there any upper limits for gromacs systems? Regards Thanks Rongliang Wu [EMAIL PROTECTED] 2006-05-10 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] after g_morph, how to calculate energies?
Hello, gmx-users， i have generated a series of conformations of my molecule using the command g_morph, but how can i get the correspongding energies for each conformation? if i want to make an estimation of the energies of each conformation of polypropelene(two chain unites), how can i get those conformations which might be beyond the ability of g_morph? Regards Thanks Rongliang Wu [EMAIL PROTECTED] 2006-04-30 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] grompp error
Hello, gmx-users， i removed the entire folder before intalling a new one. i just source GMXRC in the ~/bin but i still got the same results. my previous installs didnot need source GMXRC, but they all went well. and this time i set the GMXLIB, it still doesnot work. and the md5sum was correct! i installed a send time and it didnot change Regards Thanks Rongliang Wu [EMAIL PROTECTED] 2006-04-09 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] grompp error
Hello, gmx-users， i finished compiling the gromacs-3.3.1 but when i run genbox it said aminoacids.dat not found. then i set the GMXLIB environmental variable to find the top folder. but when i used the grompp command it said: ao7.top:11:24: ffoplsaa.itp: No such file or directory ao7.top:648:19: spc.itp: No such file or directory ao7.top:658:20: ions.itp: No such file or directory cpp exit code: 256 Tried to execute: '/usr/bin/cpp -I/export/home/wurl/software/gromacs/share/gromacs/top: ao7.top gromppDx0yaF' The '/usr/bin/cpp' command is defined in the .mdp file processing topology... Cleaning up temporary file gromppDx0yaF --- Program grompp, VERSION 3.3.1 Source code file: topio.c, line: 388 Fatal error: Invalid order for directive moleculetype, file ao7.top, line 13 --- it is clear that the program still cannot find the itp files in the top folder? why? is there anyother environmental variables that i didnot set ? Regards Thanks Rongliang Wu [EMAIL PROTECTED] 2006-04-09 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] grompp error
565960 3 56596061 3 56596062 3 56596063 3 59606364 3 59606365 3 59606366 3 61606364 3 61606365 3 61606366 3 62606364 3 62606365 3 62606366 3 60636667 3 64636667 3 65636667 3 63666768 3 63666769 3 63666770 3 66677071 3 66677072 3 66677073 3 68677071 3 68677072 3 68677073 3 69677071 3 69677072 3 69677073 3 67707374 3 71707374 3 72707374 3 70737475 3 70737476 3 70737477 3 73747778 3 73747779 3 73747780 3 75747778 3 75747779 3 75747780 3 76747778 3 76747779 3 76747780 3 74778081 3 78778081 3 79778081 3 ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include water topology #include spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include generic topology for ions #include ions.itp [ system ] ; Name GROningen MAchine for Chemical Simulation [ molecules ] ; Compound#mols Protein 1 i also met with the same problem using gromacs-3.2 why? Regards Thanks Rongliang Wu [EMAIL PROTECTED] 2006-04-07 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problem caused by removed [ pairs ] in OPLS
179.8 185010749440. 386140793778567464878080. 0.1410 50 51 179.2 1267195740946432. 204118519408757976334336. 0.1410 51 52 179.6 1126743465263104. 149197860543313666375680. 0.1090 51 53 179.6 1126743465263104. 149197860543313666375680. 0.1090 51 54 179.1 1139419390148608. 137907426349488380313600. 0.1529 54 55 179.3 809496242814976. 74584167472078312701952. 0.1090 54 56 179.3 809496242814976. 74584167472078312701952. 0.1090 54 57 178.8 670354737463296. 60551036601584767205376. 0.1410 57 58 177.5 344853258960896. 18237673468208131080192. 0.1410 58 59 178.0 256434931499008. 7318891515282200723456. 0.1090 58 60 178.0 256434931499008. 7318891515282200723456. 0.1090 58 61 177.5 242751148916736. 6663794535785167847424. 0.1529 61 62 178.5 143391006392320. 1703730175645233184768. 0.1090 61 63 178.5 143391006392320. 1703730175645233184768. 0.1090 61 64 178.6 107687001980928. 1430247962373252972544. 0.1410 64 65 178.8 34019745988608. 249595507876500078592. 0.0945 Back Off! I just backed up step867.pdb to ./#step867.pdb.5# Back Off! I just backed up step868.pdb to ./#step868.pdb.2# Wrote pdb files with previous and current coordinates --- Program mdrun, VERSION 3.3 Source code file: nsgrid.c, line: 226 Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might ehe nd up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value -2147483648. It should have been within [ 0 .. 10648 ] Please report this to the mailing list (gmx-users@gromacs.org) --- then i added the [ pairs ] for in page 91 mannual 3.2 there is a sentence The GROMACS and GROMOS force fields lists all these interactions explicitly, but this section might be empty for force fields like OPLS that calculate the 1-4 interactions by scaling. this means the [ pairs ] can be listed in OPLS and my simulation went perfectly well then is it necessary to delete those [ pairs ] in OPLS as stated in mannual3.2 page 103 ??? i've simulated systems that went well with or without [ pairs ] listed using OPLS, BUT the results didn't seem to have much difference! Regards Thanks Rongliang Wu [EMAIL PROTECTED] 2006-04-05 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] lincs warning
Hello, gmx-users， i am just simulating a single PEO chain in a large box(vacuum), the EM step went perfectly well for steep and cg, but after MD has started there came the following warnings: Step 1432, time 2.864 (ps) LINCS WARNING relative constraint deviation after LINCS: max 1.600984 (between atoms 141 and 142) rms 0.134828 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 141142 90.00.1000 0.2458 0.0945 Wrote pdb files with previous and current coordinates Step 1433, time 2.866 (ps) LINCS WARNING relative constraint deviation after LINCS: max 0.027914 (between atoms 141 and 142) rms 0.002435 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 141142 90.00.2458 0.0971 0.0945 Step 1434, time 2.868 (ps) LINCS WARNING relative constraint deviation after LINCS: max 1.672527 (between atoms 141 and 142) rms 0.140852 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 141142 90.00.0971 0.2526 0.0945 …… and in a few seconds the core dumped, and system collapsed. i was using oplsaa force field and the [ pairs ] are removed as refered by the mannual i wonder where the problem might exists. any suggestion will be greatly appreciated! Regards Thanks Rongliang Wu [EMAIL PROTECTED] 2006-04-04 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] grompp problem
hello all, the cyc.itp went well for my previous systems of tip4p and cyc, but after adding sds, i got warnings as showed below. the 296 and 153 line of sds.itp and cyc.itp respectively are the end of the file. why?!! In file included from box.top:1: sds.itp:296:1: warning: no newline at end of file In file included from box.top:3: cyc.itp:153:30: warning: no newline at end of file processing topology... Generated 332520 of the 332520 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 332520 of the 332520 1-4 parameter combinations WARNING 1 [file sds.itp, line 102]: No default Bond types, using zeroes WARNING 2 [file sds.itp, line 103]: No default Bond types, using zeroes WARNING 3 [file sds.itp, line 104]: No default Bond types, using zeroes WARNING 4 [file sds.itp, line 105]: No default Bond types, using zeroes WARNING 5 [file sds.itp, line 181]: No default Angle types, using zeroes WARNING 6 [file sds.itp, line 182]: No default Angle types, using zeroes WARNING 7 [file sds.itp, line 183]: No default Angle types, using zeroes WARNING 8 [file sds.itp, line 184]: No default Angle types, using zeroes WARNING 9 [file sds.itp, line 185]: No default Angle types, using zeroes WARNING 10 [file sds.itp, line 186]: No default Angle types, using zeroes Cleaning up temporary file gromppmL0ZER --- Program grompp, VERSION 3.3 Source code file: fatal.c, line: 416 Fatal error: Too many warnings, grompp terminated --- -- Rongliang Wu 2006-03-21 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] mpi problem
hello all, i've got a problem whem i intend to run a parallel mdrun, when i met with such error: error while loading shared libraries: libXm.so.3: cannot open shared object file: No such file or directory what's the problem and mpi is LAM -- Rongliang Wu 2006-03-20 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] keep atoms planar
hello, i found in ffoplsaa.itp : [ dihedraltypes ] ; Improper OPLS dihedrals to keep groups planar. ; (OPLS doesnt use impropers for chiral atoms). ; Since these functions are periodic of the form 1-cos(2*x), the are actually ; implemented as proper dihedrals [1+cos(2*x+180)] for the moment, ; to keep things compatible. ; The defines are used in ffoplsaa.rtp or directly in your .top ile. ; O?-C -X -Y improper torsion. C can be C_2 or C_3 too. #define improper_O_C_X_Y180.0 43.93200 2 ; X-NO-ON-NO improper torsion. #define improper_X_NO_ON_NO 180.0 43.93200 2 ; N2-X-N2-N2 improper torsion. #define improper_N2_X_N2_N2 180.0 43.93200 2 ; Z -N?-X -Y improper torsion #define improper_Z_N_X_Y180.0 4.18400 2 ; Z -CM-X -Y improper torsion. CM can be C= too. #define improper_Z_CM_X_Y 180.0 62.76000 2 ; Z -CA-X -Y improper torsion. CA is any ring carbon (CA,CB,CN,CV,CW,CR,CK,CQ,CS,C*) #define improper_Z_CA_X_Y 180.0 4.60240 2 are X Y Z designate any atom types? -- Rongliang Wu 2006-03-14 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
