[gmx-users] x2top hangs up
Hello, Trying to generate a topology from PDB file my x2top (gromacs 4.0beta) hangs up. I have the coordinates of carbon nanotube in the PDB file (generated with MOLEKEL). I also have ffencadv.n2t with: C C 1 C ; CNT Carbon with one bond C C 2 C C ; CNT double bonded Carbon === ffgmxbon.itp with: [ bondtypes ] ; i j func b0 kb C C 1 0.14210 478900. [ angletypes ] ; i j k func th0 cth C C C 1 120.000 397.480 [ dihedraltypes ] ; i l func q0 cq C C 1 0.000 167.360 x2top -f cnt.pdb -o cnt.top -ff select Then I select "8: Encad all-atom force field, using scaled-down vacuum charges" Opening library file /usr/local/gromacs/share/gromacs/top/ffencadv.rtp Opening library file /usr/local/gromacs/share/gromacs/top/ffencadv.n2t Opening library file /usr/local/gromacs/share/gromacs/top/ffencadv.n2t There are 0 name to type translations Generating bonds from distances... atom 0 And the programme hangs up. The processor load is 99% all the time before I terminate the job. The same data input works with GROMACS 3.3.1 as described by C. Stiles but not with 3.3.3 and 4.0b however. If it is not a bug then what should be modified to make a topology? Has anyone tried to make SWCNT topology in the versions newer that 3.3.1? What essential things have been changed in x2top since 3.3.1? Thanks a lot for suggestions! -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq., 4, Kharkiv 61077, Ukraine email: [EMAIL PROTECTED] skype: vvchaban ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Extending a run for different number of nodes
DimitryASuplatov wrote: Hello, I have completed a 10ns run. Now I want to extend it to 20ns. The problem is that the initial tpr was compiled for 8 processors and now I have only 4 cores. What I tried to do is used tpbconv to make a 10ns extended tpr, then used an exactly the same mdp file to grompp it all together with -np 4 to a new tpr file. What do you mean "grompp it all together?" It sounds like you are trying to use both tpbconv and grompp for some reason. The only way to change the number of processors is to use grompp, not tpbconv, providing it your .trr and .edr files with the -t and -e flags. The problem is that at the beginning of the trajectory the structure is undergoing a structural change with 0.12 nm from the initial structure. That means that the structure is actually relaxed and that is not something I want to see. How do you know this is not the normal behavior? -Justin I have used this in my mdp ; VELOCITY INITIATION --- gen-vel = no gen-temp = 300 That means that no velocities were generated and I expect to see no relaxation but the continuation of my run. What am I doing wrong? How to extend a run without relaxation. Thank you. I appreciate any help. SDA My mdp file is the following. ;-PREPROCESSING OPTIONS title = PR "1KLC FREE"; my title cpp = cpp; my C prepocessor (whereIsIt) include = ; dir to include in my topology file define = ; ;-RUN CONTROL- integrator= md; ;--OUTPUT CONTROL-- ;TRR outpur nstxout= 1 nstvout= 1 nstfout= 0 ;LOG and EDR output nstlog = 1 nstenergy = 1 ;XTC output nstxtcout = 1000 xtc-precision = 1000 ;-START TIME & TIMESTEP--- tinit =; [ps] starting time for your run (only makes sense for md, sd, bd integator) dt = 0.005 ; [ps] time step for integration (--"--) nsteps = 160 ; (0) maximum number of steps to integrate comm-mode = ; Linear(Remove center of mass translation)/Annular(Remove center of mass ;translation and rotation)/No(no restriction) nstcomm = 1 ;-NEIGHBOR SEACHING--- nstlist = 5; frequency o update neighbor list ns_type = grid; make a gid in the box and check only ;neighboring grid cell when constructing a new neighbor list rlist = 1.0; cut-off distance for the short-range neighbor list ;-ELECTROSTATICS-- coulombtype = Reaction-field ; reaction field with coulomb cut-off rcoulomb ; where rcoulomb>rlist. The dielectric constant beyond the cut-off is epsilon_r rcoulomb = 1.5 ;distance for the coulomb cut-off epsilon_rf = 80;dielectric constant epsilon_r = 1; vdwtype = cut-off; twin-range cut-off`s with neighbor list cut-off rlist ;and VdW cut-off rvdw, where rvdw>rlist rvdw = 1.0 ; distance for for the LJ or Buckingam cut-off ;-ENERGY MINIMIZATION- emtol= 200 (kJ/mol*nm); minimisation is converged when the maximum force is smaller then this value emstep = 0.01; initial step size ;-TEMTERAURE CONTROL-- tcoupl = berendsen tc-grps = System tau-t= 0.1 ref-t= 300 ;- PRESSURE CONTROL- Pcoupl = no Pcoupltype = Isotropic tau-p= 1 ref_p= 1 compressibility = 4.5E-5 ; VELOCITY INITIATION --- gen-vel = no gen-temp = 300 ;- BONDS --- constraints = all-bonds constraint-algorithm = Lincs unconstrained-start = yes Shake-SOR= no shake-tol= 0.0001 lincs-order = 8 lincs-warnangle = 30 lincs-iter = 8 morse= no [EMAIL PROTECTED]:~/klc/MD/free> cat pr_free.extendfrom12to20ns.mdp ;-PREPROCESSING OPTIONS title = PR "1KLC FREE"; my title cpp = cpp; my C prepocessor (whereIsIt) include = ; dir to include in my topology file define = ; ;-RUN CONTROL- integrator= md; ;--OUTPUT CONTROL-- ;TRR outpur nstxout= 1 nstvout= 1 nstfout= 0 ;LOG
Re: [gmx-users] kill some atoms
Omer, The situation is as follows. I simulate some pore (located at the center of the box) and solvent is both inside and outside the pore. To get a "right" density of solvent inside I make a system and let it relax itself. Then I want to stop migrating solvent inside and outside (inside an outside is intact!), so the easiest way is to reduce one side of the box to be equal to the length of my pore (and re-center the pore of course). genbox and editconf can change the box parameters but they don't want to kill the solvent which appears to be already not in the box after the manipulations. OM> What is the reason for shrinking the box? OM> If it is for technical reasons, for example - nicer visualization etc`, then perhaps this could be done OM> manually. OM> If you plan to use the smaller box later, then maybe you could do some part of high pressure simulation, OM> to reduce box size while keeping it physical. It seems that high pressure simulation reduces all side lengths (but I need to reduce only the selected one). Am I wrong? Vitaly -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq.,4, Kharkiv 61077, Ukraine email: [EMAIL PROTECTED] skype: vvchaban tel.: +38-097-8259698 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] kill some atoms
What is the reason for shrinking the box? If it is for technical reasons, for example - nicer visualization etc`, then perhaps this could be done manually. If you plan to use the smaller box later, then maybe you could do some part of high pressure simulation, to reduce box size while keeping it physical. --Omer. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Extending a run for different number of nodes
Hello, I have completed a 10ns run. Now I want to extend it to 20ns. The problem is that the initial tpr was compiled for 8 processors and now I have only 4 cores. What I tried to do is used tpbconv to make a 10ns extended tpr, then used an exactly the same mdp file to grompp it all together with -np 4 to a new tpr file. The problem is that at the beginning of the trajectory the structure is undergoing a structural change with 0.12 nm from the initial structure. That means that the structure is actually relaxed and that is not something I want to see. I have used this in my mdp ; VELOCITY INITIATION --- gen-vel = no gen-temp = 300 That means that no velocities were generated and I expect to see no relaxation but the continuation of my run. What am I doing wrong? How to extend a run without relaxation. Thank you. I appreciate any help. SDA My mdp file is the following. ;-PREPROCESSING OPTIONS title = PR "1KLC FREE"; my title cpp = cpp; my C prepocessor (whereIsIt) include = ; dir to include in my topology file define = ; ;-RUN CONTROL- integrator= md; ;--OUTPUT CONTROL-- ;TRR outpur nstxout= 1 nstvout= 1 nstfout= 0 ;LOG and EDR output nstlog = 1 nstenergy = 1 ;XTC output nstxtcout = 1000 xtc-precision = 1000 ;-START TIME & TIMESTEP--- tinit =; [ps] starting time for your run (only makes sense for md, sd, bd integator) dt = 0.005 ; [ps] time step for integration (--"--) nsteps = 160 ; (0) maximum number of steps to integrate comm-mode = ; Linear(Remove center of mass translation)/Annular(Remove center of mass ;translation and rotation)/No(no restriction) nstcomm = 1 ;-NEIGHBOR SEACHING--- nstlist = 5; frequency o update neighbor list ns_type = grid; make a gid in the box and check only ;neighboring grid cell when constructing a new neighbor list rlist = 1.0; cut-off distance for the short-range neighbor list ;-ELECTROSTATICS-- coulombtype = Reaction-field ; reaction field with coulomb cut-off rcoulomb ; where rcoulomb>rlist. The dielectric constant beyond the cut-off is epsilon_r rcoulomb = 1.5 ;distance for the coulomb cut-off epsilon_rf = 80;dielectric constant epsilon_r = 1; vdwtype = cut-off; twin-range cut-off`s with neighbor list cut-off rlist ;and VdW cut-off rvdw, where rvdw>rlist rvdw = 1.0 ; distance for for the LJ or Buckingam cut-off ;-ENERGY MINIMIZATION- emtol= 200 (kJ/mol*nm); minimisation is converged when the maximum force is smaller then this value emstep = 0.01; initial step size ;-TEMTERAURE CONTROL-- tcoupl = berendsen tc-grps = System tau-t= 0.1 ref-t= 300 ;- PRESSURE CONTROL- Pcoupl = no Pcoupltype = Isotropic tau-p= 1 ref_p= 1 compressibility = 4.5E-5 ; VELOCITY INITIATION --- gen-vel = no gen-temp = 300 ;- BONDS --- constraints = all-bonds constraint-algorithm = Lincs unconstrained-start = yes Shake-SOR= no shake-tol= 0.0001 lincs-order = 8 lincs-warnangle = 30 lincs-iter = 8 morse= no [EMAIL PROTECTED]:~/klc/MD/free> cat pr_free.extendfrom12to20ns.mdp ;-PREPROCESSING OPTIONS title = PR "1KLC FREE"; my title cpp = cpp; my C prepocessor (whereIsIt) include = ; dir to include in my topology file define = ; ;-RUN CONTROL- integrator= md; ;--OUTPUT CONTROL-- ;TRR outpur nstxout= 1 nstvout= 1 nstfout= 0 ;LOG and EDR output nstlog = 1 nstenergy = 1 ;XTC output nstxtcout = 1000 xtc-precision = 1000 ;-START TIME & TIMESTEP--- tinit =; [ps] starting time for your run (only makes sense for md, sd, bd integator) dt = 0.005 ; [ps] time step for integration (--"--) nsteps = 160 ;
[gmx-users] kill some atoms
Hi, Is there a way in gromacs to kill some atoms. For example, after the run one decreases the box volume using editconf (or genbox). Evidently then some molecules appear to be outside the MD box. The task is to kill those molecules. Please give a hint. -- Vitaly ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
