Re: [gmx-users] Problem with equilibrated lipid bilayer structure
Is there a reason to switch water models? Gromacs supports both the traditional TIP3P and the CHARMM TIP3P (TIPS3P). Since you need to reinitialize velocities, it may not be a good idea to use Nose-Hoover and Parinello-Rahman straight away. Furthermore, you need to gen_vel=yes since gromacs has no velocity from your previous charmm run and subjecting an otherwise frozen system to a parinello-rahman thermostat is asking for trouble. Also, pressure coupling for NPT should probably be semiisotropic for bilayers. Finally you may want to experiment with EnerPres; see also http://pubs.acs.org/doi/abs/10.1021/ct3003157 (although this isn't related to your crash). On 2012-10-15 01:48:47PM +0800, Jernej Zidar wrote: Hi. I used CHARMM to prepare a cholesterol/POPC lipid bilayer. I equilibrated it in CHARMM and the imported the resulting PDB to GROMACS. In CHARMM I was the TIP3P water model, so before importing the PDB I changed the atom types from the TIP3P's ones to SPCE ones. Then I used this command to import the PDB: pdb2gmx -f lipid-wat.pdb -o bilayer.gro -p bilayer.top -i bilayer-posres.itp -ff charmm36cgenff -water spce -noter -v -renum After the import I center the system in the unit cell with: editconf -f bilayer.gro -o bilayer.gro -c Problem 1: The system size (unit cell) is not properly computed/detected. The following numbers are for the same structure after the CHARMM equilibration. CHARMM reports the size as: 10.45820 x 10.45825 x 6.864382 (in nm; converted from Angstroms) GROMACS states the size is: 12.30940 x 11.81980 x 7.138100 (in nm) Problem 2: While I'm able to run MD in CHARMM if I start from the equilibrated structure, I am unable to do so in GROMACS. As the system apparently blows up with the cryptic message: Program mdrun, VERSION 4.5.5 Source code file: /build/buildd/gromacs-4.5.5/src/mdlib/pme.c, line: 538 Fatal error: 5 particles communicated to PME node 0 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. This usually means that your system is not well equilibrated. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I can minimize the system, but any attempt to run MD results in the aforementioned message. Here's the MDP file I would like to use: ;define = -DPOSRES ; position restrain the protein ; Run parameters integrator= md; leap-frog integrator nsteps= 50; 2 * 50 = 1000 ps (1 ns) dt= 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog= 100 ; update log file every 0.2 ps ; Bond parameters continuation = no; Restarting after NVT constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) rvdw = 1.2 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing= 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl= Nose-Hoover ; More accurate thermostat tc-grps = LIPID SOL ; three coupling groups - more accurate tau_t = 0.5 0.5 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl= Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype= isotropic ; uniform scaling of x-y box vectors, independent z tau_p = 5.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, x-y, z (in bar) compressibility = 4.5e-5 ; isothermal compressibility, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no; Velocity generation is off ; COM
[gmx-users] VMD problem?
hello: I've installed gromacs in my macbookPro with 10.8 OS system. I am trying to import gromacs trajectory which contains 6000 frames. However, the VMD always clashed VMD(552,0xac879a28) malloc: *** mmap(size=831488) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug libc++abi.dylib: terminate called throwing an exception /Applications/VMD 1.9.1.app/Contents/MacOS/startup.command: line 7: 552 Abort trap: 6 $p/../Resources/VMD.app/Contents/MacOS/VMD $* logout Does anybody have any idae how to solve this problem? I try to install the 64bit VMD, but it crashed as soon as it start up. thank you very much Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Problem with equilibrated lipid bilayer structure
Hello, You might want to use TIPS3P (special CHARMM TIP3P) instead of regular TIP3P because some researchers observed that regular TIP3P can impact the area per lipid significantly when simulating CHARMM lipid bilayer (see reference below). Concerning the CHARMM36 lipid force field in Gromacs, there is also an issue about cutoffs. The switch cutoff scheme in the charmm software is different than in the gromacs software. It might impact your results for some bilayers, while it does not for others. You might find that previous post on the mailing list enlightening (and the cited reference) : Hi everyone,This message is just to let people know that there is finally a reference that we ask you to cite if you publish work using the CHARMM36 lipid force field contribution available from the GROMACS website. The reference is provided in a new version of the forcefield.doc file, and is also given below: Thomas J. Piggot, Ángel Piñeiro and Syma Khalid Molecular Dynamics Simulations of Phosphatidylcholine Membranes: A Comparative Force Field Study Journal of Chemical Theory and Computation DOI: 10.1021/ct3003157 http://pubs.acs.org/doi/abs/10.1021/ct3003157 A validation of the conversion for DPPC and POPC membrane systems (in terms of single point energies calculated in both GROMACS and NAMD) is provided in the supporting information of this work. Cheers Tom Hope that helps, Sebastien Date: Mon, 15 Oct 2012 13:48:47 +0800 From: jernej.zi...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] Problem with equilibrated lipid bilayer structure Hi. I used CHARMM to prepare a cholesterol/POPC lipid bilayer. I equilibrated it in CHARMM and the imported the resulting PDB to GROMACS. In CHARMM I was the TIP3P water model, so before importing the PDB I changed the atom types from the TIP3P's ones to SPCE ones. Then I used this command to import the PDB: pdb2gmx -f lipid-wat.pdb -o bilayer.gro -p bilayer.top -i bilayer-posres.itp -ff charmm36cgenff -water spce -noter -v -renum After the import I center the system in the unit cell with: editconf -f bilayer.gro -o bilayer.gro -c Problem 1: The system size (unit cell) is not properly computed/detected. The following numbers are for the same structure after the CHARMM equilibration. CHARMM reports the size as: 10.45820 x 10.45825 x 6.864382 (in nm; converted from Angstroms) GROMACS states the size is: 12.30940 x 11.81980 x 7.138100 (in nm) Problem 2: While I'm able to run MD in CHARMM if I start from the equilibrated structure, I am unable to do so in GROMACS. As the system apparently blows up with the cryptic message: Program mdrun, VERSION 4.5.5 Source code file: /build/buildd/gromacs-4.5.5/src/mdlib/pme.c, line: 538 Fatal error: 5 particles communicated to PME node 0 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. This usually means that your system is not well equilibrated. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I can minimize the system, but any attempt to run MD results in the aforementioned message. Here's the MDP file I would like to use: ;define = -DPOSRES ; position restrain the protein ; Run parameters integrator= md; leap-frog integrator nsteps= 50; 2 * 50 = 1000 ps (1 ns) dt= 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog= 100 ; update log file every 0.2 ps ; Bond parameters continuation = no; Restarting after NVT constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) rvdw = 1.2 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing= 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl= Nose-Hoover ; More accurate thermostat tc-grps = LIPID SOL ; three coupling groups - more accurate
Re: [gmx-users] VMD problem?
Depending on the # of atoms, 6000 frames may exceed the amount of ram a 32bit application can address (4GB). If you're having problems with the 64bit version, you should probably ask the vmd-l list. The only workaround other than that is trjconv -skip and make a trajectory file that skips frames and will load under 4GB of ram. On 2012-10-15 08:15:34AM +0200, Albert wrote: hello: I've installed gromacs in my macbookPro with 10.8 OS system. I am trying to import gromacs trajectory which contains 6000 frames. However, the VMD always clashed VMD(552,0xac879a28) malloc: *** mmap(size=831488) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug libc++abi.dylib: terminate called throwing an exception /Applications/VMD 1.9.1.app/Contents/MacOS/startup.command: line 7: 552 Abort trap: 6 $p/../Resources/VMD.app/Contents/MacOS/VMD $* logout Does anybody have any idae how to solve this problem? I try to install the 64bit VMD, but it crashed as soon as it start up. thank you very much Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] VMD problem?
On 10/15/2012 08:46 AM, Peter C. Lai wrote: Depending on the # of atoms, 6000 frames may exceed the amount of ram a 32bit application can address (4GB). If you're having problems with the 64bit version, you should probably ask the vmd-l list. The only workaround other than that is trjconv -skip and make a trajectory file that skips frames and will load under 4GB of ram. thanks for kind reply. I found in VMD maillist and they claimed to be solved by installing the 64bit VMD. However, I download more than 10 different 64bit VMD, and none of them works: all of then crashed as soon as it start up.. nobody else in VMD mailist reply my thread. ;-( -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Lennard-Jones Parameters
Thanks for you email. I already had the .gro and .top files from PRODRG. Now I want to reproduce these files following the LJ parameters in a published paper (charge, sigma and epsilon values). I can change the charge in the top file, yet I do not know how to change sigma and epsilon values. Best regards, Cuong On 15 October 2012 13:57, Peter C. Lai p...@uab.edu wrote: It's hard to understand your question. What do you mean by reference parameters? You said you already obtained a .gro and .top from PRODRG, which uses the gromos 43a1 forcefield to derive the parameters, so if you need to change the LJ parameters, edit the top file it gave you. If you want to reproduce the results of a published paper, you should use the forcefield and parameters specified in that paper and contact the author(s) if more details are needed. On 2012-10-15 10:42:57AM +0800, cuong nguyen wrote: Thank you very much for your email, Justin. in case I want to use the reference parameters, which force-field and what should I do to get the .gro and .top files for this molecule? Best regards, Cuong On 12 October 2012 21:14, Justin Lemkul jalem...@vt.edu wrote: On 10/12/12 8:04 AM, cuong nguyen wrote: Dear Gromacs Users, I got the .gro and .top files of 1-octanol downloaded from PRODRG website. Please let me know if I can change charge, epsilon and sigma of the molecule as written in a paper? and How to do? Atom types from PRODRG rarely, if ever, need changing. Charges can be taken first by chemical homology (group-based approach that makes Gromos force fields convenient) and then by calculating the charges yourself. For 1-octanol, it should be very straightforward to obtain parameters, zero charges on all the C atoms except for the one in the alocohol, then standard alcohol charges for the C-O-H. Whether or not those parameters are sufficiently accurate is up to you to decide, but that's the approach one would take with this particular force field. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808| == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Lennard-Jones Parameters
Is there no [atomtypes] section in the top file? On 2012-10-15 03:53:54PM +0800, cuong nguyen wrote: Thanks for you email. I already had the .gro and .top files from PRODRG. Now I want to reproduce these files following the LJ parameters in a published paper (charge, sigma and epsilon values). I can change the charge in the top file, yet I do not know how to change sigma and epsilon values. Best regards, Cuong On 15 October 2012 13:57, Peter C. Lai p...@uab.edu wrote: It's hard to understand your question. What do you mean by reference parameters? You said you already obtained a .gro and .top from PRODRG, which uses the gromos 43a1 forcefield to derive the parameters, so if you need to change the LJ parameters, edit the top file it gave you. If you want to reproduce the results of a published paper, you should use the forcefield and parameters specified in that paper and contact the author(s) if more details are needed. On 2012-10-15 10:42:57AM +0800, cuong nguyen wrote: Thank you very much for your email, Justin. in case I want to use the reference parameters, which force-field and what should I do to get the .gro and .top files for this molecule? Best regards, Cuong On 12 October 2012 21:14, Justin Lemkul jalem...@vt.edu wrote: On 10/12/12 8:04 AM, cuong nguyen wrote: Dear Gromacs Users, I got the .gro and .top files of 1-octanol downloaded from PRODRG website. Please let me know if I can change charge, epsilon and sigma of the molecule as written in a paper? and How to do? Atom types from PRODRG rarely, if ever, need changing. Charges can be taken first by chemical homology (group-based approach that makes Gromos force fields convenient) and then by calculating the charges yourself. For 1-octanol, it should be very straightforward to obtain parameters, zero charges on all the C atoms except for the one in the alocohol, then standard alcohol charges for the C-O-H. Whether or not those parameters are sufficiently accurate is up to you to decide, but that's the approach one would take with this particular force field. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808| == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham
[gmx-users] losing data in trjconv?
Hi all, When I do the following command trjconv -f traj.trr -o traj_1.trr the file size of traj_1.trr is around 25% smaller than traj.trr. Does traj_1.trr contain less data than traj.trr? Thanks Gil -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] losing data in trjconv?
Was traj.trr output by the same machine/mdrun as the machine you are running trjconv on? Is traj.trr (or the mdrun that wrote it) double precision and trjconv is compiled float (single precision)? On 2012-10-15 02:31:00AM -0700, Gil Claudio wrote: Hi all, When I do the following command trjconv -f traj.trr -o traj_1.trr the file size of traj_1.trr is around 25% smaller than traj.trr. Does traj_1.trr contain less data than traj.trr? Thanks Gil -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Lennard-Jones Parameters
Dear, The top file downloaded from PRODRG did not consist of [atomtypes]. Please tell me how can I add and use this function? Best regards, Cuong On 15 October 2012 16:43, Peter C. Lai p...@uab.edu wrote: Is there no [atomtypes] section in the top file? On 2012-10-15 03:53:54PM +0800, cuong nguyen wrote: Thanks for you email. I already had the .gro and .top files from PRODRG. Now I want to reproduce these files following the LJ parameters in a published paper (charge, sigma and epsilon values). I can change the charge in the top file, yet I do not know how to change sigma and epsilon values. Best regards, Cuong On 15 October 2012 13:57, Peter C. Lai p...@uab.edu wrote: It's hard to understand your question. What do you mean by reference parameters? You said you already obtained a .gro and .top from PRODRG, which uses the gromos 43a1 forcefield to derive the parameters, so if you need to change the LJ parameters, edit the top file it gave you. If you want to reproduce the results of a published paper, you should use the forcefield and parameters specified in that paper and contact the author(s) if more details are needed. On 2012-10-15 10:42:57AM +0800, cuong nguyen wrote: Thank you very much for your email, Justin. in case I want to use the reference parameters, which force-field and what should I do to get the .gro and .top files for this molecule? Best regards, Cuong On 12 October 2012 21:14, Justin Lemkul jalem...@vt.edu wrote: On 10/12/12 8:04 AM, cuong nguyen wrote: Dear Gromacs Users, I got the .gro and .top files of 1-octanol downloaded from PRODRG website. Please let me know if I can change charge, epsilon and sigma of the molecule as written in a paper? and How to do? Atom types from PRODRG rarely, if ever, need changing. Charges can be taken first by chemical homology (group-based approach that makes Gromos force fields convenient) and then by calculating the charges yourself. For 1-octanol, it should be very straightforward to obtain parameters, zero charges on all the C atoms except for the one in the alocohol, then standard alcohol charges for the C-O-H. Whether or not those parameters are sufficiently accurate is up to you to decide, but that's the approach one would take with this particular force field. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808| == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before
Re: [gmx-users] amount of solvent
On 10/14/12 10:41 PM, Nur Syafiqah Abdul Ghani wrote: Dear All, I would like to do the simulation between water and other solvent. One question that i curious to know which is how i want to put the amount of solvent, HFIP before i insert the water? Its suppose 80% of HFIP and 20% of water. But the starting point of my pdb already 1 nmol which only 1 compound of HFIP. So how can i insert the other amount of HFIP before I insert the water molecule? http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Lennard-Jones Parameters
On 10/15/12 5:45 AM, cuong nguyen wrote: Dear, The top file downloaded from PRODRG did not consist of [atomtypes]. Please tell me how can I add and use this function? I see no need to change anything about the L-J parameters. Is there some reason you believe them to be incorrect? If you modify L-J parameters, you're no longer using Gromos96 43a1. In PRODRG topologies, the charges and charge groups certainly need changing, but I have never seen a need to hack the L-J parameters. -Justin Best regards, Cuong On 15 October 2012 16:43, Peter C. Lai p...@uab.edu wrote: Is there no [atomtypes] section in the top file? On 2012-10-15 03:53:54PM +0800, cuong nguyen wrote: Thanks for you email. I already had the .gro and .top files from PRODRG. Now I want to reproduce these files following the LJ parameters in a published paper (charge, sigma and epsilon values). I can change the charge in the top file, yet I do not know how to change sigma and epsilon values. Best regards, Cuong On 15 October 2012 13:57, Peter C. Lai p...@uab.edu wrote: It's hard to understand your question. What do you mean by reference parameters? You said you already obtained a .gro and .top from PRODRG, which uses the gromos 43a1 forcefield to derive the parameters, so if you need to change the LJ parameters, edit the top file it gave you. If you want to reproduce the results of a published paper, you should use the forcefield and parameters specified in that paper and contact the author(s) if more details are needed. On 2012-10-15 10:42:57AM +0800, cuong nguyen wrote: Thank you very much for your email, Justin. in case I want to use the reference parameters, which force-field and what should I do to get the .gro and .top files for this molecule? Best regards, Cuong On 12 October 2012 21:14, Justin Lemkul jalem...@vt.edu wrote: On 10/12/12 8:04 AM, cuong nguyen wrote: Dear Gromacs Users, I got the .gro and .top files of 1-octanol downloaded from PRODRG website. Please let me know if I can change charge, epsilon and sigma of the molecule as written in a paper? and How to do? Atom types from PRODRG rarely, if ever, need changing. Charges can be taken first by chemical homology (group-based approach that makes Gromos force fields convenient) and then by calculating the charges yourself. For 1-octanol, it should be very straightforward to obtain parameters, zero charges on all the C atoms except for the one in the alocohol, then standard alcohol charges for the C-O-H. Whether or not those parameters are sufficiently accurate is up to you to decide, but that's the approach one would take with this particular force field. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808| == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before
[gmx-users] bonds braking
Hi, I'm having trouble simulating a protein kinase on water. During the simulation, the molecule moves towards the box limits and some residues apear on the other side. Almost like they are interacting with water molecules on different sides of the box. I'm on my third simulation and the problem persists. I've already tried changing the periodic conditions but with no success. Waht are your thoughts on that? For additional information: Before the dynamics step I performed 4 minimization steps then i did water dynamics and the entire system dynamics. Here is all the .mdp files. Sorry in advance for the long email. FIRST MINIMIZATION STEP: title = min_steepest_descent_PR cpp = /lib/cpp define = -DFLEXIBLE -DPOSRES constraints = none integrator = steep ;l-bfgs nsteps = 2 nstlist = 10 ns_type = grid rlist = 1.0 pbc = xyz coulombtype = PME rcoulomb = 1.0 epsilon-r = 1 ;1 for CUTOFF, PME and SWITCH and, 54 for REACTIONFIELD vdw-type = Cut-off rvdw = 1.4 ; emtol = 209.2 emstep = 0.01 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes SECOND MINIMIZATION STEP title = min_steepest_descent cpp = /lib/cpp define = -DFLEXIBLE constraints = none integrator = steep nsteps = 2 nstlist = 10 ns_type = grid rlist = 1.0 pbc = xyz coulombtype = PME rcoulomb = 1.0 epsilon-r = 1.0 ;1 for CUTOFF, PME and SWITCH and, 54 for REACTIONFIELD vdw-type = Cut-off rvdw = 1.4 emtol = 104.6 emstep = 0.01 ewald_rtol = 1e-5 optimize_fft = yes THIRD MINIMIZATION STEP title = min cg cpp = /lib/cpp define = -DFLEXIBLE constraints = none integrator = cg nsteps = 2 nstlist = 10 ns_type = grid nstcgsteep = 100 rlist = 1.0 pbc = xyz coulombtype = PME rcoulomb = 1.0 vdw-type = Cut-off ;Switch rvdw = 1.4 emtol = 41.84 emstep = 0.01 ewald_rtol = 1e-5 optimize_fft = yes FOURTH MINIMIZATION STEP title = min_steepest_descent cpp = /lib/cpp define = -DFLEXIBLE constraints = none integrator = l-bfgs ;steep nsteps = 2 nstlist = 10 ns_type = grid rlist = 1.0 pbc = xyz coulombtype = PME rcoulomb = 1.0 epsilon-r = 1.0 ;1 for CUTOFF, PME and SWITCH and, 54 for REACTIONFIELD vdw-type = Cut-off rvdw = 1.4 emtol = 41.84 emstep = 0.01 ewald_rtol = 1e-5 optimize_fft = yes WATER DYNAMICS title = 500ps_pr_fixo cpp = /lib/cpp define = -DPOSRES integrator = md tinit = 0 dt = 0.002 nsteps = 25 ; total 500 ps comm-mode = Linear nstcomm = 1 nstxout = 500 nstvout = 2 nstfout = 2 nstlog = 1000 nstenergy = 100 nstxtcout = 500 xtc-precision = 1000 energygrps = Protein SOL NA nstlist = 5 ns_type = grid pbc = xyz rlist = 1.0 domain-decomposition = no coulombtype = PME rcoulomb = 1.0 epsilon-r = 1 vdw-type = Cut-off rvdw = 1.4 DispCorr = EnerPres optimize_fft = yes Tcoupl = V-rescale ;berendsen tc-grps = Protein Non-protein tau-t = .1 .1 ref-t = 310 310 gen_vel = yes gen_temp = 310 gen_seed = 173529 Pcoupl = berendsen Pcoupltype = Isotropic tau-p = 1 compressibility = 4.5e-5 ref-p = 1 constraints = all-bonds constraint-algorithm = Lincs unconstrained-start = no Shake-SOR = no shake-tol = 1e-04 lincs-order = 4 lincs-warnangle = 30 morse = no SYSTEM DYNAMICS title = 10 ns cpp = /lib/cpp include = define = integrator
Re: [gmx-users] bonds braking
On 10/15/12 8:40 AM, Eduardo Oliveira wrote: Thanks! So, if i understood correctly the correct workflow of trjconf? I posted the link for two reasons: (1) so you would understand the nature of what was actually happening in the simulation and (2) so you would be aware of the solution. In your case, a protein in water, the remedy is very easy: trjconv -pbc mol -ur compact -center Center on the protein. You can apply various fitting operations afterwards if you like. -Justin *De:* Justin Lemkul jalem...@vt.edu *Para:* Eduardo Oliveira eduardo...@yahoo.com.br; Discussion list for GROMACS users gmx-users@gromacs.org *Enviadas:* Segunda-feira, 15 de Outubro de 2012 9:14 *Assunto:* Re: [gmx-users] bonds braking On 10/15/12 8:09 AM, Eduardo Oliveira wrote: Hi, I'm having trouble simulating a protein kinase on water. During the simulation, the molecule moves towards the box limits and some residues apear on the other side. Almost like they are interacting with water molecules on different sides of the box. I'm on my third simulation and the problem persists. I've already tried changing the periodic conditions but with no success. Waht are your thoughts on that? For additional information: Before the dynamics step I performed 4 minimization steps then i did water dynamics and the entire system dynamics. Here is all the .mdp files. Sorry in advance for the long email. This is a perfectly normal consequence of PBC. http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] bonds braking
Thanks a lot! De: Justin Lemkul jalem...@vt.edu Para: Discussion list for GROMACS users gmx-users@gromacs.org Enviadas: Segunda-feira, 15 de Outubro de 2012 9:42 Assunto: Re: [gmx-users] bonds braking On 10/15/12 8:40 AM, Eduardo Oliveira wrote: Thanks! So, if i understood correctly the correct workflow of trjconf? I posted the link for two reasons: (1) so you would understand the nature of what was actually happening in the simulation and (2) so you would be aware of the solution. In your case, a protein in water, the remedy is very easy: trjconv -pbc mol -ur compact -center Center on the protein. You can apply various fitting operations afterwards if you like. -Justin *De:* Justin Lemkul jalem...@vt.edu *Para:* Eduardo Oliveira eduardo...@yahoo.com.br; Discussion list for GROMACS users gmx-users@gromacs.org *Enviadas:* Segunda-feira, 15 de Outubro de 2012 9:14 *Assunto:* Re: [gmx-users] bonds braking On 10/15/12 8:09 AM, Eduardo Oliveira wrote: Hi, I'm having trouble simulating a protein kinase on water. During the simulation, the molecule moves towards the box limits and some residues apear on the other side. Almost like they are interacting with water molecules on different sides of the box. I'm on my third simulation and the problem persists. I've already tried changing the periodic conditions but with no success. Waht are your thoughts on that? For additional information: Before the dynamics step I performed 4 minimization steps then i did water dynamics and the entire system dynamics. Here is all the .mdp files. Sorry in advance for the long email. This is a perfectly normal consequence of PBC. http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] about equilibrium
Dear Gromacs Users, I have one system consists of: surfactant, solvent and additives. I made one box with only solvent and one box with only additives and equilibrated them little separable for better placing into the box, and then made one box with surfactant and then placed box of solvent and additives (that before I had equilibrated them separable) in the box of surfactant (by genbox) and equilibrated it totally. May I know that this work is correct or not, Please? Best Regards Sara -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] losing data in trjconv?
Hi Justin, My original intention was to lessen the 5 ns trajectory to transfer to another drive. I did trjconv -f traj.trr -o traj_1.trr -b 0 -e 4000 When I saw the resulting file greatly lessened in size, that's when I tried as a test trjconv -f traj.trr -o traj_1.trr I knew that it was not supposed to do anything, hence my surprise upon seeing the file size decrease by ~25%. No other flags were used. I'll do your suggestion in 2 days. Am out of the lab till then. Thanks Gil Claudio On Oct 15, 2012, at 7:55 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/15/12 7:50 AM, Gil Claudio wrote: Hi Peter, Same machine, all single precision. Run gmxcheck -f -f2 on the two trajectories to see what's going on. Can you explain what you were trying to do? I see no point in the trjconv command you ran. Were there other flags that you haven't shown? Other commands that produced strange results that led you to simplify the trjconv command down to something that (in theory) doesn't do anything? -Justin On Oct 15, 2012, at 5:39 PM, Peter C. Lai p...@uab.edu wrote: Was traj.trr output by the same machine/mdrun as the machine you are running trjconv on? Is traj.trr (or the mdrun that wrote it) double precision and trjconv is compiled float (single precision)? On 2012-10-15 02:31:00AM -0700, Gil Claudio wrote: Hi all, When I do the following command trjconv -f traj.trr -o traj_1.trr the file size of traj_1.trr is around 25% smaller than traj.trr. Does traj_1.trr contain less data than traj.trr? Thanks Gil -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst| KAUL 752A Genetics, Div. of Research| 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808| == -- Justin A. Lemkul, Ph.D. Research Scientist 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/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Concerning a Fatal Error!
Dear Justin, Thank you for your help, however, the problem was originated from absence of -table table_d1.xvg flag in my mdrun command. Now it is fixed. BR Arman On Sat, Oct 13, 2012 at 10:30 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/13/12 9:49 AM, Arman Mahboubi Soufiani wrote: Dear Justin, The followings are the two successive commands I used: *grompp -f justPLA.mdp -c 20LA-2layer-4chains.gro -p t-PLA.top -o justPLA-em.tpr mdrun -deffnm justPLa-em* These commands would not produce the error posted previously. The error would have resulted from: mdrun -deffnm justPLA-em.tpr The fact that the capitalization is different and the nature of the suffix supports this conclusion. It is better to copy directly from the terminal rather than try to recreate what you did. In any case, proper invocation of the command should solve the issue. mdrun is looking for an .xvg file containing parameters for a tabulated dihedral; it needs to be named appropriately to function correctly. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Force calculations were truncated at a distance of 1.2 nm
On 10/15/12 9:04 AM, Ali Alizadeh wrote: Dear All users I want to specify this statement in my input files but Where does it specify?( i don't know!) I know but i do not certain, Force calculations were truncated at a distance of 1.2 nm That likely refers to cutoff values. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] about equilibrium
On 10/15/12 8:56 AM, mohammad agha wrote: Dear Gromacs Users, I have one system consists of: surfactant, solvent and additives. I made one box with only solvent and one box with only additives and equilibrated them little separable for better placing into the box, and then made one box with surfactant and then placed box of solvent and additives (that before I had equilibrated them separable) in the box of surfactant (by genbox) and equilibrated it totally. May I know that this work is correct or not, Please? Maybe. It's hard to tell. Note that when you post the same thing four times and do not get a reply, it's usually due to the fact that it's hard for us to figure out what's going on. I don't know what your goal is but your approach is a bit hard to comprehend as written. One can usually build a multi-component system rather easily with a few invocations of genbox -ci -nmol, but then too, I don't know if you need some particular configuration (surfactant micelles?) or if random positions will suffice. Prior equilibration of solvent is probably a good approach. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] The problem of converting CGenff parameters to those of Gromacs
Hello, everyone. I used the Mark's script's to convert the CGenff (version 2b7 ) parameter file to Gromacs .itp files. In the ffcharmmnb.itp, the script gave the c6 and c12, while the charmm's ffnonbond.itp showed epsilon and sigma.I do not understand the relation between the c6/c12 and epsilon and sigma, and I have a poor Perl skill. Can someone give me a solution? In addition, the script makes all atoms' charge zero in the file, which is not the case in the ffnonbond.itp. Why is it? Thank you! Qing Liu -- View this message in context: http://gromacs.5086.n6.nabble.com/The-problem-of-converting-CGenff-parameters-to-those-of-Gromacs-tp5002042.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_dipole
Hello, I am calculating the dipole moment auto-correlation function for my system which have 128 cation and 128 anion. Due to the PBC, the function of the total dipole moment in time is not continuous. Can I removed PBC for g_dipole? Thanks Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] The problem of converting CGenff parameters to those of Gromacs
Isn't Mark's script outdated for this purpose? charmm forcefields specify epsilon and sigmas so you only need to convert them: gromacs(sigma) = (charmm(Rmin/2)/10) * (2/(2^(1/6))) gromacs(epsilon) = charmm(eps) * 4.184 For 1-4 pair interactions, gromacs(sigma1,4 i,j) = (charmm(Rmin/2_1,4_i) + charmm(Rmin/2_1,4_j))/(2^1/6) gromacs(eps1,4 i,j) = sqrt(charmm(eps_1,4_i) * charmm(eps_1,4_j)) * 4.184 On 2012-10-15 07:27:51AM -0700, spin wrote: Hello, everyone. I used the Mark's script's to convert the CGenff (version 2b7 ) parameter file to Gromacs .itp files. In the ffcharmmnb.itp, the script gave the c6 and c12, while the charmm's ffnonbond.itp showed epsilon and sigma.I do not understand the relation between the c6/c12 and epsilon and sigma, and I have a poor Perl skill. Can someone give me a solution? In addition, the script makes all atoms' charge zero in the file, which is not the case in the ffnonbond.itp. Why is it? Thank you! Qing Liu -- View this message in context: http://gromacs.5086.n6.nabble.com/The-problem-of-converting-CGenff-parameters-to-those-of-Gromacs-tp5002042.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] The problem of converting CGenff parameters to those of Gromacs
On 2012-10-15 16:53, Peter C. Lai wrote: Isn't Mark's script outdated for this purpose? I just uploaded a new script that seems to work: http://www.gromacs.org/@api/deki/files/185/=charmm2gromacs-pvm.py Please check the comment on http://www.gromacs.org/Downloads/User_contributions/Other_software charmm forcefields specify epsilon and sigmas so you only need to convert them: gromacs(sigma) = (charmm(Rmin/2)/10) * (2/(2^(1/6))) gromacs(epsilon) = charmm(eps) * 4.184 For 1-4 pair interactions, gromacs(sigma1,4 i,j) = (charmm(Rmin/2_1,4_i) + charmm(Rmin/2_1,4_j))/(2^1/6) gromacs(eps1,4 i,j) = sqrt(charmm(eps_1,4_i) * charmm(eps_1,4_j)) * 4.184 On 2012-10-15 07:27:51AM -0700, spin wrote: Hello, everyone. I used the Mark's script's to convert the CGenff (version 2b7 ) parameter file to Gromacs .itp files. In the ffcharmmnb.itp, the script gave the c6 and c12, while the charmm's ffnonbond.itp showed epsilon and sigma.I do not understand the relation between the c6/c12 and epsilon and sigma, and I have a poor Perl skill. Can someone give me a solution? In addition, the script makes all atoms' charge zero in the file, which is not the case in the ffnonbond.itp. Why is it? Thank you! Qing Liu -- View this message in context: http://gromacs.5086.n6.nabble.com/The-problem-of-converting-CGenff-parameters-to-those-of-Gromacs-tp5002042.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Diatomic in MeCN NPT (NH and PR) simulation segfaults after 1 us
As a further check I ran a neat solvent box and the simulation ends abruptly at 1.07 us. -- View this message in context: http://gromacs.5086.n6.nabble.com/Diatomic-in-MeCN-NPT-NH-and-PR-simulation-segfaults-after-1-us-tp5001845p5002046.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] no groups in indexfile!
Hi ! I want to use g_sgangle to find distance between two groups (each group includes 3 atoms). I use this command: g_sgangle -s md_1.tpr -f md_1_noPBC.xtc -n index.ndx -oa 12_angle.xvg -od 12_dist.xvg but i got this error Fatal error: Error: no groups in indexfile my index file: [ G3 ] 76 81 85 [ G4 ] 110 115 119 Best Regards, Amir -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] calculating the water mol
On 10/15/12 10:12 AM, Rajiv Gandhi wrote: Dear Gromacs. In experimental it says that the number of water molecule present in dimer interface could be varied upon time of ligation process. I want to calculate the number of water molecules in the protein dimer interface during the simulation. Could advice me how it can be done? Thanks in advance. g_select can likely do this. Others have attempted similar tasks in the past; check the archive for tips and the lengthy help documentation provided with g_select -select 'help all' -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] about equilibrium
Dear Justin, Thank you very much from your response. This question was because of my previous problems about equilibration the box that I sent it with subject equilibrium for box of simulation. When I equilibrate solvent and additives separated and then add to surfactant and after that equilibrate totally, there are not previous problems and I wanted to know that this method is correct? Best Regards Sara From: Justin Lemkul jalem...@vt.edu To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, October 15, 2012 5:21 PM Subject: Re: [gmx-users] about equilibrium On 10/15/12 8:56 AM, mohammad agha wrote: Dear Gromacs Users, I have one system consists of: surfactant, solvent and additives. I made one box with only solvent and one box with only additives and equilibrated them little separable for better placing into the box, and then made one box with surfactant and then placed box of solvent and additives (that before I had equilibrated them separable) in the box of surfactant (by genbox) and equilibrated it totally. May I know that this work is correct or not, Please? Maybe. It's hard to tell. Note that when you post the same thing four times and do not get a reply, it's usually due to the fact that it's hard for us to figure out what's going on. I don't know what your goal is but your approach is a bit hard to comprehend as written. One can usually build a multi-component system rather easily with a few invocations of genbox -ci -nmol, but then too, I don't know if you need some particular configuration (surfactant micelles?) or if random positions will suffice. Prior equilibration of solvent is probably a good approach. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Diatomic in MeCN NPT (NH and PR) simulation segfaults after 1 us
On 10/15/12 11:45 AM, benjfitz wrote: As a further check I ran a neat solvent box and the simulation ends abruptly at 1.07 us. These results suggest that your physical model is unstable. A linear model of a triatomic species is not stable. A more appropriate approach is to use virtual sites as in the following tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/vsites/index.html Also note that your cutoffs should not be dictated by your box size, rather the opposite should be true. The cutoffs are an essential part of the force field model and changing them haphazardly can easily invalidate that force field model. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] no groups in indexfile!
On 10/15/12 11:48 AM, Amir Abbasi wrote: Hi ! I want to use g_sgangle to find distance between two groups (each group includes 3 atoms). I use this command: g_sgangle -s md_1.tpr -f md_1_noPBC.xtc -n index.ndx -oa 12_angle.xvg -od 12_dist.xvg but i got this error Fatal error: Error: no groups in indexfile my index file: [ G3 ] 768185 [ G4 ] 110115119 The most likely explanation is that you have some problem with non-Unix line endings in the file. Note that if you just need distances between groups, g_dist is more efficient for that calculation. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] about equilibrium
On 10/15/12 12:11 PM, mohammad agha wrote: Dear Justin, Thank you very much from your response. This question was because of my previous problems about equilibration the box that I sent it with subject equilibrium for box of simulation. When I equilibrate solvent and additives separated and then add to surfactant and after that equilibrate totally, there are not previous problems and I wanted to know that this method is correct? Please provide a link to the previous thread. I read hundreds of posts per week; I don't recall this one. A sequence of commands would also be helpful here, as I cannot clearly envision what you are describing. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] about equilibrium
Dear Justin, The previous problems was as is following: Dear GROMACS Users, I asked this question before but I don't understand it! I placed several materials in my box of simulation for example box with 6nm*6nm*6nm and my materials are not placed in the smaller box but when I equilibrate my system, the box became smaller and temperature and pressure also equilibrate. my question is: is my system and equilibrate mistake, because of reach to smaller box? Is there equilibriums with reach to smaller box? What do you mean by my materials are not placed in the smaller box? If a box compresses, it is because the initial configuration was incompatible with the desired equilibration conditions and it contracted produce the desired quantity (likely pressure). -Justin Dear Justin, my materials are not placed in the smaller box means if I select box with dimensions 5.99 nm, space is low and insufficient for my molecules! but after equilibrate the box become small. Please define what you mean here. You start with a 6-nm cubic box. How small does it get? Are the box vectors trending downward, or do they converge? What is the change in density, and is it acceptable? According what you said, when the box become smaller in equilibrium, there is not mistake and it is natural? That depends on the magnitude of the change. Compression indicates that the pressure (and thus density of the system) was not at the desired value and the system is contracting. The manner in which the contraction occurs (magnitude, speed) is the deciding factor as to whether or not there is a problem. also, Dear Mark, May I know your idea about cause of my doubt, Please? As I said yesterday: At least one of your volume, contents or model physics are not consistent with the others, but only you can say which. Since only you know anything about your volume, contents and model physics, or that of the work you think you should be replicating, we can't help at the moment. See previous comment about relevant information :-) Mark Best Regards Sara - Original Message - From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Friday, October 5, 2012 9:34 AM Subject: Re: [gmx-users] equilibrium for box of simulation On 5/10/2012 3:55 PM, mohammad agha wrote: Dear Justin, Thank you very much. So, decreasing of box dimensions is not bad, if all thing process natural, yes? The cause of my doubt was because of in the most of articles was said for example we select box with dimensions 10nm that after equilibrium was converted to 11nm and I didn't see the report of decreasing of box dimensions! May I know your idea about it, Please? Following a published method closely and observing an opposite result is a cause for concern. You have to judge closely, however. You should have said earlier this was one of your reasons for doubt, rather than leave us to guess. The quality of the help you might receive is often in direct proportion to the quantity of relevant information you give in asking for it. Mark - Forwarded Message - From: Justin Lemkul jalem...@vt.edu To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Monday, October 15, 2012 7:50 PM Subject: Re: [gmx-users] about equilibrium On 10/15/12 12:11 PM, mohammad agha wrote: Dear Justin, Thank you very much from your response. This question was because of my previous problems about equilibration the box that I sent it with subject equilibrium for box of simulation. When I equilibrate solvent and additives separated and then add to surfactant and after that equilibrate totally, there are not previous problems and I wanted to know that this method is correct? Please provide a link to the previous thread. I read hundreds of posts per week; I don't recall this one. A sequence of commands would also be helpful here, as I cannot clearly envision what you are describing. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] about equilibrium
I didn't see anything inherently wrong with your previous observations, so I suspect your new approach is probably fine. There are several ways to do just about anything; you just need to find one that works to your satisfaction and represents a reasonable model of whatever you're trying to simulate. -Justin On 10/15/12 12:37 PM, mohammad agha wrote: Dear Justin, The previous problems was as is following: Dear GROMACS Users, I asked this question before but I don't understand it! I placed several materials in my box of simulation for example box with 6nm*6nm*6nm and my materials are not placed in the smaller box but when I equilibrate my system, the box became smaller and temperature and pressure also equilibrate. my question is: is my system and equilibrate mistake, because of reach to smaller box? Is there equilibriums with reach to smaller box? What do you mean by my materials are not placed in the smaller box? If a box compresses, it is because the initial configuration was incompatible with the desired equilibration conditions and it contracted produce the desired quantity (likely pressure). -Justin Dear Justin, my materials are not placed in the smaller box means if I select box with dimensions 5.99 nm, space is low and insufficient for my molecules! but after equilibrate the box become small. Please define what you mean here. You start with a 6-nm cubic box. How small does it get? Are the box vectors trending downward, or do they converge? What is the change in density, and is it acceptable? According what you said, when the box become smaller in equilibrium, there is not mistake and it is natural? That depends on the magnitude of the change. Compression indicates that the pressure (and thus density of the system) was not at the desired value and the system is contracting. The manner in which the contraction occurs (magnitude, speed) is the deciding factor as to whether or not there is a problem. also, Dear Mark, May I know your idea about cause of my doubt, Please? As I said yesterday: At least one of your volume, contents or model physics are not consistent with the others, but only you can say which. Since only you know anything about your volume, contents and model physics, or that of the work you think you should be replicating, we can't help at the moment. See previous comment about relevant information :-) Mark Best Regards Sara - Original Message - From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Friday, October 5, 2012 9:34 AM Subject: Re: [gmx-users] equilibrium for box of simulation On 5/10/2012 3:55 PM, mohammad agha wrote: Dear Justin, Thank you very much. So, decreasing of box dimensions is not bad, if all thing process natural, yes? The cause of my doubt was because of in the most of articles was said for example we select box with dimensions 10nm that after equilibrium was converted to 11nm and I didn't see the report of decreasing of box dimensions! May I know your idea about it, Please? Following a published method closely and observing an opposite result is a cause for concern. You have to judge closely, however. You should have said earlier this was one of your reasons for doubt, rather than leave us to guess. The quality of the help you might receive is often in direct proportion to the quantity of relevant information you give in asking for it. Mark - Forwarded Message - From: Justin Lemkul jalem...@vt.edu To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Monday, October 15, 2012 7:50 PM Subject: Re: [gmx-users] about equilibrium On 10/15/12 12:11 PM, mohammad agha wrote: Dear Justin, Thank you very much from your response. This question was because of my previous problems about equilibration the box that I sent it with subject equilibrium for box of simulation. When I equilibrate solvent and additives separated and then add to surfactant and after that equilibrate totally, there are not previous problems and I wanted to know that this method is correct? Please provide a link to the previous thread. I read hundreds of posts per week; I don't recall this one. A sequence of commands would also be helpful here, as I cannot clearly envision what you are describing. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to
Re: [gmx-users] no groups in indexfile!
On 10/15/12 1:03 PM, Amir Abbasi wrote: tnx But I need these two planes angle too. what should I do? can I convert all of trajectory file to pdb? in order to do these manually? That would be extremely inefficient. Determining what's wrong with your index file is probably a much better solution. -Justin *From:* Justin Lemkul jalem...@vt.edu *To:* Amir Abbasi amir.abbas...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Monday, October 15, 2012 7:47 PM *Subject:* Re: [gmx-users] no groups in indexfile! On 10/15/12 11:48 AM, Amir Abbasi wrote: Hi ! I want to use g_sgangle to find distance between two groups (each group includes 3 atoms). I use this command: g_sgangle -s md_1.tpr -f md_1_noPBC.xtc -n index.ndx -oa 12_angle.xvg -od 12_dist.xvg but i got this error Fatal error: Error: no groups in indexfile my index file: [ G3 ] 768185 [ G4 ] 110115119 The most likely explanation is that you have some problem with non-Unix line endings in the file. Note that if you just need distances between groups, g_dist is more efficient for that calculation. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] about equilibrium
Dear Justin, Thank you very much from your time. Best Regards Sara - Original Message - From: Justin Lemkul jalem...@vt.edu To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Monday, October 15, 2012 9:54 PM Subject: Re: [gmx-users] about equilibrium I didn't see anything inherently wrong with your previous observations, so I suspect your new approach is probably fine. There are several ways to do just about anything; you just need to find one that works to your satisfaction and represents a reasonable model of whatever you're trying to simulate. -Justin On 10/15/12 12:37 PM, mohammad agha wrote: Dear Justin, The previous problems was as is following: Dear GROMACS Users, I asked this question before but I don't understand it! I placed several materials in my box of simulation for example box with 6nm*6nm*6nm and my materials are not placed in the smaller box but when I equilibrate my system, the box became smaller and temperature and pressure also equilibrate. my question is: is my system and equilibrate mistake, because of reach to smaller box? Is there equilibriums with reach to smaller box? What do you mean by my materials are not placed in the smaller box? If a box compresses, it is because the initial configuration was incompatible with the desired equilibration conditions and it contracted produce the desired quantity (likely pressure). -Justin Dear Justin, my materials are not placed in the smaller box means if I select box with dimensions 5.99 nm, space is low and insufficient for my molecules! but after equilibrate the box become small. Please define what you mean here. You start with a 6-nm cubic box. How small does it get? Are the box vectors trending downward, or do they converge? What is the change in density, and is it acceptable? According what you said, when the box become smaller in equilibrium, there is not mistake and it is natural? That depends on the magnitude of the change. Compression indicates that the pressure (and thus density of the system) was not at the desired value and the system is contracting. The manner in which the contraction occurs (magnitude, speed) is the deciding factor as to whether or not there is a problem. also, Dear Mark, May I know your idea about cause of my doubt, Please? As I said yesterday: At least one of your volume, contents or model physics are not consistent with the others, but only you can say which. Since only you know anything about your volume, contents and model physics, or that of the work you think you should be replicating, we can't help at the moment. See previous comment about relevant information :-) Mark Best Regards Sara - Original Message - From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Friday, October 5, 2012 9:34 AM Subject: Re: [gmx-users] equilibrium for box of simulation On 5/10/2012 3:55 PM, mohammad agha wrote: Dear Justin, Thank you very much. So, decreasing of box dimensions is not bad, if all thing process natural, yes? The cause of my doubt was because of in the most of articles was said for example we select box with dimensions 10nm that after equilibrium was converted to 11nm and I didn't see the report of decreasing of box dimensions! May I know your idea about it, Please? Following a published method closely and observing an opposite result is a cause for concern. You have to judge closely, however. You should have said earlier this was one of your reasons for doubt, rather than leave us to guess. The quality of the help you might receive is often in direct proportion to the quantity of relevant information you give in asking for it. Mark - Forwarded Message - From: Justin Lemkul jalem...@vt.edu To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Monday, October 15, 2012 7:50 PM Subject: Re: [gmx-users] about equilibrium On 10/15/12 12:11 PM, mohammad agha wrote: Dear Justin, Thank you very much from your response. This question was because of my previous problems about equilibration the box that I sent it with subject equilibrium for box of simulation. When I equilibrate solvent and additives separated and then add to surfactant and after that equilibrate totally, there are not previous problems and I wanted to know that this method is correct? Please provide a link to the previous thread. I read hundreds of posts per week; I don't recall this one. A sequence of commands would also be helpful here, as I cannot clearly envision what you are describing. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080
[gmx-users] Re: amount of solvent
Not answering your main question here, just pointing out that you should try: trjconv -pbc mol -ur compact and then visualize with VMD to see if you are actually getting what you want after all. Chris. -- original message -- I already pack the mixed solvent by using packmol cause the box that i used octahedron.Therefore the error that coming out is that topology and the gro file does not same. When I view the solvent by VMD its just shows that the mixture only fill in the cubic form even though the starting box that i need was octahedron. So I would like to ask you guys if I already pack all the molecule,i need to create the new topology right? before start to minimize? Regards, SHika -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Load imbalance logging, how to limit it?
I'm getting control over my .mdp files, cutting down on the generation of data for which I currently have no use. I just changed the nstenergy parameter to 2500 cycles, much larger than its default value of 100 cycles. This reduced logging still gives me plenty of data for monitoring the stability of long runs. In my .log file, however, load imbalances are still being reported every 10 cycles. Once in a while, I'll get a 15% to 20% load imbalance, but most of the time it's under 2%. It's nothing that I seem to need to worry about at this time. I would like to reduce the load imbalance reporting frequency as well. What is the .mdp file key word that accomplishes this? Thanks once again. -- View this message in context: http://gromacs.5086.n6.nabble.com/Load-imbalance-logging-how-to-limit-it-tp5002063.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
