[gmx-users] About the example case A toy peptide in water and other protein case (CG martini force field )
Dear Sir , I used your CG parameters and gromacs V3.3 to simulate protein aggregation. And my command is : grompp_mpi_d -np 2 -f aggre.mdp -c aggre.gro -p aggre.top -o aggre.trp The error message is : double-checking input for internal consistency... Velocities were taken from a Maxwell distribution at 300 K renumbering atomtypes... converting bonded parameters... # BONDS: 1935 # G96ANGLES: 2565 # IDIHS: 225 # CONSTR: 900 Walking down the molecule graph to make shake-blocks initialising group options... processing index file... Analysing residue names: Opening library file /opt/gromacs//share/gromacs/top/aminoacids.dat There are: 76048 OTHER residues There are: 1170 PROTEIN residues There are: 0 DNA residues Analysing Protein... Analysing Other... --- Program grompp_mpi_d, VERSION 3.3.3 Source code file: readir.c, line: 798 Fatal error: Group Protein1 not found in indexfile. Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n' option. But I tried your example case A toy peptide in water , I still got the same error . My command is : 1.grompp_mpi_d -np 2 -f toypeptide.mdp -p toypeptide.top -c toypeptide.gro -n index.ndx -o toypeptide.tpr 2.grompp_mpi_d -np 2 -f toypeptide.mdp -p toypeptide.top -c toypeptide.gro -o toypeptide.tpr index.ndx : [ prot_sort ] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 The error message : Walking down the molecule graph to make shake-blocks initialising group options... processing index file... --- Program grompp_mpi_d, VERSION 3.3.3 Source code file: readir.c, line: 798 Fatal error: Group TOYPEP not found in indexfile. Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n' option. Sir, could you tell me how to fix the problem? By the way, I test other cases in your website and I didn't get any error message . Best regards Wang Yeng-tseng begin:vcard fn:Yeng-Tseng Wang n:Wang;Yeng-Tseng org;quoted-printable;quoted-printable:=E7=94=9F=E6=8A=80=E9=86=AB=E7=99=82=E8=B3=87=E8=A8=8A=E7=B5=84;=E5=8D=97=E9=83=A8=E4=BA=8B=E6=A5=AD=E7=BE=A4 adr;quoted-printable;quoted-printable;quoted-printable;quoted-printable:;;=E5=8F=B0=E5=8D=97=E7=B8=A3=E6=96=B0=E5=B8=82=E9=84=89=E5=8D=97=E7=A7=91=E4= =B8=89=E8=B7=AF28=E8=99=9F;=E5=8F=B0=E5=8D=97=E7=B8=A3;=E6=96=B0=E5=B8=82=E9=84=89;74114;=E4=B8=AD=E8=8F=AF=E6=B0=91=E5=9C=8B(=E5=8F=B0=E7=81=A3) email;internet:[EMAIL PROTECTED] title;quoted-printable:=E8=B2=A1=E5=9C=98=E6=B3=95=E4=BA=BA=E5=9C=8B=E5=AE=B6=E5=AF=A6=E9=A9=97=E7= =A0=94=E7=A9=B6=E9=99=A2=E5=9C=8B=E5=AE=B6=E9=AB=98=E9=80=9F=E7=B6=B2=E8=B7= =AF=E8=88=87=E8=A8=88=E7=AE=97=E4=B8=AD=E5=BF=83 tel;work:+886-5050940 ext.738 tel;cell:+886-939875770 url:http://www.nchc.org.tw version:2.1 end:vcard ___ 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] About the example case A toy peptide in water and other protein case (CG martini force field )
Dear Sir , I used your CG parameters and gromacs V3.3 to simulate protein aggregation. And my command is : grompp_mpi_d -np 2 -f aggre.mdp -c aggre.gro -p aggre.top -o aggre.trp The error message is : double-checking input for internal consistency... Velocities were taken from a Maxwell distribution at 300 K renumbering atomtypes... converting bonded parameters... # BONDS: 1935 # G96ANGLES: 2565 # IDIHS: 225 # CONSTR: 900 Walking down the molecule graph to make shake-blocks initialising group options... processing index file... Analysing residue names: Opening library file /opt/gromacs//share/gromacs/top/aminoacids.dat There are: 76048 OTHER residues There are: 1170 PROTEIN residues There are: 0 DNA residues Analysing Protein... Analysing Other... --- Program grompp_mpi_d, VERSION 3.3.3 Source code file: readir.c, line: 798 Fatal error: Group Protein1 not found in indexfile. Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n' option. But I tried your example case A toy peptide in water , I still got the same error . My command is : 1.grompp_mpi_d -np 2 -f toypeptide.mdp -p toypeptide.top -c toypeptide.gro -n index.ndx -o toypeptide.tpr 2.grompp_mpi_d -np 2 -f toypeptide.mdp -p toypeptide.top -c toypeptide.gro -o toypeptide.tpr index.ndx : [ prot_sort ] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 The error message : Walking down the molecule graph to make shake-blocks initialising group options... processing index file... --- Program grompp_mpi_d, VERSION 3.3.3 Source code file: readir.c, line: 798 Fatal error: Group TOYPEP not found in indexfile. Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n' option. Sir, could you tell me how to fix the problem? By the way, I test other cases in your website and I didn't get any error message . Best regards Wang Yeng-tseng begin:vcard fn:Yeng-Tseng Wang n:Wang;Yeng-Tseng org;quoted-printable;quoted-printable:=E7=94=9F=E6=8A=80=E9=86=AB=E7=99=82=E8=B3=87=E8=A8=8A=E7=B5=84;=E5=8D=97=E9=83=A8=E4=BA=8B=E6=A5=AD=E7=BE=A4 adr;quoted-printable;quoted-printable;quoted-printable;quoted-printable:;;=E5=8F=B0=E5=8D=97=E7=B8=A3=E6=96=B0=E5=B8=82=E9=84=89=E5=8D=97=E7=A7=91=E4= =B8=89=E8=B7=AF28=E8=99=9F;=E5=8F=B0=E5=8D=97=E7=B8=A3;=E6=96=B0=E5=B8=82=E9=84=89;74114;=E4=B8=AD=E8=8F=AF=E6=B0=91=E5=9C=8B(=E5=8F=B0=E7=81=A3) email;internet:[EMAIL PROTECTED] title;quoted-printable:=E8=B2=A1=E5=9C=98=E6=B3=95=E4=BA=BA=E5=9C=8B=E5=AE=B6=E5=AF=A6=E9=A9=97=E7= =A0=94=E7=A9=B6=E9=99=A2=E5=9C=8B=E5=AE=B6=E9=AB=98=E9=80=9F=E7=B6=B2=E8=B7= =AF=E8=88=87=E8=A8=88=E7=AE=97=E4=B8=AD=E5=BF=83 tel;work:+886-5050940 ext.738 tel;cell:+886-939875770 url:http://www.nchc.org.tw version:2.1 end:vcard ___ 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] About the example case A toy peptide in water and other protein case (CG martini force field )
Dear Sir , I used your CG parameters and gromacs V3.3 to simulate protein aggregation. And my command is : grompp_mpi_d -np 2 -f aggre.mdp -c aggre.gro -p aggre.top -o aggre.trp The error message is : double-checking input for internal consistency... Velocities were taken from a Maxwell distribution at 300 K renumbering atomtypes... converting bonded parameters... # BONDS: 1935 # G96ANGLES: 2565 # IDIHS: 225 # CONSTR: 900 Walking down the molecule graph to make shake-blocks initialising group options... processing index file... Analysing residue names: Opening library file /opt/gromacs//share/gromacs/top/aminoacids.dat There are: 76048 OTHER residues There are: 1170 PROTEIN residues There are: 0 DNA residues Analysing Protein... Analysing Other... --- Program grompp_mpi_d, VERSION 3.3.3 Source code file: readir.c, line: 798 Fatal error: Group Protein1 not found in indexfile. Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n' option. But I tried your example case A toy peptide in water , I still got the same error . My command is : 1.grompp_mpi_d -np 2 -f toypeptide.mdp -p toypeptide.top -c toypeptide.gro -n index.ndx -o toypeptide.tpr 2.grompp_mpi_d -np 2 -f toypeptide.mdp -p toypeptide.top -c toypeptide.gro -o toypeptide.tpr index.ndx : [ prot_sort ] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 The error message : Walking down the molecule graph to make shake-blocks initialising group options... processing index file... --- Program grompp_mpi_d, VERSION 3.3.3 Source code file: readir.c, line: 798 Fatal error: Group TOYPEP not found in indexfile. Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n' option. Sir, could you tell me how to fix the problem? By the way, I test other cases in your website and I didn't get any error message . Best regards Wang Yeng-tseng begin:vcard fn:Yeng-Tseng Wang n:Wang;Yeng-Tseng org;quoted-printable;quoted-printable:=E7=94=9F=E6=8A=80=E9=86=AB=E7=99=82=E8=B3=87=E8=A8=8A=E7=B5=84;=E5=8D=97=E9=83=A8=E4=BA=8B=E6=A5=AD=E7=BE=A4 adr;quoted-printable;quoted-printable;quoted-printable;quoted-printable:;;=E5=8F=B0=E5=8D=97=E7=B8=A3=E6=96=B0=E5=B8=82=E9=84=89=E5=8D=97=E7=A7=91=E4= =B8=89=E8=B7=AF28=E8=99=9F;=E5=8F=B0=E5=8D=97=E7=B8=A3;=E6=96=B0=E5=B8=82=E9=84=89;74114;=E4=B8=AD=E8=8F=AF=E6=B0=91=E5=9C=8B(=E5=8F=B0=E7=81=A3) email;internet:[EMAIL PROTECTED] title;quoted-printable:=E8=B2=A1=E5=9C=98=E6=B3=95=E4=BA=BA=E5=9C=8B=E5=AE=B6=E5=AF=A6=E9=A9=97=E7= =A0=94=E7=A9=B6=E9=99=A2=E5=9C=8B=E5=AE=B6=E9=AB=98=E9=80=9F=E7=B6=B2=E8=B7= =AF=E8=88=87=E8=A8=88=E7=AE=97=E4=B8=AD=E5=BF=83 tel;work:+886-5050940 ext.738 tel;cell:+886-939875770 url:http://www.nchc.org.tw version:2.1 end:vcard ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] cannot generate .top file
Hi. I seem having some problem in running ./pdb2gmx. Here is the output file. Can you help me in giving me some idea to deal with this? bcsb09s-imac52:bin bcsb09$ pdb2gmx -f 1aml.pdb -p 1aml.top -o 1aml.gro :-) G R O M A C S (-: Getting the Right Output Means no Artefacts in Calculating Stuff :-) VERSION 3.3.3 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) pdb2gmx (-: Option Filename Type Description -f 1aml.pdb InputGeneric structure: gro g96 pdb tpr tpb tpa xml -o 1aml.gro Output Generic structure: gro g96 pdb xml -p 1aml.top Output Topology file -i posre.itp Output Include file for topology -n clean.ndx Output, Opt. Index file -q clean.pdb Output, Opt. Generic structure: gro g96 pdb xml Option Type Value Description -- -[no]h bool no Print help info and quit -niceint0 Set the nicelevel -[no]merge bool no Merge chains into one molecule definition -ff string select Force field, interactive by default. Use -h for information. -water enum spc Water model to use: with GROMOS we recommend SPC, with OPLS, TIP4P: spc, spce, tip3p, tip4p, tip5p or f3c -[no]inter bool no Set the next 6 options to interactive -[no]ss bool no Interactive SS bridge selection -[no]ter bool no Interactive termini selection, iso charged -[no]lys bool no Interactive Lysine selection, iso charged -[no]arg bool no Interactive Arganine selection, iso charged -[no]asp bool no Interactive Aspartic Acid selection, iso charged -[no]glu bool no Interactive Glutamic Acid selection, iso charged -[no]gln bool no Interactive Glutamine selection, iso neutral -[no]his bool no Interactive Histidine selection, iso checking H-bonds -angle real 135 Minimum hydrogen-donor-acceptor angle for a H-bond (degrees) -distreal 0.3 Maximum donor-acceptor distance for a H-bond (nm) -[no]una bool no Select aromatic rings with united CH atoms on Phenylalanine, Tryptophane and Tyrosine -[no]ignhbool no Ignore hydrogen atoms that are in the pdb file -[no]missing bool no Continue when atoms are missing, dangerous -[no]v bool no Be slightly more verbose in messages -posrefc real 1000Force constant for position restraints -vsite enum noneConvert atoms to virtual sites: none, hydrogens or aromatics -[no]heavyh bool no Make hydrogen atoms heavy -[no]deuterate bool no Change the mass of hydrogens to 2 amu Opening library file /usr/local/gromacs/share/gromacs/top/FF.dat Select the Force Field: 0: GROMOS96 43a1 force field 1: GROMOS96 43b1 vacuum force field 2: GROMOS96 43a2 force field (improved alkane dihedrals) 3: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 4: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 5: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 6: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 7: Encad all-atom force field, using scaled-down vacuum charges 8: Encad all-atom force field, using full solvent charges 2 Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2.rtp Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat Reading 1aml.pdb... Read 'AMYLOID A4', 598 atoms Opening library file /usr/local/gromacs/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file There are 1 chains and 0 blocks of water and 40 residues with 598 atoms chain #res #atoms 1 ' '40598 All occupancies are one Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2.atp Atomtype 50 Reading residue database... (ffG43a2) Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2.rtp Residue 96 Sorting it all out... Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2.hdb Opening library file
RE: [gmx-users] stochastic dynamics , langevin
From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: RE: [gmx-users] stochastic dynamics , langevin Date: Thu, 23 Oct 2008 15:32:02 -0700 Along these same lines... (a)is there an thermostat setting in GROMACS that comes close to the DPD thermostat as described in (T. Soddemann, B. D¨unweg, and K. Kremer. Dissipative particle dynamics: A useful thermostat for equilibrium and nonequilibrium molecular dynamics simulations. Phys. Rev. E, 68:046702, 2003.) No. (b) if nothing approaches DPD, how would a one go about starting to write a new thermostat in GROMACS? Implementing a new thermostat in Gromacs is easy, except for DPD, since it interferes both with the neighborlist and the integration. I have considered implementing DPD, but it is a lot of work and also difficult to do efficiently, since the DPD interactions are more expensive that the Coulomb and LJ interactions. Note that you only really need DPD for non-equilibrium phenomena where hydrodynamics plays a role. Berk -Matt - Matthew Hoopes Biophysics Graduate Group University of California, Davis [EMAIL PROTECTED] 530-752-6452 - Hi, Brownina dynamics is a Langevin equation for the coordinates (no inertia). Stochastic dynamics is a Langevin equation for the velocities (with inertia). Everything depends on what you want to do, which you do not tell in detail. If you want to leave out the solvent, but you want to simulate a system in solvent, SD is not going to help you, since there is no implicit solvent potential, so your potential and therefore your sampling is nonsense. tau_t has no effect on the distribution, only on the dynamics. If you want the correct dynamics, you will have fit tau_t to reproduce some kinetic quantity that you are interested in. For different quantities tau_t can be different. Berk Date: Thu, 23 Oct 2008 15:31:16 +0200 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: [gmx-users] stochastic dynamics , langevin Dear All, I am trying to perform Langevin dynamics of large peptides / proteins. After reading the manual going over some old mails in this list, I have two points I hope you could clear for me: [Gromacs version 3.3.3] 1) I am a bit confused with Brownian vs. Langevin dynamics. Is this the proper keywords I should use for Langevin dynamics: integrator = sd ; bd-fric= 0 ; tau_t = 10 ; ref_t = 300 ; With bd-fric=0, the friction is taken as the inverse tau_t. 2) From your experience, what are good values of tau_t (or 1/tau_t) for simulating a protein? In 2006 list, David has commented that choosing tau_t is very important ( http://www.gromacs.org/pipermail/gmx-users/2006-July/023089.html ). Your help is appreciated. Omer. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ ___ 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 _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ 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] table_bonded.xvg
Dear Users In gromacs 4.0, in file force.c in function make_bonded_tables line (1007) sprintf(tabfn + strlen(basefn) - strlen(ftp2ext(efXVG)) - 1,_%s%d.%s, tabext, i, ftp2ext(efXVG)); produces table_bonded_bonded.xvg instead of table_bonded.xvg Greetings Andrzej Rzepiela ___ 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] cannot generate .top file
Kwee Hong wrote: Hi. I seem having some problem in running ./pdb2gmx. Here is the output file. Can you help me in giving me some idea to deal with this? bcsb09s-imac52:bin bcsb09$ pdb2gmx -f 1aml.pdb -p 1aml.top -o 1aml.gro snip --- Program pdb2gmx, VERSION 3.3.3 Source code file: futil.c, line: 313 File input/output error: 1aml.top --- This means it can't write 1aml.top, which likely means you don't have write permission to the directory in which pdb2gmx resides. This is a Good Thing. You should do daily work in a suitable subdirectory of (say) your home directory, and adjust your environment variables to give you ready access to GROMACS stuff by using source /path/to/GMXRC using the path in which you installed the GROMACS binaries. I guess this is your attempted working directory above. I seem to be having problem in running the test tun as well. Below is its output: bcsb09s-imac52:bin bcsb09$ ./gmxtest.pl Usage: ./gmxtest.pl [ -np N ] [-verbose ] [ -double ] [ simple | complex | kernel | pdb2gmx | all ] or: ./gmxtest.pl clean | refclean | dist Again this won't work in a directory in which you don't have write permissions. The above message tells you that an empty command line isn't acceptable to gmxtest.pl. *Technically* it ought to be acceptable per the usage line, since square brackets denote optional things and |-symbols denote a series of mutually-exclusive possibilities. I think the brackets should be missing around simple | complex | kernel | pdb2gmx | all. 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] Warning with L-BFGS minimization
Hi, with l-bfgs minimzation, grompp always reports WARNING 1 [file em.mdp, line unknown]: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. even if the mdp gives ; Method for doing electrostatics coulombtype = PME rcoulomb_switch = 0 rcoulomb = 1. I could't find anything on that in the archive. Is that a known issue? Cheers, Jochen -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312 ___ 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] Warning with L-BFGS minimization
Jochen Hub wrote: Hi, with l-bfgs minimzation, grompp always reports WARNING 1 [file em.mdp, line unknown]: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. even if the mdp gives ; Method for doing electrostatics coulombtype = PME rcoulomb_switch = 0 rcoulomb = 1. I could't find anything on that in the archive. Is that a known issue? Maybe it's case-sensitive... try pme 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] Gromacs 4 SRC RPM?
Is there any eta on when the gromacs-4.0-1.src.rpm is going to show up on: ftp://ftp.gromacs.org/pub/gromacs/rpm Thanks, Mike ___ 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] Warning with L-BFGS minimization
Mark Abraham wrote: Jochen Hub wrote: Hi, with l-bfgs minimzation, grompp always reports WARNING 1 [file em.mdp, line unknown]: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. even if the mdp gives ; Method for doing electrostatics coulombtype = PME rcoulomb_switch = 0 rcoulomb = 1. I could't find anything on that in the archive. Is that a known issue? Maybe it's case-sensitive... try pme No, same warning. :-( Jochen 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 . -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312 ___ 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] Warning with L-BFGS minimization
Jochen Hub wrote: Mark Abraham wrote: Jochen Hub wrote: Hi, with l-bfgs minimzation, grompp always reports WARNING 1 [file em.mdp, line unknown]: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. even if the mdp gives ; Method for doing electrostatics coulombtype = PME rcoulomb_switch = 0 rcoulomb = 1. I could't find anything on that in the archive. Is that a known issue? Maybe it's case-sensitive... try pme No, same warning. :-( src/kernel/readir.c Jochen 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 . -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Warning with L-BFGS minimization
Hi, The problem is you vdwtype setting, not coulombtype. Berk Date: Fri, 24 Oct 2008 16:08:14 +0200 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: Re: [gmx-users] Warning with L-BFGS minimization Mark Abraham wrote: Jochen Hub wrote: Hi, with l-bfgs minimzation, grompp always reports WARNING 1 [file em.mdp, line unknown]: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. even if the mdp gives ; Method for doing electrostatics coulombtype = PME rcoulomb_switch = 0 rcoulomb = 1. I could't find anything on that in the archive. Is that a known issue? Maybe it's case-sensitive... try pme No, same warning. :-( Jochen 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 . -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312 ___ 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 _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ 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 4 SRC RPM?
On Fri, 2008-10-24 at 09:06 -0500, Mike Hanby wrote: Is there any eta on when the gromacs-4.0-1.src.rpm is going to show up on: ftp://ftp.gromacs.org/pub/gromacs/rpm You may be able to use the one in Fedora, e.g. http://download.fedora.redhat.com/pub/fedora/linux/updates/9/SRPMS.newkey/gromacs-4.0-3.fc9.src.rpm Or, if you have Fedora / RHEL, just use the compiled RPMS available from the mirror nearest to you. -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto [EMAIL PROTECTED], p. 191 50632 -- Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of Physics, University of Helsinki, Finland [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] Gromacs 4 SRC RPM?
Thanks for the link, I'll take a look at that one. I have to build my own RPM to compile it with Intel compilers and OpenMPI. -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Jussi Lehtola Sent: Friday, October 24, 2008 9:44 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Gromacs 4 SRC RPM? On Fri, 2008-10-24 at 09:06 -0500, Mike Hanby wrote: Is there any eta on when the gromacs-4.0-1.src.rpm is going to show up on: ftp://ftp.gromacs.org/pub/gromacs/rpm You may be able to use the one in Fedora, e.g. http://download.fedora.redhat.com/pub/fedora/linux/updates/9/SRPMS.newke y/gromacs-4.0-3.fc9.src.rpm Or, if you have Fedora / RHEL, just use the compiled RPMS available from the mirror nearest to you. -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto [EMAIL PROTECTED], p. 191 50632 -- Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of Physics, University of Helsinki, Finland [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] Warning with L-BFGS minimization
Hi Jochen,
It's probably the rvdw cutoff (from readir.c):
if (ir-eI == eiLBFGS (ir-coulombtype==eelCUT || ir-vdwtype==evdwCUT)
ir-rvdw != 0) {
warning(For efficient BFGS minimization, use switch/shift/pme
instead of cut-off.);
}
Bummer!
Tsjerk
On 10/24/08, Jochen Hub [EMAIL PROTECTED] wrote:
Hi,
with l-bfgs minimzation, grompp always reports
WARNING 1 [file em.mdp, line unknown]:
For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
even if the mdp gives
; Method for doing electrostatics
coulombtype = PME
rcoulomb_switch = 0
rcoulomb = 1.
I could't find anything on that in the archive. Is that a known issue?
Cheers,
Jochen
--
Dr. Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
Tel.: +49 (0)551 201-2312
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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RE: [gmx-users] table_bonded.xvg
Hi, According to me it does not. I never change the default names. But with the default names the table file name option is table.xvg and for a tabulated bond table number 0, it correctly opens table_b0.xvg Berk From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Date: Fri, 24 Oct 2008 13:45:53 +0200 Subject: [gmx-users] table_bonded.xvg Dear Users In gromacs 4.0, in file force.c in function make_bonded_tables line (1007) sprintf(tabfn + strlen(basefn) - strlen(ftp2ext(efXVG)) - 1,_%s%d.%s, tabext, i, ftp2ext(efXVG)); produces table_bonded_bonded.xvg instead of table_bonded.xvg Greetings Andrzej Rzepiela ___ 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 _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ 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] atoms not part of any of the T-coupling groups
I am a novice at Gromacs (although I used Gromos 20+ years ago!)I have a dimer with two zincs per monomer, and I get the following complaint when running the grompp with pr.dmp, which I assume is referring to the 4 zincs. There are: 6789 OTHER residues There are: 262PROTEIN residues There are: 0DNA residues Analysing Protein... Analysing Other... --- Program grompp, VERSION 3.3.2 Source code file: readir.c, line: 865 Fatal error: 4 atoms are not part of any of the T-Coupling groups --- the zincs are in the pdb file as (properly formatted in the pdb file!): ATOM 2103 SG CYS B 133 -10.574 -5.438 18.502 1.00 51.42 S ATOM 2104 C CYS B 133 -10.084 -9.287 20.134 1.00 50.50 C ATOM 2105 O CYS B 133 -9.171 -9.545 20.923 1.00 50.69 O HETATM 2106 ZN ZN2+C 1 -12.350 1.941 1.066 1.00 43.80 ZN HETATM 2107 ZN ZN2+C 2 -21.690 2.493 -3.958 1.00 38.99 ZN HETATM 2109 ZN ZN2+C 3 -11.783 11.509 10.159 1.00 28.52 ZN HETATM 2108 ZN ZN2+C 4 -17.911 8.618 18.155 1.00 32.42 ZN What am I doing wrong ? Many thanks Garry ___ 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] atoms not part of any of the T-coupling groups
garry wrote: I am a novice at Gromacs (although I used Gromos 20+ years ago!)I have a dimer with two zincs per monomer, and I get the following complaint when running the grompp with pr.dmp, which I assume is referring to the 4 zincs. There are: 6789 OTHER residues There are: 262PROTEIN residues There are: 0DNA residues Analysing Protein... Analysing Other... --- Program grompp, VERSION 3.3.2 Source code file: readir.c, line: 865 Fatal error: 4 atoms are not part of any of the T-Coupling groups --- the zincs are in the pdb file as (properly formatted in the pdb file!): ATOM 2103 SG CYS B 133 -10.574 -5.438 18.502 1.00 51.42 S ATOM 2104 C CYS B 133 -10.084 -9.287 20.134 1.00 50.50 C ATOM 2105 O CYS B 133 -9.171 -9.545 20.923 1.00 50.69 O HETATM 2106 ZN ZN2+C 1 -12.350 1.941 1.066 1.00 43.80 ZN HETATM 2107 ZN ZN2+C 2 -21.690 2.493 -3.958 1.00 38.99 ZN HETATM 2109 ZN ZN2+C 3 -11.783 11.509 10.159 1.00 28.52 ZN HETATM 2108 ZN ZN2+C 4 -17.911 8.618 18.155 1.00 32.42 ZN What am I doing wrong ? What does your .mdp file look like? Have you included the Zn2+ within one of your tc-grps? -Justin Many thanks Garry ___ 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 -- 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 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] How to assign/make ionion bonds ?
Hi How to assign / make ionion bonds? 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] Does gromacs simulate rotation correctly?
Hi, all, Just curious. Does gromacs simulate rotation correctly? From my observation, it would appear that every object in the simulation both small and large has a similar rotational correlation time, which is not reality. I would expect water for example to have an extremely short rotational correlation time with respect to a protein. I appreciate your input. Best wishes, Art Roberts University of Washington Seattle, WA ___ 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 assign/make ionion bonds ?
Chih-Ying Lin wrote: Hi How to assign / make ionion bonds? Assign them yourself in the [ bonds ] section of the topology. As for what parameters to assign to such a species, that's up to you; they probably don't exist in the standard force fields within Gromacs... -Justin 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 -- 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 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 simulate rotation correctly?
On Fri, 24 Oct 2008 10:42:26 -0700 Arthur Roberts [EMAIL PROTECTED] wrote: Hi, all, Just curious. Does gromacs simulate rotation correctly? From my observation, it would appear that every object in the simulation both small and large has a similar rotational correlation time, which is not reality. I would expect water for example to have an extremely short rotational correlation time with respect to a protein. I appreciate your input. The answer has actually nothing to do with gromacs itself, as it is only a software. It has to do with the force field used to describe the system. This said the current force fields describe the rotational diffusion of water and proteins quite reasonably well. The correlation times are a bit too small (a factor 2-4) for both water and proteins. For water (SPC, TIP3P, etc) it would be of the order of picoseconds For proteins depending (on the size) from one to a few nanoseconds. So the force fields do reproduce the relative rotational diffusion in function of the size of the objects. Best, XAvier. Best wishes, Art Roberts University of Washington Seattle, WA ___ 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 - XAvier Periole - PhD - Molecular Dynamics Group - NMR and Computation University of Groningen The Netherlands - ___ 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] The structure property
Hi From the following tutorial, the protein pdb file is downloaded from the Protein Data Bank. Before running the MD simulation, we have to make sure the structure property. I have some questions about this tutorials. http://nmr.chem.uu.nl/~tsjerk/course/md-tutorial/ 1. Make sure that there are NO Missing residues, missing atoms- http://www.rcsb.org/pdb/files/1lw9.pdb Search for the presence of REMARK entries with numbers 465 and/or 470. = there are no REMARK 465 and REMARK 470 ??? 2. The protonation state and side chain orientation of histidine residues may be problematic. = How could I know if they are problematic? = How to do the protonation process on the system? 3. From the tutorial = Note the numbers of ions added, and verify that an excess of 8 chloride ions is added for neutralization. Having replaced a number of water molecules with ions, the system topology in 1LW9.top is not correct anymore. Edit the topology file and decrease the number of solvent molecules. Also add a line specifying the number of NA+ ions and a line specifying the amount of CL-. = Would you please explain this more? Thank you very much 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
Re: [gmx-users] The structure property
Chih-Ying Lin wrote: Hi From the following tutorial, the protein pdb file is downloaded from the Protein Data Bank. Before running the MD simulation, we have to make sure the structure property. I have some questions about this tutorials. http://nmr.chem.uu.nl/~tsjerk/course/md-tutorial/ 1. Make sure that there are NO Missing residues, missing atoms- http://www.rcsb.org/pdb/files/1lw9.pdb Search for the presence of REMARK entries with numbers 465 and/or 470. = there are no REMARK 465 and REMARK 470 ??? These REMARK lines would correspond to missing atoms or residues. You should always search a .pdb file for such lines; I believe that is the point being made. 2. The protonation state and side chain orientation of histidine residues may be problematic. = How could I know if they are problematic? = How to do the protonation process on the system? It is dependent on the protein, and histidines should be protonated according to hydrogen bonding networks, whether or not they are involved in catalysis (and how the protonation state might affect the active site!), coordination of metal ions, etc. Gromacs will try to guess the appropriate protonation state. It is your job to thoroughly research your system and determine if any special considerations are necessary. 3. From the tutorial = Note the numbers of ions added, and verify that an excess of 8 chloride ions is added for neutralization. Having replaced a number of water molecules with ions, the system topology in 1LW9.top is not correct anymore. Edit the topology file and decrease the number of solvent molecules. Also add a line specifying the number of NA+ ions and a line specifying the amount of CL-. = Would you please explain this more? What genion does is replace water molecules with ions. So if 8 Cl- are added, then 8 water molecules are removed. The corrections to the topology are thus trivial to implement. Otherwise, you can pass the -p flag to genion and have it make the changes for you. -Justin Thank you very much 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 -- 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 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] atoms not part of any of the T-coupling groups
Wouldn't it be better to couple the Protein and Zn2+ together (i.e., index group Protein_Zn2+)? Coupling ions separately often leads to weird behavior/explosions when they're free in the solvent. I've never dealt with proteins that have ions bound, so I'm curious to see what everyone else thinks about this, just as a point of curiosity. -Justin Andy Shelley wrote: Garry, I believe you are trying to not temperature couple the 4 zincs. To do this put the 4 zincs in one group and include that group in the listing of tc_grps and then correspondingly assign tau_t. tau_t=0 means no temperature coupling, but I think you will also need to give a temperature for the tau_t=0 even though that group does not have temperature coupling. See section 7.3.13 in the gromacs user manual. Andy garry wrote: I am a novice at Gromacs (although I used Gromos 20+ years ago!)I have a dimer with two zincs per monomer, and I get the following complaint when running the grompp with pr.dmp, which I assume is referring to the 4 zincs. There are: 6789 OTHER residues There are: 262PROTEIN residues There are: 0DNA residues Analysing Protein... Analysing Other... -- - Program grompp, VERSION 3.3.2 Source code file: readir.c, line: 865 Fatal error: 4 atoms are not part of any of the T-Coupling groups --- the zincs are in the pdb file as (properly formatted in the pdb file!): ATOM 2103 SG CYS B 133 -10.574 -5.438 18.502 1.00 51.42 S ATOM 2104 C CYS B 133 -10.084 -9.287 20.134 1.00 50.50 C ATOM 2105 O CYS B 133 -9.171 -9.545 20.923 1.00 50.69 O HETATM 2106 ZN ZN2+C 1 -12.350 1.941 1.066 1.00 43.80 ZN HETATM 2107 ZN ZN2+C 2 -21.690 2.493 -3.958 1.00 38.99 ZN HETATM 2109 ZN ZN2+C 3 -11.783 11.509 10.159 1.00 28.52 ZN HETATM 2108 ZN ZN2+C 4 -17.911 8.618 18.155 1.00 32.42 ZN What am I doing wrong ? What does your .mdp file look like? Have you included the Zn2+ within one of your tc-grps? -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 -- 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 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 structure property
Hi Lin, Justin is right on all points. The first is indeed a check you should always perform, but in this case (1LW9), there are no missing residues/atoms. The point is that one should be aware that there could. The same thing goes with the hint for the histidines. I could have not written you should check for missing residues/atoms and mind protonation states, but then you might take it for granted in any structure, thus running into problems or just making the MD program an expensive random number generator. Anyway, I'll probably polish the tutorial somewhat in the near future (and expand the analysis part). Do note that this mailing list is not the mailing list for the tutorial ;) Comments and questions primarily relating to the tutorial rather than to Gromacs are better sent to me personally. Cheers, Tsjerk On Fri, Oct 24, 2008 at 9:23 PM, Justin A. Lemkul [EMAIL PROTECTED] wrote: Chih-Ying Lin wrote: Hi From the following tutorial, the protein pdb file is downloaded from the Protein Data Bank. Before running the MD simulation, we have to make sure the structure property. I have some questions about this tutorials. http://nmr.chem.uu.nl/~tsjerk/course/md-tutorial/ 1. Make sure that there are NO Missing residues, missing atoms- http://www.rcsb.org/pdb/files/1lw9.pdb Search for the presence of REMARK entries with numbers 465 and/or 470. = there are no REMARK 465 and REMARK 470 ??? These REMARK lines would correspond to missing atoms or residues. You should always search a .pdb file for such lines; I believe that is the point being made. 2. The protonation state and side chain orientation of histidine residues may be problematic. = How could I know if they are problematic? = How to do the protonation process on the system? It is dependent on the protein, and histidines should be protonated according to hydrogen bonding networks, whether or not they are involved in catalysis (and how the protonation state might affect the active site!), coordination of metal ions, etc. Gromacs will try to guess the appropriate protonation state. It is your job to thoroughly research your system and determine if any special considerations are necessary. 3. From the tutorial = Note the numbers of ions added, and verify that an excess of 8 chloride ions is added for neutralization. Having replaced a number of water molecules with ions, the system topology in 1LW9.top is not correct anymore. Edit the topology file and decrease the number of solvent molecules. Also add a line specifying the number of NA+ ions and a line specifying the amount of CL-. = Would you please explain this more? What genion does is replace water molecules with ions. So if 8 Cl- are added, then 8 water molecules are removed. The corrections to the topology are thus trivial to implement. Otherwise, you can pass the -p flag to genion and have it make the changes for you. -Justin Thank you very much 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 -- 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 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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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] f(x) g(x) h(x)in the user defined potential functions
Hi Mark, Thank you for your reply. From your point of view, I wonder whether you mean I need to write a table based on different interaction types and then change the source code for recognition when running my case in the gromacs .I just have no idea about that .Can you give me further suggestion about that? I am stuck by this point Thank you very much. Yang From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Mark Abraham [EMAIL PROTECTED] Sent: Thursday, October 23, 2008 6:11 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] f(x) g(x) h(x)in the user defined potential functions He, Yang wrote: Hi all users, When I am defining the user potential functions using the table, I encountered a problem that there are several unstable parameters in the separate f(x),g(x),h(x) .For example, in the g(x), there is a parameter epsilon whose value will depend on different pairs.In this situation, I can not get a specific value in the table file . I don't know how to solve this problem. Can anyone of you give me some suggestions about that? So your nonbonded interaction depends on your atom types. You could write a table for each interaction type, modify GROMACS to read them all in, and then modify the routine that calls the kernels to use the correct one. This additional memory usage would grow as the square of the number of atom types. You would also see some performance loss which you could minimize by arranging to evaluate all of one type of nonbonded interaction close together in the nonbonded routines, to minimize cache misses. Better would be if some of these functions (conveniently) differed only by a multiplicative or additive constant so that you could re-use the same table and then apply a correction function, but you'll have to look at your own maths for that. 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] gromacs 3.3.1/4.0 and fftw 3.1.2
Hello, can anybody confirm if fftw-3.1.2 is compatible with gromacs 3.3.1 and gromacs 4.0? A colleague has recently indicated that I must use fftw 2.1.5 for gromacs mpi. However, I have been using fftw-3.1.2 for quite a while now. It compiles fine and my searching today turned up some other usage here: http://lindahl.sbc.su.se/outgoing/workshop2007/tutorial1/tutorial1.pdf I did find mention of some problems with fftw 3.0.1 and gromacs here: http://www.pathscale.com/building_code/gromacs.html and also on the gromacs users mailing list, but I am hoping that fftw 3.1.2 is fine. Second question, if there is some problem with fftw 3.1.2 and mpi gromacs then is this a problem of a) inability to compile, b) slow execution with PME, or c) incorrect dynamics? Thanks, Chris. ___ 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] Is there a way to measure the shortest distance between two groups of atoms?
Hi, all, I was wondering if there is a way to measure the shortest distance between two groups of atoms? g_dist seems to only measure the average distance between the two groups. Your input would be greatly appreciated. Sincerely, Art Roberts ___ 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] Is there a way to measure the shortest distance between two groups of atoms?
g_mindist (with or without -pi depending on what you want) Hi, all, I was wondering if there is a way to measure the shortest distance between two groups of atoms? g_dist seems to only measure the average distance between the two groups. Your input would be greatly appreciated. ___ 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 3.3.1/4.0 and fftw 3.1.2
[EMAIL PROTECTED] a écrit : Hello, can anybody confirm if fftw-3.1.2 is compatible with gromacs 3.3.1 and gromacs 4.0? A colleague has recently indicated that I must use fftw 2.1.5 for gromacs mpi. However, I have been using fftw-3.1.2 for quite a while now. It compiles fine and my searching today turned up some other usage here: http://lindahl.sbc.su.se/outgoing/workshop2007/tutorial1/tutorial1.pdf I did find mention of some problems with fftw 3.0.1 and gromacs here: http://www.pathscale.com/building_code/gromacs.html and also on the gromacs users mailing list, but I am hoping that fftw 3.1.2 is fine. Second question, if there is some problem with fftw 3.1.2 and mpi gromacs then is this a problem of a) inability to compile, I have compiled several times gromacs-3.3.3 with fftw-3.1.2 on different machines and never had any problem related to fftw, but I'm really not a gcc wizard. Same think with gmx-3.3.1 and gromacs-4 b) slow execution with PME I have never noticed any slowdown with fftw-3.1.2 on any gromacs version 3.3.1 or c) incorrect dynamics? I have briefly compare gromacs-3.3.1 + fftw-2.1.5 (on cluster X) and gromacs-3.3.3+fftw-3.1.2 (on cluster Y) and didn't notice any significant difference, but as I said, it was a quick comparison. Additionally, it is said on the website that Gromacs is compatible with fftw-3.x: http://www.gromacs.org/content/view/23/33/ Nicolas Thanks, Chris. ___ 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 begin:vcard fn:Nicolas Sapay n:Sapay;Nicolas org:University of Calgary;Biological department adr:;;2500 University drive NW;Calgary;AB;T2N 1N4;Canada email;internet:[EMAIL PROTECTED] title:Post-doctoral fellow tel;work:403-220-6869 x-mozilla-html:TRUE url:http://moose.bio.ucalgary.ca/ version:2.1 end:vcard ___ 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] The code : from .pdb to .gro
Hi Could anyone please to direct me the code / the command (pdb2gmx) , which can transfer .pdb file to .gro file? 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
Re: [gmx-users] gromacs 3.3.1/4.0 and fftw 3.1.2
[EMAIL PROTECTED] wrote: Hello, can anybody confirm if fftw-3.1.2 is compatible with gromacs 3.3.1 and gromacs 4.0? A colleague has recently indicated that I must use fftw 2.1.5 for gromacs mpi. However, I have been using fftw-3.1.2 for quite a while now. It compiles fine and my searching today turned up some other usage here: http://lindahl.sbc.su.se/outgoing/workshop2007/tutorial1/tutorial1.pdf Possibly your colleague's memory is antiquated. FFTW 2.x had parallel FFTs that might have been used by GROMACS at the time. This might explain your colleague's association of MPI GROMACS and FFTW 2.1.5. However certainly by 3.3.1, GROMACS is perfectly happy with any FFTW version, since it handles the parallelism itself and so needs only serial FFT routines. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] f(x) g(x) h(x)in the user defined potential functions
He, Yang wrote: Hi Mark, Thank you for your reply. From your point of view, I wonder whether you mean I need to write a table based on different interaction types and then change the source code for recognition when running my case in the gromacs. Yes that's what I said. I just have no idea about that .Can you give me further suggestion about that? I am stuck by this point I'm afraid you'll have to look carefully at the data structures GROMACS builds during neighbour-searching and build in some hook to allow you to use the correct tables later in src/gmxlib/nonbonded.c. You're own your own there. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] The code : from .pdb to .gro
Chih-Ying Lin wrote: Hi Could anyone please to direct me the code / the command (pdb2gmx) , which can transfer .pdb file to .gro file? It's unlikely you actually need a .gro file for your purpose. pdb2gmx is a tool for making topology files. editconf is the easiest tool for making simple changes to coordinate files. 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] gromacs 3.3.1/4.0 and fftw 3.1.2
Hi Mark, did you post something on this topic? There is a link indicating that you did but it is broken for some reason. The links above and below work fine. If you wouldn't mind, could you please repost? Thanks, Chris. ___ 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
