Re: [gmx-users] Potential Energy = -nan
shikha agarwal wrote: hi i m doing simulation membrane protein while scaling down the lipids by a factor of 0.95 then performing EM Steepest Descents converged to Fmax 10 in 18 steps Potential Energy = -nan Maximum force = 4.7791553e+02 on atom 5440 Norm of force = -nan ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator= steep; Algorithm (steep = steepest descent minimization) emtol= 10.0 ; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.1 ; Energy step size nsteps= 25000 ; Maximum number of (minimization) steps to perform ; 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= 1.2; Cut-off for making neighbor list (short range forces) coulombtype= Shift; Treatment of long range electrostatic interactions rcoulomb= 1.2; Short-range electrostatic cut-off rvdw= 1.2; Short-range Van der Waals cut-off pbc= xyz ; Periodic Boundary Conditions (yes/no) define = -DSTRONG_POSRES earlier when i was using ; minim.mdp - used as input into grompp to generate em.tpr ; 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 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps= 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist= 1; Frequency to update the neighbor list and long range forces ns_type= grid; Method to determine neighbor list (simple, grid) rlist= 1.2; Cut-off for making neighbor list (short range forces) coulombtype= PME; Treatment of long range electrostatic interactions rcoulomb= 1.2; Short-range electrostatic cut-off rvdw= 1.2; Short-range Van der Waals cut-off pbc= xyz ; Periodic Boundary Conditions (yes/no) define = -DFLEXIBLE then problem was same Which version of Gromacs? On what hardware? I discovered a platform-specific bug that looked a lot like this, but I hesitate to suggest that until I know more. In all likelihood, you simply have unresolvable atomic overlap (i.e., you're packing too much) such that energy minimization cannot complete, since nan = not a number, or something is infinitely large or small. -Justin help me ! with regards: shikha -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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] Potential Energy = -nan
shikha agarwal wrote: hi I m using gromacs4.5.3 . hardware 1GB ram 320 hard disk . What is the hardware type? PowerPC, Intel 32- or 64-bit, etc? when i skiped scaling by factor 0.95 then , after EM step I m getting same potential energy nan result. Do other simple systems work? Can you do simple tutorial systems like lysozyme in water? Otherwise, you've got some topology problem that prevents the system from being properly minimized. Set nstxout=1 in your .mdp file and watch what's happening. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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] Potential Energy = -nan
shikha agarwal wrote: hi, I m tried nstxout=1 in my .mdp file. Potential Energy = -nan Maximum force = 3.5637456e+07 on atom 2455 Norm of force = -nan help me! The purpose of nstxout=1 is not to give you a different result. It might aid you in watching the trajectory to determine what is going wrong. From these values, and everything I have seen thus far, you have a physically unreasonable system. Either you have atomic overlap or a topology problem. Unless you provide substantially more diagnostic information, then pleas like help me will get you nowhere. You haven't even provided a description of your system beyond membrane protein. The contents, topology sources, steps taken up until now, etc are all necessary pieces of information. Please read the last sentence of the following page, and visit the link therein: http://www.gromacs.org/Support/Mailing_Lists#Mailing_List_Etiquette -Justin regards: shikha -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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] Potential Energy = -nan
shikha agarwal wrote: hi, I tried on other system , 4GB ram , core i3 ,64bit processor ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator= steep; Algorithm (steep = steepest descent minimization) emtol= 10.0 ; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps= 25000 ; Maximum number of (minimization) steps to perform ; 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= 1.2; Cut-off for making neighbor list (short range forces) coulombtype= Shift; Treatment of long range electrostatic interactions rcoulomb= 1.2; Short-range electrostatic cut-off rvdw= 1.2; Short-range Van der Waals cut-off pbc= xyz ; Periodic Boundary Conditions (yes/no) nstxout = 1 result Steepest Descents: Tolerance (Fmax) = 1.0e+01 Number of steps=25000 Step= 14, Dmax= 1.2e-06 nm, Epot= -nan Fmax= 3.56233e+07, atom= 2455 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 10 Double precision normally gives you higher accuracy. writing lowest energy coordinates. Back Off! I just backed up after_em2.gro to ./#after_em2.gro.1# Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 10. Potential Energy = -nan Maximum force = 3.5637456e+07 on atom 2455 Norm of force = -nan help me! You've proven that the problem is not platform-specific, but you've provided none of the other details I requested before. Something is wrong with either the way you're building the system or constructed the topology. If you want free help, you have to make it easy to help you. So far, you haven't. Please consult my previous message and provide all the details I requested. Otherwise, you're unlikely to get anyone to help you. -Justin shikha -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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] potential energy NaN and strange dependence on cut-offs
Jennifer Williams wrote: Hi users, I am running a very simple simulation of methane inside a pore (v.much like a carbon nanotube but in my case the tube is supposed to represent silica.) I keep this tube frozen. I start with an energy minimisation-however this runs to completion almost instantly and I keep get NaN for my potential energy: Steepest Descents converged to machine precision in 18 steps, but did not reach the requested Fmax 10. Potential Energy =nan Maximum force = 6.5738518e+01 on atom 2133 Norm of force = 1.5461593e+00 This nan suggests some kind of severe atomic overlap. Reconsider your coordinates and the box size implied by your coordinate file. Mark Otherwise the trajectory looks OK (methane moving around inside the cylinder). If I go on to use the conf.gro file for an mdrun, it runs to completion and generates what looks like a reasonable trajectory, however the output again contains NaN i.e: Energies (kJ/mol) LJ (SR) Coulomb (SR) PotentialKinetic En. Total Energy nan0.0e+00nan3.36749e+01nan Conserved En.Temperature Pressure (bar) nan3.00010e+02nan and calculating the Diffusion coefficient gives: D[ CH4] 613.6682 (+/- 97.0563) 1e-5 cm^2/s If I do the same calculation but reduce the cut-offs to 0.9. I get Energies (kJ/mol) LJ (SR) Coulomb (SR) PotentialKinetic En. Total Energy nan0.0e+00nan3.36750e+01nan Conserved En.Temperature Pressure (bar) nan3.00011e+02nan D[ CH4] 237.8712 (+/- 53.5975) 1e-5 cm^2/s And for a cut-off of 1.3nm I get Energies (kJ/mol) LJ (SR) Coulomb (SR) PotentialKinetic En. Total Energ y nan0.0e+00nan3.36737e+01na n Conserved En.Temperature Pressure (bar) nan2.9e+02nan D[ CH4] 19.7953 (+/- 154.0168) 1e-5 cm^2/s For this system, the cut-off shouldn?t need to be larger than 0.8 (I have plotted graphs of calculated V vs r) so it is worrying that the diffusion coefficient is showing such dependence on the cut-offs when they should all give the same result. Can anyone offer any insight into this? I?ve tried changing the timestep making it both larger and smaller and many other things. I?ve pasted the relevant parts of my files below: I?m using gromacs 4.0.5 ?at the moment running in serial. Thanks for any advice, Top file [ defaults ] ; nbfunccomb-rulegen-pairsfudgeLJfudgeQQ 12yes1.0 1.0 ; ; [ atomtypes ] ; typemasschargeptype c6c12 OSM15.99940.00 A 0.2708 1.538176 ; ; Include forcefield parameters #include CH4.itp ; ; [ moleculetype ] ;Namenrexcl MCM3 [ atoms ] ;nrtyperesnrresidueatomcgnrcharge mass 1 OSM 1 MCM OSM 1 0 15.9994 2 OSM 1 MCM OSM 2 0 15.9994 ..etc 2127OSM 1 MCM OSM 21270 15.9994 2128OSM 1 MCM OSM 21280 15.9994 [ system ] ; Name CH4 in MCM [ molecules ] ; Compound#mols MCM1 CH410 CH4.itp file [ atomtypes ] ; type masschargeptype c6c12 CH416.043 0.00 A0.37321.24650457 ; [ moleculetype ] ; name nrexcl CH42 [ atoms ] ; nr typeresnr residu atomcgnrchargemass 1 CH4 1 CH4 CH4 10.00 16.043 .mdp file ; ;File 'mdout.mdp' was generated ;By user: jwillia4 (353773) ;On host: vlxhead2 ;At date: Fri Jun 26 15:47:37 2009 ; ; VARIOUS PREPROCESSING OPTIONS ; Preprocessor information: use cpp syntax. ; e.g.: -I/home/joe/doe -I/home/mary/hoe include = -I../top ; e.g.: -DI_Want_Cookies -DMe_Too define = ; RUN CONTROL PARAMETERS integrator = steep ; Start time and timestep in ps tinit= 0 dt = 0.0001 nsteps = 10 ; For exact run continuation or redoing part of a run ; Part index is updated automatically on checkpointing (keeps files separate) simulation_part = 1 init_step= 0 ; mode for center of mass motion removal comm-mode= linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= ; LANGEVIN DYNAMICS OPTIONS ; Friction coefficient (amu/ps) and random seed bd-fric = 0 ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size emtol= emstep =
Re: [gmx-users] potential energy NaN and strange dependence on cut-offs
Manik Mayur wrote: 2009/9/8 Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au Jennifer Williams wrote: Hi users, I am running a very simple simulation of methane inside a pore (v.much like a carbon nanotube but in my case the tube is supposed to represent silica.) I keep this tube frozen. I start with an energy minimisation-however this runs to completion almost instantly and I keep get NaN for my potential energy: Steepest Descents converged to machine precision in 18 steps, but did not reach the requested Fmax 10. Potential Energy =nan Maximum force = 6.5738518e+01 on atom 2133 Norm of force = 1.5461593e+00 This nan suggests some kind of severe atomic overlap. Reconsider your coordinates and the box size implied by your coordinate file. Mark Otherwise the trajectory looks OK (methane moving around inside the cylinder). If I go on to use the conf.gro file for an mdrun, it runs to completion and generates what looks like a reasonable trajectory, however the output again contains NaN i.e: Energies (kJ/mol) LJ (SR) Coulomb (SR) PotentialKinetic En. Total Energy nan0.0e+00nan3.36749e+01 nan Conserved En.Temperature Pressure (bar) nan3.00010e+02nan and calculating the Diffusion coefficient gives: D[ CH4] 613.6682 (+/- 97.0563) 1e-5 cm^2/s If I do the same calculation but reduce the cut-offs to 0.9. I get Energies (kJ/mol) LJ (SR) Coulomb (SR) PotentialKinetic En. Total Energy nan0.0e+00nan3.36750e+01 nan Conserved En.Temperature Pressure (bar) nan3.00011e+02nan D[ CH4] 237.8712 (+/- 53.5975) 1e-5 cm^2/s And for a cut-off of 1.3nm I get Energies (kJ/mol) LJ (SR) Coulomb (SR) PotentialKinetic En. Total Energ y nan0.0e+00nan3.36737e+01 na n Conserved En.Temperature Pressure (bar) nan2.9e+02nan D[ CH4] 19.7953 (+/- 154.0168) 1e-5 cm^2/s For this system, the cut-off shouldn?t need to be larger than 0.8 (I have plotted graphs of calculated V vs r) so it is worrying that the diffusion coefficient is showing such dependence on the cut-offs when they should all give the same result. Can anyone offer any insight into this? I?ve tried changing the timestep making it both larger and smaller and many other things. I?ve pasted the relevant parts of my files below: I?m using gromacs 4.0.5 ?at the moment running in serial. Thanks for any advice, Top file [ defaults ] ; nbfunccomb-rulegen-pairsfudgeLJfudgeQQ 12yes1.0 1.0 ; ; [ atomtypes ] ; typemasschargeptype c6c12 OSM15.99940.00 A 0.2708 1.538176 Check your tpr file: are the C6 and C12 reasonable? If you get NaN something is wrong. ; ; Include forcefield parameters #include CH4.itp ; ; [ moleculetype ] ;Namenrexcl MCM3 [ atoms ] ;nrtyperesnrresidueatomcgnrcharge mass 1 OSM 1 MCM OSM 1 0 15.9994 2 OSM 1 MCM OSM 2 0 15.9994 .etc 2127OSM 1 MCM OSM 21270 15.9994 2128OSM 1 MCM OSM 21280 15.9994 [ system ] ; Name CH4 in MCM [ molecules ] ; Compound#mols MCM1 CH410 CH4.itp file [ atomtypes ] ; type masschargeptype c6c12 CH416.043 0.00 A0.37321.24650457 ; [ moleculetype ] ; name nrexcl CH42 [ atoms ] ; nr typeresnr residu atomcgnrchargemass 1 CH4 1 CH4 CH4 10.00 16.043 .mdp file ; ;File 'mdout.mdp' was generated ;By user: jwillia4 (353773) ;On host: vlxhead2 ;At date: Fri Jun 26 15:47:37 2009 ; ; VARIOUS PREPROCESSING OPTIONS ; Preprocessor
Re: [gmx-users] potential energy NaN and strange dependence on cut-offs
2009/9/8 Mark Abraham mark.abra...@anu.edu.au Jennifer Williams wrote: Hi users, I am running a very simple simulation of methane inside a pore (v.much like a carbon nanotube but in my case the tube is supposed to represent silica.) I keep this tube frozen. I start with an energy minimisation-however this runs to completion almost instantly and I keep get NaN for my potential energy: Steepest Descents converged to machine precision in 18 steps, but did not reach the requested Fmax 10. Potential Energy =nan Maximum force = 6.5738518e+01 on atom 2133 Norm of force = 1.5461593e+00 This nan suggests some kind of severe atomic overlap. Reconsider your coordinates and the box size implied by your coordinate file. Mark Otherwise the trajectory looks OK (methane moving around inside the cylinder). If I go on to use the conf.gro file for an mdrun, it runs to completion and generates what looks like a reasonable trajectory, however the output again contains NaN i.e: Energies (kJ/mol) LJ (SR) Coulomb (SR) PotentialKinetic En. Total Energy nan0.0e+00nan3.36749e+01nan Conserved En.Temperature Pressure (bar) nan3.00010e+02nan and calculating the Diffusion coefficient gives: D[ CH4] 613.6682 (+/- 97.0563) 1e-5 cm^2/s If I do the same calculation but reduce the cut-offs to 0.9. I get Energies (kJ/mol) LJ (SR) Coulomb (SR) PotentialKinetic En. Total Energy nan0.0e+00nan3.36750e+01nan Conserved En.Temperature Pressure (bar) nan3.00011e+02nan D[ CH4] 237.8712 (+/- 53.5975) 1e-5 cm^2/s And for a cut-off of 1.3nm I get Energies (kJ/mol) LJ (SR) Coulomb (SR) PotentialKinetic En. Total Energ y nan0.0e+00nan3.36737e+01na n Conserved En.Temperature Pressure (bar) nan2.9e+02nan D[ CH4] 19.7953 (+/- 154.0168) 1e-5 cm^2/s For this system, the cut-off shouldn?t need to be larger than 0.8 (I have plotted graphs of calculated V vs r) so it is worrying that the diffusion coefficient is showing such dependence on the cut-offs when they should all give the same result. Can anyone offer any insight into this? I?ve tried changing the timestep making it both larger and smaller and many other things. I?ve pasted the relevant parts of my files below: I?m using gromacs 4.0.5 ?at the moment running in serial. Thanks for any advice, Top file [ defaults ] ; nbfunccomb-rulegen-pairsfudgeLJfudgeQQ 12yes1.0 1.0 ; ; [ atomtypes ] ; typemasschargeptype c6c12 OSM15.99940.00 A 0.2708 1.538176 ; ; Include forcefield parameters #include CH4.itp ; ; [ moleculetype ] ;Namenrexcl MCM3 [ atoms ] ;nrtyperesnrresidueatomcgnrcharge mass 1 OSM 1 MCM OSM 1 0 15.9994 2 OSM 1 MCM OSM 2 0 15.9994 ..etc 2127OSM 1 MCM OSM 21270 15.9994 2128OSM 1 MCM OSM 21280 15.9994 [ system ] ; Name CH4 in MCM [ molecules ] ; Compound#mols MCM1 CH410 CH4.itp file [ atomtypes ] ; type masschargeptype c6c12 CH416.043 0.00 A0.37321.24650457 ; [ moleculetype ] ; name nrexcl CH42 [ atoms ] ; nr typeresnr residu atomcgnrchargemass 1 CH4 1 CH4 CH4 10.00 16.043 .mdp file ; ;File 'mdout.mdp' was generated ;By user: jwillia4 (353773) ;On host: vlxhead2 ;At date: Fri Jun 26 15:47:37 2009 ; ; VARIOUS PREPROCESSING OPTIONS ; Preprocessor information: use cpp syntax. ; e.g.: -I/home/joe/doe -I/home/mary/hoe include = -I../top ; e.g.: -DI_Want_Cookies -DMe_Too define = ; RUN CONTROL PARAMETERS integrator = steep ; Start time and timestep in ps tinit= 0 dt = 0.0001 dt = 0.1 fs are you sure?? nsteps = 10 ; For exact run continuation or redoing part of a run ; Part index is updated automatically on checkpointing (keeps files separate) simulation_part = 1 init_step= 0 ; mode for center of mass motion removal comm-mode= linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= ; LANGEVIN DYNAMICS OPTIONS ; Friction coefficient (amu/ps) and random seed bd-fric = 0
Re: [gmx-users] potential energy =nan
Am Mittwoch, 20. Juni 2007 schrieb Sheyore Omovie: I am doing an Energy Minimisation run for two polypeptides in a box. I get the range checking error, variable ci= and the simulation crashes. After changing ns_type to simple, the simulation is running, but very slowly and the first few steps return Epot=nan. What could I have done wrong? If you're using SPC water, try to make it flexible. This helped me several times. Cheers Martin ___ 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] potential energy =nan
Sheyore Omovie wrote: I am doing an Energy Minimisation run for two polypeptides in a box. I get the range checking error, variable ci= and the simulation crashes. After changing ns_type to simple, the simulation is running, but very slowly and the first few steps return Epot=nan. What could I have done wrong? It's hard to tell from your description, since an energy minimization is not a simulation... but please try following this general scheme http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] potential energy =nan
Hi Mark, I'm sorry, I assume you'll understand that I've carried out all the steps before an EM run. David said is because the coordinates are on top of each other, I'll appreciate any more specific advice on how to fix this. Meanwhile, I'll try Martin's advice on making the water flexible. Rgds John From: Mark Abraham [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] potential energy =nan Date: Wed, 20 Jun 2007 23:09:03 +1000 Sheyore Omovie wrote: I am doing an Energy Minimisation run for two polypeptides in a box. I get the range checking error, variable ci= and the simulation crashes. After changing ns_type to simple, the simulation is running, but very slowly and the first few steps return Epot=nan. What could I have done wrong? It's hard to tell from your description, since an energy minimization is not a simulation... but please try following this general scheme http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ Picture this share your photos and you could win big! http://www.GETREALPhotoContest.com?ocid=TXT_TAGHMloc=us ___ 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] potential energy =nan
Hi, I figured it might be neccessary to show my *.top file and coordinate file (b4 solvation) so I could easily get help. Rgds John ; File 'twopoly.top' was generated ; By user: sjomovie (1028) ; On host: bmp041.biophysics.net ; At date: Tue Jun 19 23:12:16 2007 ; ; This is your topology file ; Great Red Oystrich Makes All Chemists Sane ; ; Include forcefield parameters #include ffG43a1.itp ; Include chain topologies #include twopoly_B.itp #include twopoly_A.itp ; Include water topology #include spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include generic topology for ions #include ions.itp [ system ] ; Name Great Red Oystrich Makes All Chemists Sane in water [ molecules ] ; Compound#mols Protein_B 1 Protein_A 1 SOL 314583 TITLE Great Red Oystrich Makes All Chemists Sane REMARKTHIS IS A SIMULATION BOX CRYST1 10.2665.7232.981 90.00 90.00 90.00 P 1 1 MODEL1 ATOM1 N ALA B 1 -0.677 -1.23 -0.491 1 0 ATOM2 H1 ALA B 1 -1.667 -1.089 -0.491 1 0 ATOM3 H2 ALA B 1 -0.414 -1.744 -1.307 1 0 ATOM4 H3 ALA B 1 -0.414 -1.744 0.325 1 0 ATOM5 CA ALA B 1 -0.001 0.064 -0.491 1 0 ATOM6 CB ALA B 1 -0.509 0.856 0.727 1 0 ATOM7 C ALA B 1 1.499 -0.11 -0.491 1 0 ATOM8 O ALA B 1 2.065 -0.922 0.251 1 0 ATOM9 N GLY B 2 2.311 0.711 -1.41 0 ATOM10 H GLY B 2 1.979 1.399 -2.045 1 0 ATOM11 CA GLY B 2 3.7 0.321 -1.173 1 0 ATOM12 C GLY B 2 4.606 1.528 -1.169 1 0 ATOM13 O GLY B 2 4.515 2.418 -2.019 1 0 ATOM14 N ALA B 3 5.629 1.648 -0.12 1 0 ATOM15 H ALA B 3 5.805 1.002 0.622 1 0 ATOM16 CA ALA B 3 6.336 2.899 -0.378 1 0 ATOM17 CB ALA B 3 5.719 3.979 0.528 1 0 ATOM18 C ALA B 3 7.821 2.735 -0.164 1 0 ATOM19 O1 ALA B 3 8.258 1.505 0.219 1 0 ATOM20 O2 ALA B 3 8.599 3.831 -0.372 1 0 ATOM21 N ALA A 4 -0.677 -1.23 -0.491 1 0 ATOM22 H1 ALA A 4 -1.667 -1.089 -0.491 1 0 ATOM23 H2 ALA A 4 -0.414 -1.744 -1.307 1 0 ATOM24 H3 ALA A 4 -0.414 -1.744 0.325 1 0 ATOM25 CA ALA A 4 -0.001 0.064 -0.491 1 0 ATOM26 CB ALA A 4 -0.509 0.856 0.727 1 0 ATOM27 C ALA A 4 1.499 -0.11 -0.491 1 0 ATOM28 O ALA A 4 2.065 -0.922 0.251 1 0 ATOM29 N ALA A 5 2.311 0.711 -1.41 0 ATOM30 H ALA A 5 1.979 1.399 -2.045 1 0 ATOM31 CA ALA A 5 3.7 0.321 -1.173 1 0 ATOM32 CB ALA A 5 4.079 -0.705 -2.254 1 0 ATOM33 C ALA A 5 4.606 1.529 -1.169 1 0 ATOM34 O ALA A 5 4.515 2.421 -2.021 1 0 ATOM35 N ALA A 6 5.629 1.648 -0.119 1 0 ATOM36 H ALA A 6 5.806 1.001 0.623 1 0 ATOM37 CA ALA A 6 6.335 2.9 -0.377 1 0 ATOM38 CB ALA A 6 5.718 3.979 0.529 1 0 ATOM39 C ALA A 6 7.821 2.736 -0.163 1 0 ATOM40 O1 ALA A 6 8.258 1.506 0.219 1 0 ATOM41 O2 ALA A 6 8.599 3.832 -0.37 1 0 TER ENDMDL From: Sheyore Omovie [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: gmx-users@gromacs.org Subject: Re: [gmx-users] potential energy =nan Date: Wed, 20 Jun 2007 11:44:32 -0500 Hi Mark, I'm sorry, I assume you'll understand that I've carried out all the steps before an EM run. David said is because the coordinates are on top of each other, I'll appreciate any more specific advice on how to fix this. Meanwhile, I'll try Martin's
Re: [gmx-users] potential energy =nan
Sheyore Omovie wrote: Hi Mark, I'm sorry, I assume you'll understand that I've carried out all the steps before an EM run. David said is because the coordinates are on top of each other, I'll appreciate any more specific advice on how to fix this. use a molecule viewer Meanwhile, I'll try Martin's advice on making the water flexible. Rgds John From: Mark Abraham [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] potential energy =nan Date: Wed, 20 Jun 2007 23:09:03 +1000 Sheyore Omovie wrote: I am doing an Energy Minimisation run for two polypeptides in a box. I get the range checking error, variable ci= and the simulation crashes. After changing ns_type to simple, the simulation is running, but very slowly and the first few steps return Epot=nan. What could I have done wrong? It's hard to tell from your description, since an energy minimization is not a simulation... but please try following this general scheme http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ Picture this – share your photos and you could win big! http://www.GETREALPhotoContest.com?ocid=TXT_TAGHMloc=us ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
