Re: [gmx-users] Re: LINCS error
I did few changes ie decreased the time step/ increased the equilibration steps/ omitted the generation of velocity in production run / did 2 steps of equilibration / checked the starting structure for steric clashes. I don't understand what else should I try to fix the lincs warnings. Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: Mark Abraham mark.abra...@anu.edu.au Sender: gmx-users-boun...@gromacs.org Date: Wed, 21 Dec 2011 00:15:15 To: Discussion list for GROMACS usersgmx-users@gromacs.org Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] Re: LINCS error -- 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
[gmx-users] Re: LINCS error
i went through the mailing list, but i dont understand when i run the same protein on my computer it runs correctly without any LINCS warning. On the cluster with 64 processors the job runs but crashes in between and shows the LINCS warning. Please anyone tell me what could be the reason. Is anything wrong with my protein. On Sun, Dec 18, 2011 at 7:35 PM, aiswarya pawar aiswarya.pa...@gmail.comwrote: Hi users, I did energy minimization of a protein complex using the following minimization mdp file. ; Lines starting with ';' ARE COMMENTS ; Everything following ';' is also comment title = Energy Minimization ; Title of run ; The following line tell the program the standard locations where to find certain files cpp = /lib/cpp ; Preprocessor ; Define can be used to control processes define = -DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0 ; Stop minimization when the maximum force 1.0 kJ/mol emstep = 0.01 nsteps = 5000 ; Maximum number of (minimization) steps to perform nstenergy = 10 ; Write energies to disk every nstenergy steps energygrps = Protein ; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 10 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 1.0 ; long range electrostatic cut-off rvdw = 1.4 ; long range Van der Waals cut-off constraints = none ; Bond types to replace by constraints pbc= xyz ; Periodic Boundary Conditions (yes/no) and the pr.mdp = ; VARIOUS PREPROCESSING OPTIONS title= Position Restrained Molecular Dynamics define = -DPOSRES constraints = all-bonds integrator = md dt = 0.001 ; ps ! nsteps = 25000 ; total 50 ps. nstcomm = 10 nstxout = 500 ; collect data every 1 ps nstxtcout= 500 nstvout = 0 nstfout = 0 nstlist = 10 ns_type = grid rlist= 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.4 pme_order= 4 ewald_rtol = 1e-5 optimize_fft = yes DispCorr = no ; Berendsen temperature coupling is on Tcoupl = v-rescale tau_t= 0.1 0.1 tc-grps = protein non-protein ref_t= 300 300 ; Pressure coupling is on Pcoupl = parrinello-rahman Pcoupltype = isotropic tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = -1 and md.mdp file = ; VARIOUS PREPROCESSING OPTIONS title= Position Restrained Molecular Dynamics ; RUN CONTROL PARAMETERS constraints = all-bonds integrator = md dt = 0.002 ; 2fs ! nsteps = 250 ; total 5000 ps. nstcomm = 10 nstxout = 500 ; collect data every 1 ps nstxtcout = 0 nstvout = 0 nstfout = 0 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.4 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes DispCorr = no ; Berendsen temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 0.1 tc-grps = protein non-protein ref_t = 300 300 ; Pressure coupling is on Pcoupl = parrinello-rahman Pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = -1 The minimization step went well. but while doing the final mdrun am getting LINCS error. i read through the numerous mailing list on grimaces but still couldn't understand how would i fix this. am getting this error for all the 10 protein complex i did minimization for. Please help. Thanks, Aiswarya -- 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: LINCS error
On 20/12/11, aiswarya pawar aiswarya.pa...@gmail.com wrote: i went through the mailing list, but i dont understand when i run the same protein on my computer it runs correctly without any LINCS warning. On the cluster with 64 processors the job runs but crashes in between and shows the LINCS warning. That happens. Your different computers are running different versions of the calculation. Numerical artefacts do happen, especially if you use algorithms that are known to be unstable when not in equilibrium, like I said three days ago. Why have you repeated your question instead of trying my suggestion? Please anyone tell me what could be the reason. Is anything wrong with my protein. Something is very likely wrong with your system preparation. The links people have been giving you detail the advice on how to diagnose the problem or how to be more gentle. There's little else for me to say. Mark On Sun, Dec 18, 2011 at 7:35 PM, aiswarya pawar aiswarya.pa...@gmail.com wrote: Hi users, I did energy minimization of a protein complex using the following minimization mdp file. ; Lines starting with ';' ARE COMMENTS ; Everything following ';' is also comment title = Energy Minimization ; Title of run ; The following line tell the program the standard locations where to find certain files cpp = /lib/cpp ; Preprocessor ; Define can be used to control processes define = -DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0 ; Stop minimization when the maximum force 1.0 kJ/mol emstep = 0.01 nsteps = 5000 ; Maximum number of (minimization) steps to perform nstenergy = 10; Write energies to disk every nstenergy steps energygrps = Protein ; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 10; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb= 1.0 ; long range electrostatic cut-off rvdw= 1.4 ; long range Van der Waals cut-off constraints = none ; Bond types to replace by constraints pbc = xyz ; Periodic Boundary Conditions (yes/no) and the pr.mdp = ; VARIOUS PREPROCESSING OPTIONS title = Position Restrained Molecular Dynamics define = -DPOSRES constraints = all-bonds integrator = md dt = 0.001 ; ps ! nsteps = 25000 ; total 50 ps. nstcomm = 10 nstxout = 500 ; collect data every 1 ps nstxtcout = 500 nstvout = 0 nstfout = 0 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.4 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes DispCorr = no ; Berendsen temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 0.1 tc-grps = protein non-protein ref_t = 300 300 ; Pressure coupling is on Pcoupl = parrinello-rahman Pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = -1 and md.mdp file = ; VARIOUS PREPROCESSING OPTIONS title = Position Restrained Molecular Dynamics ; RUN CONTROL PARAMETERS constraints = all-bonds integrator = md dt = 0.002 ; 2fs ! nsteps = 250 ; total 5000 ps. nstcomm = 10 nstxout = 500 ; collect data every 1 ps nstxtcout = 0 nstvout = 0 nstfout = 0 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.4 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes DispCorr = no ; Berendsen temperature coupling
