Re: [gmx-users] Error while pulling a settled tip4p water molecule
chris.ne...@utoronto.ca wrote: I have done a similar thing in the past (without using the pull code), renaming the crystal waters around the protein so that they were easier to track. I eventually figured out that it was necessary for me to place the waters sequentially in the .top file. e.g: ; This is OK Protein 1 SOL 999 XSOL 1 ; This crashed SOL 999 Protein 1 XSOL 1 I realize that I was getting different errors than you are, but it's worth checking if this fix works for you. My old post is here http://lists.gromacs.org/pipermail/gmx-users/2006-September/024003.html although it doesn't contain any relevant information other than what I have mentioned above. Ah thanks. For me it was already fine to replace the settle-line by 3 constraints: ; [ settles ] ; OWfunct dohdhh ; 1 1 0.095720.15139 [ constraints ] ; turned settle into normal constraint 1 2 1 0.09572 1 3 1 0.09572 2 3 1 0.15139 Jochen Chris. --- original message --- Berk Hess wrote: Hi, I don't understand why you got this error message. Do you have two different types of water molecules with different geometries? In that case Gromacs would give this error message, because currently only one geometry is supported for settle, so you'll have to replace the others by 3 normal constraints. Ah, all right. I have indeed a separate topology for the water used in the pulling (to be able to give it a different residue name). I have replaced the settle by 3 constraints and now everything works fine. But if the you make the geometry identical, it should still work with settle, since then the two settle geometries are identical. Berk Then there is something odd. The two settles are definitely identical since I simply copied the tip4p.itp. I also just rechecked with xxdiff, the two settle lines are the same. Jochen -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- -- 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] Unstable Minimizations
Hi, Okay, they're read in some cases. But not in pdb2gmx related to building a topology as far as I can see. I should've written: pdb2gmx doesn't distinguish between ATOM and HETATM entries. pdb2gmx does not read CONECT records. Now the 'TER' recoord... That makes a difference. Cheers, Tsjerk On Thu, Jan 14, 2010 at 9:23 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Tsjerk Wassenaar skrev: Hi Jack, On Thu, Jan 14, 2010 at 5:41 PM, Jack Shultz j...@drugdiscoveryathome.com mailto:j...@drugdiscoveryathome.com wrote: Problem Solved. I replaced HETATM with ATOM, I fixed BOTH N-terminal and C-terminal. I kept TER and END. Removed all CONECT. Renamed the CYS to CYS2. No other non-AminoAcid residues were present. Most of this is described by the FFAmber site http://chemistry.csulb.edu/ffamber/ Gromacs doesn't distinguish between ATOM and HETATM entries. Gromacs does not read CONECT records. Now the 'TER' recoord... That makes a difference. I may be wrong, but I think Gromacs reads CONNECT records nowadays. /Erik Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- --- Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 4537 fax: +46 18 511 755 er...@xray.bmc.uu.se http://xray.bmc.uu.se/molbiophys -- gmx-users mailing list gmx-us...@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 -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- 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
[gmx-users] Re: Configuration of Gaussian for QM/MM
The instruction says: To find the fortran source file that contains the function you need, you can use the grep command: grep -i d1e $GAUSS_DIR/*.F What is it that you do misunderstand about this? Gerrit Is there any misunderstand about instruction ? -- 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] 10-4-3 implicit wall potential
Dear prof. Berk, Since it is the first time I use the tabulated potential, I have lots of questions about it. Could you help me out? Thanks a lot! I make the test in the system with only some waters between 2 implicit walls. 1. some related parameters of the .mdp file are listed below. Is there anything wrong? energygrps = SOL pbc= xy rlist = 1.2 coulombtype = pme rcoulomb = 1.2 vdw-type = cut-off rvdw = 1.2 DispCorr = EnerPres table-extension = 1 energygrp_table = ;Walls nwall = 2 wall_type = table wall_r_linpot = 0.0 wall_atomtype = opls_135 opls_135 wall_density = ;(the wall_density is included in the tabulated potential, right?) wall_ewald_zfac = 3 2. The flags of mdrun are: mdrun -deffnm table -tablep table_SOL_wall0.xvg table_SOL_wall1.xvg -table table.xvg where table.xvg is copied from gmx_top_path/table6-12.xvg, and table_SOL_wall0.xvg and table_SOL_wall1.xvg are the self-generated 9-3 potential (9-3 potential is used for the aim of testing and compare with the default 9-3 potential of gromacs.) Since I use only the tabulated potential between SOL-wall0 and SOL-wall1, why do I need the table.xvg? Does it affect the coulomb/vdw potential between SOL-SOL? 3. In the table_SOL_wall0.xvg and table_SOL_wall1.xvg, the distance range of 0-3nm is generated. max(rvdw, rcoulomb)=1.2 nm and table-extension=1. The question is what is the cutoff distance for the tabulated SOL-wall0/wall1 potential, 2.2nm or 3nm? 4. In the output file table.log, Table routines are used for coulomb: TRUE Table routines are used for vdw: FALSE Using a Gaussian width (1/beta) of 0.384195 nm for Ewald Cut-off's: NS: 1.2 Coulomb: 1.2 LJ: 1.2 System total charge: 0.000 Generated table with 1100 data points for Ewald. Tabscale = 500 points/nm Generated table with 1100 data points for LJ6. Tabscale = 500 points/nm Generated table with 1100 data points for LJ12. Tabscale = 500 points/nm Reading user tables for 1 energy groups with 2 walls Read user tables from table_SOL_wall0.xvg with 1501 data points. Tabscale = 500 points/nm Read user tables from table_SOL_wall1.xvg with 1501 data points. Tabscale = 500 points/nm The question are: a) Since Table is not used for vdw (FALSE), why table is generated for LJ6/LJ12? b) Where does the value of "1100" data points come from? (Since rvdw=1.2, tabscale=500, it should be 1400, not 1100!?) c) 1501 data points is generated for table_SOL_wall0/wall1, the answer of the 3rd question (cutoff value for the tabulated potential calculation) should be 3nm, right? Sorry for the lots of questions! best wishes, Baofu Qiao Berk Hess wrote: Hi, Why not use the tabulated wall potential? That does not require are changes to the code. Berk Date: Tue, 5 Jan 2010 14:13:30 +0100 From: qia...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] 10-4-3 implicit wall potential HI all, Does anyone have experience to implement the 10-4-3 implicit wall potential? If I want to use it, which files do I need to change, except wall.c? Can anyone give some suggestions? Thanks a lot! best wishes, Baofu Qiao -- 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 _ 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://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] 10-4-3 implicit wall potential
Hi, Do you really need all those tables? I would think you onkly need to specify your wall table and no other tables. As the documentation says (I think), the cut-off for the wall table is the length of the table you specify. Berk Date: Fri, 15 Jan 2010 11:02:40 +0100 From: qia...@gmail.com To: gmx-users@gromacs.org Subject: Re: [gmx-users] 10-4-3 implicit wall potential Dear prof. Berk, Since it is the first time I use the tabulated potential, I have lots of questions about it. Could you help me out? Thanks a lot! I make the test in the system with only some waters between 2 implicit walls. 1. some related parameters of the .mdp file are listed below. Is there anything wrong? energygrps = SOL pbc= xy rlist= 1.2 coulombtype = pme rcoulomb = 1.2 vdw-type = cut-off rvdw = 1.2 DispCorr = EnerPres table-extension = 1 energygrp_table = ;Walls nwall = 2 wall_type = table wall_r_linpot = 0.0 wall_atomtype = opls_135 opls_135 wall_density = ;(the wall_density is included in the tabulated potential, right?) wall_ewald_zfac = 3 2. The flags of mdrun are: mdrun -deffnm table -tablep table_SOL_wall0.xvg table_SOL_wall1.xvg -table table.xvg where table.xvg is copied from gmx_top_path/table6-12.xvg, and table_SOL_wall0.xvg and table_SOL_wall1.xvg are the self-generated 9-3 potential (9-3 potential is used for the aim of testing and compare with the default 9-3 potential of gromacs.) Since I use only the tabulated potential between SOL-wall0 and SOL-wall1, why do I need the table.xvg? Does it affect the coulomb/vdw potential between SOL-SOL? 3. In the table_SOL_wall0.xvg and table_SOL_wall1.xvg, the distance range of 0-3nm is generated. max(rvdw, rcoulomb)=1.2 nm and table-extension=1. The question is what is the cutoff distance for the tabulated SOL-wall0/wall1 potential, 2.2nm or 3nm? 4. In the output file table.log, Table routines are used for coulomb: TRUE Table routines are used for vdw: FALSE Using a Gaussian width (1/beta) of 0.384195 nm for Ewald Cut-off's: NS: 1.2 Coulomb: 1.2 LJ: 1.2 System total charge: 0.000 Generated table with 1100 data points for Ewald. Tabscale = 500 points/nm Generated table with 1100 data points for LJ6. Tabscale = 500 points/nm Generated table with 1100 data points for LJ12. Tabscale = 500 points/nm Reading user tables for 1 energy groups with 2 walls Read user tables from table_SOL_wall0.xvg with 1501 data points. Tabscale = 500 points/nm Read user tables from table_SOL_wall1.xvg with 1501 data points. Tabscale = 500 points/nm The question are: a) Since Table is not used for vdw (FALSE), why table is generated for LJ6/LJ12? b) Where does the value of 1100 data points come from? (Since rvdw=1.2, tabscale=500, it should be 1400, not 1100!?) c) 1501 data points is generated for table_SOL_wall0/wall1, the answer of the 3rd question (cutoff value for the tabulated potential calculation) should be 3nm, right? Sorry for the lots of questions! best wishes, Baofu Qiao Berk Hess wrote: Hi, Why not use the tabulated wall potential? That does not require are changes to the code. Berk Date: Tue, 5 Jan 2010 14:13:30 +0100 From: qia...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] 10-4-3 implicit wall potential HI all, Does anyone have experience to implement the 10-4-3 implicit wall potential? If I want to use it, which files do I need to change, except wall.c? Can anyone give some suggestions? Thanks a lot! best wishes, Baofu Qiao -- 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 _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ _ New Windows 7: Simplify what you do everyday. Find the right PC for you. http://windows.microsoft.com/shop-- 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
Re: [gmx-users] 10-4-3 implicit wall potential
Hi, Thanks a lot! I just tried again. mdrun -table table works. best regards, Baofu Qiao Berk Hess wrote: Hi, Do you really need all those tables? I would think you onkly need to specify your wall table and no other tables. As the documentation says (I think), the cut-off for the wall table is the length of the table you specify. Berk Date: Fri, 15 Jan 2010 11:02:40 +0100 From: qia...@gmail.com To: gmx-users@gromacs.org Subject: Re: [gmx-users] 10-4-3 implicit wall potential Dear prof. Berk, Since it is the first time I use the tabulated potential, I have lots of questions about it. Could you help me out? Thanks a lot! I make the test in the system with only some waters between 2 implicit walls. 1. some related parameters of the .mdp file are listed below. Is there anything wrong? energygrps = SOL pbc= xy rlist= 1.2 coulombtype = pme rcoulomb = 1.2 vdw-type = cut-off rvdw = 1.2 DispCorr = EnerPres table-extension = 1 energygrp_table = ;Walls nwall = 2 wall_type = table wall_r_linpot = 0.0 wall_atomtype = opls_135 opls_135 wall_density = ;(the wall_density is included in the tabulated potential, right?) wall_ewald_zfac = 3 2. The flags of mdrun are: mdrun -deffnm table -tablep table_SOL_wall0.xvg table_SOL_wall1.xvg -table table.xvg where table.xvg is copied from gmx_top_path/table6-12.xvg, and table_SOL_wall0.xvg and table_SOL_wall1.xvg are the self-generated 9-3 potential (9-3 potential is used for the aim of testing and compare with the default 9-3 potential of gromacs.) Since I use only the tabulated potential between SOL-wall0 and SOL-wall1, why do I need the table.xvg? Does it affect the coulomb/vdw potential between SOL-SOL? 3. In the table_SOL_wall0.xvg and table_SOL_wall1.xvg, the distance range of 0-3nm is generated. max(rvdw, rcoulomb)=1.2 nm and table-extension=1. The question is what is the cutoff distance for the tabulated SOL-wall0/wall1 potential, 2.2nm or 3nm? 4. In the output file table.log, Table routines are used for coulomb: TRUE Table routines are used for vdw: FALSE Using a Gaussian width (1/beta) of 0.384195 nm for Ewald Cut-off's: NS: 1.2 Coulomb: 1.2 LJ: 1.2 System total charge: 0.000 Generated table with 1100 data points for Ewald. Tabscale = 500 points/nm Generated table with 1100 data points for LJ6. Tabscale = 500 points/nm Generated table with 1100 data points for LJ12. Tabscale = 500 points/nm Reading user tables for 1 energy groups with 2 walls Read user tables from table_SOL_wall0.xvg with 1501 data points. Tabscale = 500 points/nm Read user tables from table_SOL_wall1.xvg with 1501 data points. Tabscale = 500 points/nm The question are: a) Since Table is not used for vdw (FALSE), why table is generated for LJ6/LJ12? b) Where does the value of 1100 data points come from? (Since rvdw=1.2, tabscale=500, it should be 1400, not 1100!?) c) 1501 data points is generated for table_SOL_wall0/wall1, the answer of the 3rd question (cutoff value for the tabulated potential calculation) should be 3nm, right? Sorry for the lots of questions! best wishes, Baofu Qiao Berk Hess wrote: Hi, Why not use the tabulated wall potential? That does not require are changes to the code. Berk Date: Tue, 5 Jan 2010 14:13:30 +0100 From: qia...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] 10-4-3 implicit wall potential HI all, Does anyone have experience to implement the 10-4-3 implicit wall potential? If I want to use it, which files do I need to change, except wall.c? Can anyone give some suggestions? Thanks a lot! best wishes, Baofu Qiao -- 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] MPI ERROR while installing GMX4.0.7
Hello! I had the same problem, and for me the solution was to set up the openmpi/lib directory. The compiler is not able to find it alone. I'm using bash, so for me the solution was: export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/your/directory/openmpi/lib of course you have to change /your/directory with the correct path in your system. I hope this will help. Nuno Azoia On Fri, 2010-01-15 at 12:30 +0530, Chandan Choudhury wrote: Hello gmx-users !! I am trying to install gromacs 4.0.7 double precision with mpi. I downloaded openmpi-1.4. and installed it. Then executed ./configure --enable-mpi --program-suffix=_mpi_d --prefix=/usr/local/gromacs407_double_mpi --enable-double It showed checking for mpicc... mpicc checking whether the MPI cc command works... yes checking for catamount... no checking how to run the C preprocessor... mpicc -E checking whether mpicc accepts -O3... yes checking whether mpicc accepts -funroll-all-loops... yes checking whether mpicc accepts -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops... yes checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... no checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking whether byte ordering is bigendian... no checking for int... yes
Re: [gmx-users] Density
Thank you Mark, for your answer. This time I have another issue: temperature. What are the ways to control temperature in gromacs (during heating or equilibration phases), other than temperature coupling? Thank you Carla On Thu, Jan 14, 2010 at 10:40 PM, Mark Abraham mark.abra...@anu.edu.auwrote: Carla Jamous wrote: Hello, I'm experiencing some difficulties with gromacs. In order to control my system's density, I have to use g_energy or g_density. Those tools report density-related quantities, they do not control it. However, when I use g_energy, in my list, Density doesn't appear. g_energy doesn't report the density if you have a constant-volume simulation (but grompp probably reported it when you generated the .tpr) Else, if I use g_density, it needs a file traj.xtc which I don't have. Per Erik's point, you can usually use any coordinate file or trajectory file. Mark So please can anyone tell me how to check my system's density in gromacs? Thank you Carla -- 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 -- 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
[gmx-users] Ammonia in Water
Hello, I created a topology file for 1 ammonia in water. Could someone please have a look at the file and let me know if it looks okay. Thanks Nisha Patel ; Include forcefield parameters #include ffoplsaa.itp [ moleculetype ] ; Namenrexcl Ammonia 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB 1 opls_237 1NH3 N 1 -0.7614.0067 ; qtot -0.76 2 opls_240 1NH3 H1 1 0.38 1.008 ; qtot -0.38 3 opls_240 1NH3 H2 1 0.38 1.008 ; qtot 0 4 opls_240 1NH3 H3 1 0.38 1.008 ; qtot 0.38 [ bonds ] ; aiaj functc0c1c2c3 1 2 1 1 3 1 1 4 1 [ angles ] ; aiajak functc0c1c2 c3 2 1 3 1 2 1 4 1 3 1 4 1 ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include water topology #include spc.itp [ system ] ; Name ammonia in water [ molecules ] ; Compound#mols Ammonia 1 SOL 345 -- 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
[gmx-users] polymer-protein
Dear Gromacs users, I have to attach a chemical polymer to a protein and when I created peptide bonds and saved it, the entire format of the pdb file changed. That is the entire identity of the protein was lost and the pdb file was saved in the form of ATOMS and not residues. Are there any solutions to this or can I Use the same in gromacs??? If yes, how can I use it in the pdb2gmx command Please help, Thanking you, regards, Anand The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. http://in.yahoo.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/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] implicit wall doesn't recognize the wall_atomtype correctly?
Hi all, I want to know whether it is a bug or not: When I use some nonsense wall_atomtype for the implicit wall, the grompp doesn't complain about it. Or it is a mistake I make myself. I am using gmx 4.0.7. See the following flags of wall_atomtype. nwall = 2 wall_type = 9-3 wall_r_linpot = 0.1 wall_atomtype = abc 123 ;opls_abc opls_abc wall_density = 144 144 wall_ewald_zfac = 3 best wishes, Baofu Qiao -- 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] Ammonia in Water
nishap.pa...@utoronto.ca wrote: Hello, I created a topology file for 1 ammonia in water. Could someone please have a look at the file and let me know if it looks okay. With a fractional charge of +0.38, I'd say these parameters (at least as far as the charges) are inappropriate. The only way to determine if parameters are appropriate is to derive them in a manner consistent with the original force field. This is not a trivial task. Consult the list archive and Gromacs wiki for tips. -Justin Thanks Nisha Patel ; Include forcefield parameters #include ffoplsaa.itp [ moleculetype ] ; Namenrexcl Ammonia 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB 1 opls_237 1NH3 N 1 -0.7614.0067 ; qtot -0.76 2 opls_240 1NH3 H1 1 0.38 1.008 ; qtot -0.38 3 opls_240 1NH3 H2 1 0.38 1.008 ; qtot 0 4 opls_240 1NH3 H3 1 0.38 1.008 ; qtot 0.38 [ bonds ] ; aiaj functc0c1c2c3 1 2 1 1 3 1 1 4 1 [ angles ] ; aiajak functc0c1c2 c3 2 1 3 1 2 1 4 1 3 1 4 1 ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include water topology #include spc.itp [ system ] ; Name ammonia in water [ molecules ] ; Compound#mols Ammonia 1 SOL 345 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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://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] polymer-protein
P.R.Anand Narayanan wrote: Dear Gromacs users, I have to attach a chemical polymer to a protein and when I created peptide bonds and saved it, the entire format of the pdb file changed. That is the entire identity of the protein was lost and the pdb file was saved in the form of ATOMS and not residues. You'll have to give some example of what you mean. Otherwise, we're left to assume that you improperly generated the coordinate file, but you haven't even mentioned how you've done what you're attempting. Are there any solutions to this or can I Use the same in gromacs??? If yes, how can I use it in the pdb2gmx command You cannot use pdb2gmx unless you have the appropriate .rtp entries (and perhaps specbond.dat entries) defined. See the numerous discussions in the list archive as well as pdb2gmx usage information and errors (and how to deal with them) on the Gromacs site. -Justin Please help, Thanking you, regards, Anand The INTERNET now has a personality. YOURS! See your Yahoo! Homepage http://in.rd.yahoo.com/tagline_yyi_1/*http://in.yahoo.com/. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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://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
[gmx-users] Ammonia in Water
First, I doubt that you want a molecule with a partial charge. Second, just because the bonds, angles, and LJ parameters will be generated doesn't mean they will be correct. What are the N-H bond lengths of ammonia? Are those the same as the ones that you are including here? Take a look at ffoplsaabon.itp and, for LJ parameters, ffoplsaanb.itp. Third, ammonia has a lone pair if memory serves. Are your angles sufficient to reproduce the geometry? i.e. will you get the correct pyramidal structure or will you perhaps get a planar structure? Hint: I think that your topology will pick up the following angles from ffoplsaabon.itp H N H 1 120.000292.880 ; ADE,CYT,GUA,GLN,ASN ** Finally, it is often said -- though rarely heard -- that parameterization is a very advanced topic best attempted after you have sufficient simulation experience: http://www.gromacs.org/index.php?title=Documentation/How-tos/Parameterizationhighlight=exotic Hello, I created a topology file for 1 ammonia in water. Could someone please have a look at the file and let me know if it looks okay. Thanks Nisha Patel ; Include forcefield parameters #include ffoplsaa.itp [ moleculetype ] ; Namenrexcl Ammonia 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB 1 opls_237 1NH3 N 1 -0.7614.0067 ; qtot -0.76 2 opls_240 1NH3 H1 1 0.38 1.008 ; qtot -0.38 3 opls_240 1NH3 H2 1 0.38 1.008 ; qtot 0 4 opls_240 1NH3 H3 1 0.38 1.008 ; qtot 0.38 [ bonds ] ; aiaj functc0c1c2c3 1 2 1 1 3 1 1 4 1 [ angles ] ; aiajak functc0c1c2 c3 2 1 3 1 2 1 4 1 3 1 4 1 ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include water topology #include spc.itp [ system ] ; Name ammonia in water [ molecules ] ; Compound#mols Ammonia 1 SOL 345 -- Message: 4 Date: Fri, 15 Jan 2010 21:26:47 +0530 (IST) From: P.R.Anand Narayanan nandu_coolde...@yahoo.co.in Subject: [gmx-users] polymer-protein To: gromacs gmx-users@gromacs.org Message-ID: 61710.4449...@web95203.mail.in2.yahoo.com Content-Type: text/plain; charset=utf-8 Dear Gromacs users, I have to attach a chemical polymer to a protein and when I created peptide bonds and saved it, the entire format of the pdb file changed. That is the entire identity of the protein was lost and the pdb file was saved in the form of ATOMS and not residues. Are there any solutions to this or can I Use the same in gromacs??? If yes, how can I use it in the pdb2gmx command Please help, Thanking you, regards, Anand The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. http://in.yahoo.com/ -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100115/49eed6ff/attachment-0001.html -- Message: 5 Date: Fri, 15 Jan 2010 17:06:25 +0100 From: Baofu Qiao qia...@gmail.com Subject: [gmx-users] implicit wall doesn't recognize the wall_atomtype correctly? To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4b509281.9050...@gmail.com Content-Type: text/plain; charset=us-ascii An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100115/e1f3bab3/attachment.html -- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! End of gmx-users Digest, Vol 69, Issue 78 * -- 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] Density
Carla Jamous wrote: Thank you Mark, for your answer. This time I have another issue: temperature. What are the ways to control temperature in gromacs (during heating or equilibration phases), other than temperature coupling? I don't see how that's even possible. By definition, temperature control is the job of a thermostat. The sd integrator provides this function as well, by way of a Langevin thermostat, but that's really the same thing as using temperature coupling, anyway, it's just not a tcoupl option. -Justin Thank you Carla On Thu, Jan 14, 2010 at 10:40 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: Carla Jamous wrote: Hello, I'm experiencing some difficulties with gromacs. In order to control my system's density, I have to use g_energy or g_density. Those tools report density-related quantities, they do not control it. However, when I use g_energy, in my list, Density doesn't appear. g_energy doesn't report the density if you have a constant-volume simulation (but grompp probably reported it when you generated the .tpr) Else, if I use g_density, it needs a file traj.xtc which I don't have. Per Erik's point, you can usually use any coordinate file or trajectory file. Mark So please can anyone tell me how to check my system's density in gromacs? Thank you Carla -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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://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] MPI ERROR while installing GMX4.0.7
Dear Nuno
thanks for your helpful suggestion. It worked successful.
But the following command mpirun -np 2 mdrun_mpi_d -v -s em_1.tpr -c
em_1.pdb doesnt seem to run parallely. I have mentiond the output below.
ban...@corsica:~/CKC/L2PJR mpirun -np 2 mdrun_mpi_d -v -s em_1.tpr -c
em_1.pdb
[corsica:17339] [NO-NAME] ORTE_ERROR_LOG: Not found in file
runtime/orte_init_stage1.c at line 182
--
It looks like orte_init failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during orte_init; some of which are due to configuration or
environment problems. This failure appears to be an internal failure;
here's some additional information (which may only be relevant to an
Open MPI developer):
orte_rml_base_select failed
-- Returned value -13 instead of ORTE_SUCCESS
--
[corsica:17339] [NO-NAME] ORTE_ERROR_LOG: Not found in file
runtime/orte_system_init.c at line 42
[corsica:17339] [NO-NAME] ORTE_ERROR_LOG: Not found in file
runtime/orte_init.c at line 52
--
Open RTE was unable to initialize properly. The error occured while
attempting to orte_init(). Returned value -13 instead of ORTE_SUCCESS.
--
Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Fri, Jan 15, 2010 at 5:04 PM, Nuno Azoia naz...@det.uminho.pt wrote:
Hello!
I had the same problem, and for me the solution was to set up the
openmpi/lib directory. The compiler is not able to find it alone.
I'm using bash, so for me the solution was:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/your/directory/openmpi/lib
of course you have to change /your/directory with the correct path in
your system.
I hope this will help.
Nuno Azoia
On Fri, 2010-01-15 at 12:30 +0530, Chandan Choudhury wrote:
Hello gmx-users !!
I am trying to install gromacs 4.0.7 double precision with mpi. I
downloaded openmpi-1.4. and installed it.
Then executed
./configure --enable-mpi --program-suffix=_mpi_d
--prefix=/usr/local/gromacs407_double_mpi --enable-double
It showed checking for mpicc...
mpicc
checking whether the MPI cc command works...
yes
checking for catamount...
no
checking how to run the C preprocessor... mpicc
-E
checking whether mpicc accepts -O3...
yes
checking whether mpicc accepts -funroll-all-loops...
yes
checking whether mpicc accepts -O3 -fomit-frame-pointer
-finline-functions -Wall -Wno-unused -funroll-all-loops...
yes
checking for grep that handles long lines and
-e... /usr/bin/grep
checking for egrep... /usr/bin/grep
-E
checking for ANSI C header files...
no
checking for sys/types.h...
yes
checking for sys/stat.h...
yes
checking for stdlib.h...
yes
checking for string.h...
yes
checking for memory.h...
yes
checking for strings.h...
yes
checking for inttypes.h...
yes
checking for stdint.h...
yes
checking for unistd.h...
yes
checking whether byte ordering is bigendian...
no
checking for int...
yes
checking size of int... configure: error: cannot compute sizeof
(int)
See `config.log' for more details.
The part of the config.log reads as:
--configure:4577: checking whether the MPI cc command works
configure:4601: mpicc -o conftest -g -O2 conftest.c 5
configure:4607: $? = 0
configure:4613: result: yes
configure:4636: checking for catamount
configure:4664: mpicc -c -g -O2 conftest.c 5
conftest.c:20:2: error: #error not catamount
configure:4670: $? = 1
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME gromacs
| #define PACKAGE_TARNAME gromacs
| #define PACKAGE_VERSION 4.0.7
| #define PACKAGE_STRING gromacs 4.0.7
| #define PACKAGE_BUGREPORT gmx-users@gromacs.org
| #define PACKAGE gromacs
| #define VERSION 4.0.7
| #define GMX_DOUBLE
| #define GMX_SOFTWARE_SQRT
| #define GMX_QMMM_GAUSSIAN
| #define BUILD_TIME Sun Jan 17 01:26:27 EST 2010
| #define BUILD_USER r...@corsica
| #define BUILD_MACHINE Linux 2.6.31.5-0.1-desktop i686
| #define GMX_MPI
| /* end confdefs.h. */
|
| #if defined __QK_USER__
| #else
| #error not catamount
| #endif
|
| int
| main ()
| {
|
| ;
| return 0;
| }
configure:4706: result: no
configure:5590: checking how to run the C preprocessor
configure:5630: mpicc -E conftest.c
configure:5636: $? = 0
configure:5667: mpicc -E conftest.c
conftest.c:19:28: error: ac_nonexistent.h: No such file or directory
|
| int
| main ()
| {
|
| ;
| return 0;
| }
configure:4706: result: no
configure:5590: checking how to run the C preprocessor
configure:5630: mpicc -E conftest.c
configure:5636: $? = 0
configure:5667: mpicc
[gmx-users] CHarmm and popc membrane
I am trying to equilibrate a POPC membrane with 128 POPC molecules, but grompp gives out the following notes and minimization with mdrun does not work. The output on screen of mdrun comes out like this: Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 10. Potential Energy = 1.4422483e+17 Maximum force =inf on atom 4082 Norm of force =inf And grompp notes are: NOTE 2 [file topol.top, line unknown]: The largest charge group contains 12 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts. For efficiency and accuracy, charge group should consist of a few atoms. For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc. NOTE 3 [file topol.top, line unknown]: The largest charge group contains 16 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts. For efficiency and accuracy, charge group should consist of a few atoms. For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc. Here is my minimization mdp file, I have used the first one with PME but then changed to Reaction-field and no PBC (just as curiosity to see if it worked). integrator= steep emtol= 1000.0 emstep = 0.01 nsteps= 5 nstlist= 1 ns_type= grid rlist= 1.2 coulombtype= PME rcoulomb= 1.2 rvdw= 1.2 pbc= xyz Thank you -- 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
[gmx-users] CHarmm and popc membrane
I think the notes from grompp are pretty clear. You need to redivide your charge groups so that they contain fewer atoms. You can do this in the .top or .itp file and you can find out how to do that in the manual. Feel free to post your original and charge-group-modified topologies back here if you want people to take a look at them. Chris. -- original message -- I am trying to equilibrate a POPC membrane with 128 POPC molecules, but grompp gives out the following notes and minimization with mdrun does not work. The output on screen of mdrun comes out like this: Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 10. Potential Energy = 1.4422483e+17 Maximum force =inf on atom 4082 Norm of force =inf And grompp notes are: NOTE 2 [file topol.top, line unknown]: The largest charge group contains 12 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts. For efficiency and accuracy, charge group should consist of a few atoms. For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc. NOTE 3 [file topol.top, line unknown]: The largest charge group contains 16 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts. For efficiency and accuracy, charge group should consist of a few atoms. For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc. Here is my minimization mdp file, I have used the first one with PME but then changed to Reaction-field and no PBC (just as curiosity to see if it worked). integrator= steep emtol= 1000.0 emstep = 0.01 nsteps= 5 nstlist= 1 ns_type= grid rlist= 1.2 coulombtype= PME rcoulomb= 1.2 rvdw= 1.2 pbc= xyz -- 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
[gmx-users] Missing Residues are list ind pdb file
I'm trying to prep Fe-Hydrogenase again (1YQW). I took out all the non-standard residues. Re-named n-terminal and c-terminal residues. Took out connects because that worked last time though I'm uncertain if connect really maters. Another issue with preping a protein. Its says I a missing H and HA for this residue, but have those atoms listed there. Why does it say CYSH instead of CYS2 on residue 15 ??? ffamber99sb.hdb does not list CYSH as a resdue. http://boinc.drugdiscoveryathome.com/protein.pdb.txt http://boinc.drugdiscoveryathome.com/pdb2gmx.txt ATOM 232 N CYS2 15 5.467 7.021 7.435 1.00 0.00 ATOM 233 H CYS2 15 6.122 7.731 7.139 1.00 0.00 ATOM 234 CA CYS2 15 5.957 5.650 7.604 1.00 0.00 ATOM 235 HA CYS2 15 5.114 4.975 7.752 1.00 0.00 ATOM 236 CB CYS2 15 6.737 5.195 6.365 1.00 0.00 ATOM 237 2HB CYS2 15 6.774 4.106 6.322 1.00 0.00 ATOM 238 3HB CYS2 15 6.264 5.578 5.461 1.00 0.00 ATOM 239 SG CYS2 15 8.466 5.762 6.309 1.00 0.00 ATOM 240 HG CYS2 15 8.764 5.185 5.148 1.00 0.00 ATOM 241 C CYS2 15 6.841 5.543 8.845 1.00 0.00 ATOM 242 O CYS2 15 7.324 4.457 9.169 1.00 0.00 WARNING: atom H is missing in residue CYSH 15 in the pdb file You might need to add atom H to the hydrogen database of residue CYSH in the file ff???.hdb (see the manual) WARNING: atom HA is missing in residue CYSH 15 in the pdb file You might need to add atom HA to the hydrogen database of residue CYSH in the file ff???.hdb (see the manual) WARNING: atom HB1 is missing in residue CYSH 15 in the pdb file You might need to add atom HB1 to the hydrogen database of residue CYSH in the file ff???.hdb (see the manual) WARNING: atom HB2 is missing in residue CYSH 15 in the pdb file You might need to add atom HB2 to the hydrogen database of residue CYSH in the file ff???.hdb (see the manual) -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- 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
[gmx-users] Pressure Coupling: Scaling of Coordinates is Occurring - why?
Hi Gromacs Users, Pressure coupling is not supposed to scale the coordinates of my frozen group, yet it is. My frozen group is a crystal structure that does not have any topology assigned to them: no bond, angle, dihedral constants etc. specified. I find that a crystal structure gets compressed. A sample of the pressure coupling section of my .mdp file is given below: ; PRESSURE COUPLING pcoupl = parrinello-rahman pcoupltype = isotropic tau_p = 50.0 compressibility = 0.1 0.1 0.1 0.1 0.1 0.1 refcoord_scaling = no ref_p = 1000.0 1000.0 1000.0 0.0 0.0 0.0 I'm using Gromacs 4.0.5. Any suggestions appreciated, Chris Rowan -- 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
