Re: [gmx-users] energy-minimisation problem
On 1/29/13 4:43 AM, SANTU BISWAS wrote: dear users, I am performing an energy minimization of polypeptide(formed by 10-residues of alanine, lysine,leucine,glutamic acid ) in vacuum box by using Steepest Descent(initially) and then Conjugate Gradient methods in gromacs_4.5.5_doubleprecision using charmm-27 force field for all system.I saw that for lysine and alanine potential energy value is positive but for leucine and glutamic acid potential energy value is nagative for both energy- minimisation methods. I do not understand why this is happening. How are you extracting this information? You don't even have energygrps set in the .mdp file, so I'm not sure how you've got energies per amino acid, which are relatively useless numbers anyway. In vacuo, you probably have a lot of unsatisfied interactions that would not occur in the condensed phase. Positive potential energies can thus arise. As long as the EM converged to an acceptable value of Fmax, that's what you should be most concerned with. -Justin Input file for energy-minimisation is ;title= cpp = /lib/cpp ;include =-I../top/ define = -DFLEXIBLE ; Input file integrator = cg nsteps = 1 pbc = no ns_type= simple nstlist = 0 rlist = 0 rcoulomb = 0 rvdw = 0 ; Energy minimizing stuff emtol = 0.001 emstep = 0.1 nstcgsteep= 10 --- santu -- 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: RE: [gmx-users] energy minimisation of carbon nanotubes.
I recommend use the double precision just to check the better result to your system. In my case, i've got much better results using emtol=0.004 and double precision. My system is too much unstable and i tried. I have no regrets... Marcelo Depolo Em 15/09/2012 22:11, Elie M elie.mouj...@hotmail.co.ukescreveu: Thank you for your reply and help. Regards Elie Date: Sat, 15 Sep 2012 13:32:06 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] energy minimisation of carbon nanotubes. On 9/15/12 12:49 PM, Elie M wrote: Dear all, I have a small question regardin... -- 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] energy minimisation of carbon nanotubes.
On 9/15/12 12:49 PM, Elie M wrote: Dear all, I have a small question regarding energy minimization. I am minimizing a carbon naotube in vaccuo and my (mdp )input file is: ; ; SWNT (10,0) on its own ; Elie Moujaes, SWNT+polymers project ; Energy minimization input file ; cpp =/usr/bin/cpp define = -DFLEXIBLE constraints = none integrator = cg nsteps = 2000 ; ; Energy minimizing stuff ; emtol = 0.1 emstep = 0.03 nstcomm = 1 pbc = xyz periodic_molecules = yes ns_type = grid rlist = 1 rcoulomb= 1.0 rvdw= 1.0 Tcoupl = no Pcoupl = no gen_vel = no I have put emstep very loww toa chieve accuracy.In the output i got: Reading file SWNT-EM.tpr, VERSION 4.0.5 (single precision)Polak-Ribiere Conjugate Gradients: Tolerance (Fmax) = 1.0e-05 Number of steps= 2000 F-max = 3.48055e+03 on atom 799 F-Norm = 9.67779e+02 Stepsize too small, or no change in energy.Converged to machine precision,but not to the requested precision Fmax 1e-05 Double precision normally gives you higher accuracy. writing lowest energy coordinates. Polak-Ribiere Conjugate Gradients converged to machine precision in 359 steps,but did not reach the requested Fmax 1e-05.Potential Energy = 8.7646348e+03Maximum force = 1.6186214e+01 on atom 701Norm of force = 5.4860659e+00 It seems that I have to use the double precision version but as the single precision is concerned,Is the minimization fine (as the maximum force on atom 701 is 16...)? The outcome seems reasonable. I doubt that any algorithm, in single or double precision, would ever reach Fmax 1e-05. Values of Fmax 10 are generally suitable for just about any purpose and Fmax 1000 will generally result in stable simulations for most systems. -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] energy minimisation of carbon nanotubes.
Thank you for your reply and help. Regards Elie Date: Sat, 15 Sep 2012 13:32:06 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] energy minimisation of carbon nanotubes. On 9/15/12 12:49 PM, Elie M wrote: Dear all, I have a small question regarding energy minimization. I am minimizing a carbon naotube in vaccuo and my (mdp )input file is: ; ; SWNT (10,0) on its own ; Elie Moujaes, SWNT+polymers project ; Energy minimization input file ; cpp =/usr/bin/cpp define = -DFLEXIBLE constraints = none integrator = cg nsteps = 2000 ; ; Energy minimizing stuff ; emtol = 0.1 emstep = 0.03 nstcomm = 1 pbc = xyz periodic_molecules = yes ns_type = grid rlist = 1 rcoulomb= 1.0 rvdw= 1.0 Tcoupl = no Pcoupl = no gen_vel = no I have put emstep very loww toa chieve accuracy.In the output i got: Reading file SWNT-EM.tpr, VERSION 4.0.5 (single precision)Polak-Ribiere Conjugate Gradients: Tolerance (Fmax) = 1.0e-05 Number of steps = 2000 F-max = 3.48055e+03 on atom 799 F-Norm = 9.67779e+02 Stepsize too small, or no change in energy.Converged to machine precision,but not to the requested precision Fmax 1e-05 Double precision normally gives you higher accuracy. writing lowest energy coordinates. Polak-Ribiere Conjugate Gradients converged to machine precision in 359 steps,but did not reach the requested Fmax 1e-05.Potential Energy = 8.7646348e+03Maximum force = 1.6186214e+01 on atom 701Norm of force = 5.4860659e+00 It seems that I have to use the double precision version but as the single precision is concerned,Is the minimization fine (as the maximum force on atom 701 is 16...)? The outcome seems reasonable. I doubt that any algorithm, in single or double precision, would ever reach Fmax 1e-05. Values of Fmax 10 are generally suitable for just about any purpose and Fmax 1000 will generally result in stable simulations for most systems. -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 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] Energy Minimisation
Ravi Kumar Venkatraman wrote: *Dear all, I am trying to minimize the energy of the single molecule using gromacs. I tried with the following mdp ; VARIOUS PREPROCESSING OPTIONS FOR ENERGY MINIMIZATION OF ISOLATED MOLECULE include = define = ; RUN CONTROL PARAMETERS integrator = steep nsteps = 5000 init_step= ; ENERGY MINIMIZATION OPTIONS emtol= 10 emstep = 0.01 nstcgsteep = nbfgscorr= nstcheckpoint= 100 nstlog = 100 nstenergy= 1 ; SIMULATED ANNEALING annealing = no annealing_npoints= annealing_time = annealing_temp= But it shows the following error, ERROR: The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease rlist. I have not included any the cut-off in the mdp file, but it still shows the error. Am I supposed to include something to mdp to run single molecule energy minimisation. You should explicitly provide the settings you wish to use. The default of 1.0 nm will be applied (which may or may not be appropriate), and the error suggests your box is too small, so you should build a proper one. http://www.gromacs.org/Documentation/Errors#The_cut-off_length_is_longer_than_half_the_shortest_box_vector_or_longer_than_the_smallest_box_diagonal_element._Increase_the_box_size_or_decrease_rlist -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] Energy minimisation query
nikhil damle wrote: Hi, I am trying to simulate a dimeric structure and I have already simulated its monomeric form. I use exactly same parameters which i use for monomer during dimer minimisation in solvent. System Details: # Atoms = 4488 (# Res = 582) octahedron box with d = 0.9 Solvent (spce water model) density = 1050.6 g/L (During monomer MD it was 1048.86 g/L) System subjected to energy minimisation, Only warning arising during grompp: --- WARNING 1 [file dimer.top, line 46]: 86974 non-matching atom names atom names from dimer.top will be used atom names from neutral.pdb will be ignored --- This was neglected using -maxwarn option and contd... Error during minimisation run (mdrun): --- Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps=5 Step= 14, Dmax= 1.2e-06 nm, Epot= 7.04150e+23 Fmax= inf, atom= 37 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 Double precision normally gives you higher accuracy. writing lowest energy coordinates. Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 1000. Potential Energy = 6.9065950e+23 Maximum force =inf on atom 37 Norm of force =inf - 1) I thought that the box size is too small so that dimer is not able to move at all and hence the energy is too high. But I am getting same error even if box size is increased to 2.0 nm 2) I checked my initial structure and even the neutralised structure post solvation only to find that it is not broken. (My system has a missing loop which I have modeled using modeler9v8 and then subjected it to MD in solvent.) What could possibly go wrong ? Could it be really the step size or precision although I do not think so ! Nearly 87,000 atoms are being assigned parameters that do not belong to them. The order of the [molecules] directive and the coordinate file must match. Otherwise, grompp (and then mdrun) will think that water is protein, and protein residues are other residues, etc. I would be a fan of making -maxwarn a hidden option; it really should not be used unless one knows the exact consequences of doing so. -Justin Regards, Nikhil -- 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] Energy minimisation problems - coordinate file and topology file not matching.
Hi, Natalie, Obviously, number of coordinates still doesn't match the topology file even you updated the topol.top *carefully*. Check the topol.top thoroughly or paste several line of your coordinate and topology files may be good ideas. Note that the topology file is lacking information for *28* atoms. Does that number remind you anything? Terry On Wed, Sep 22, 2010 at 6:42 PM, Natalie Stephenson natalie.stephen...@postgrad.manchester.ac.uk wrote: Hi everyone, I was hoping you could clear up a problem I'm having when performing energy minimisation. I'm following the instructions from one of the tutorials (Justin's Umbrella Sampling) with my own protein, however, this time when I try to perform the energy minimisation it throws out this 'fatal error message' ... number of coordinates in coordinate file (nrr_solv_ions.gro, 33181) does not match topology (topol.top, 33153) I've been updating the topol.top file every time I've done something, so I'm not really sure what's happened. Can anyone throw some light on what I've gone wrong!! Thanks loads! Natalie -- 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] Energy minimisation problems - coordinate file and topology file not matching.
Natalie Stephenson wrote: Hi everyone, I was hoping you could clear up a problem I'm having when performing energy minimisation. I'm following the instructions from one of the tutorials (Justin's Umbrella Sampling) with my own protein, however, this time when I try to perform the energy minimisation it throws out this 'fatal error message' ... number of coordinates in coordinate file (nrr_solv_ions.gro, 33181) does not match topology (topol.top, 33153) I've been updating the topol.top file every time I've done something, so I'm not really sure what's happened. Are you making manual updates, or allowing genbox/genion to make changes for you? In the case of the former, check your work :) In the case of the latter, I'd be more concerned. There really is nothing diagnostic that can be done. You simply have to check how many of each molecule are in your system. Something has gone wrong somewhere along the way. http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology -Justin Can anyone throw some light on what I've gone wrong!! Thanks loads! Natalie -- 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] Energy minimisation problems - coordinate file and topology file not matching.
Thanks for your help Justin Terry I've been letting genion etc update it ... so there must be somewhere where i've missed it or something. I'll check through the files and see if I can see what's missing... xxx From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Terry [terrence...@gmail.com] Sent: 22 September 2010 11:55 To: Discussion list for GROMACS users Subject: Re: [gmx-users] Energy minimisation problems - coordinate file and topology file not matching. Hi, Natalie, Obviously, number of coordinates still doesn't match the topology file even you updated the topol.top *carefully*. Check the topol.top thoroughly or paste several line of your coordinate and topology files may be good ideas. Note that the topology file is lacking information for *28* atoms. Does that number remind you anything? Terry On Wed, Sep 22, 2010 at 6:42 PM, Natalie Stephenson natalie.stephen...@postgrad.manchester.ac.ukmailto:natalie.stephen...@postgrad.manchester.ac.uk wrote: Hi everyone, I was hoping you could clear up a problem I'm having when performing energy minimisation. I'm following the instructions from one of the tutorials (Justin's Umbrella Sampling) with my own protein, however, this time when I try to perform the energy minimisation it throws out this 'fatal error message' ... number of coordinates in coordinate file (nrr_solv_ions.gro, 33181) does not match topology (topol.top, 33153) I've been updating the topol.top file every time I've done something, so I'm not really sure what's happened. Can anyone throw some light on what I've gone wrong!! Thanks loads! Natalie -- gmx-users mailing listgmx-users@gromacs.orgmailto: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.orgmailto: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] Energy minimisation problems - coordinate file and topology file not matching.
Ok ... think I've worked out what's happened ... There were two 'SOL' groups. So when replacing solvent with ions it has added double the amount of ions to the topol.top file. Think I'll go back a couple of steps and try to sort out why there are two 'SOL' groups. Thanks for the help! xxx From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Natalie Stephenson [natalie.stephen...@postgrad.manchester.ac.uk] Sent: 22 September 2010 13:02 To: Discussion list for GROMACS users Subject: RE: [gmx-users] Energy minimisation problems - coordinate file and topology file not matching. Thanks for your help Justin Terry I've been letting genion etc update it ... so there must be somewhere where i've missed it or something. I'll check through the files and see if I can see what's missing... xxx From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Terry [terrence...@gmail.com] Sent: 22 September 2010 11:55 To: Discussion list for GROMACS users Subject: Re: [gmx-users] Energy minimisation problems - coordinate file and topology file not matching. Hi, Natalie, Obviously, number of coordinates still doesn't match the topology file even you updated the topol.top *carefully*. Check the topol.top thoroughly or paste several line of your coordinate and topology files may be good ideas. Note that the topology file is lacking information for *28* atoms. Does that number remind you anything? Terry On Wed, Sep 22, 2010 at 6:42 PM, Natalie Stephenson natalie.stephen...@postgrad.manchester.ac.ukmailto:natalie.stephen...@postgrad.manchester.ac.uk wrote: Hi everyone, I was hoping you could clear up a problem I'm having when performing energy minimisation. I'm following the instructions from one of the tutorials (Justin's Umbrella Sampling) with my own protein, however, this time when I try to perform the energy minimisation it throws out this 'fatal error message' ... number of coordinates in coordinate file (nrr_solv_ions.gro, 33181) does not match topology (topol.top, 33153) I've been updating the topol.top file every time I've done something, so I'm not really sure what's happened. Can anyone throw some light on what I've gone wrong!! Thanks loads! Natalie -- gmx-users mailing listgmx-users@gromacs.orgmailto: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.orgmailto: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] Energy minimisation problems - coordinate file and topology file not matching.
Natalie Stephenson wrote: Ok ... think I've worked out what's happened ... There were two 'SOL' groups. So when replacing solvent with ions it has added double the amount of ions to the topol.top file. Think I'll go back a couple of steps and try to sort out why there are two 'SOL' groups. Were there water molecules (i.e., from a crystal structure) in the initial structure passed to pdb2gmx? -Justin Thanks for the help! xxx *From:* gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Natalie Stephenson [natalie.stephen...@postgrad.manchester.ac.uk] *Sent:* 22 September 2010 13:02 *To:* Discussion list for GROMACS users *Subject:* RE: [gmx-users] Energy minimisation problems - coordinate file and topology file not matching. Thanks for your help Justin Terry I've been letting genion etc update it ... so there must be somewhere where i've missed it or something. I'll check through the files and see if I can see what's missing... xxx *From:* gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Terry [terrence...@gmail.com] *Sent:* 22 September 2010 11:55 *To:* Discussion list for GROMACS users *Subject:* Re: [gmx-users] Energy minimisation problems - coordinate file and topology file not matching. Hi, Natalie, Obviously, number of coordinates still doesn't match the topology file even you updated the topol.top *carefully*. Check the topol.top thoroughly or paste several line of your coordinate and topology files may be good ideas. Note that the topology file is lacking information for *28* atoms. Does that number remind you anything? Terry On Wed, Sep 22, 2010 at 6:42 PM, Natalie Stephenson natalie.stephen...@postgrad.manchester.ac.uk mailto:natalie.stephen...@postgrad.manchester.ac.uk wrote: Hi everyone, I was hoping you could clear up a problem I'm having when performing energy minimisation. I'm following the instructions from one of the tutorials (Justin's Umbrella Sampling) with my own protein, however, this time when I try to perform the energy minimisation it throws out this 'fatal error message' ... number of coordinates in coordinate file (nrr_solv_ions.gro, 33181) does not match topology (topol.top, 33153) I've been updating the topol.top file every time I've done something, so I'm not really sure what's happened. Can anyone throw some light on what I've gone wrong!! Thanks loads! Natalie -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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] Energy minimisation problems - coordinate file and topology file not matching.
Yeah ... hadn't realised they were there when I began the simulating Natalie xxx From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: 22 September 2010 13:37 To: Discussion list for GROMACS users Subject: Re: [gmx-users] Energy minimisation problems - coordinate file and topology file not matching. Natalie Stephenson wrote: Ok ... think I've worked out what's happened ... There were two 'SOL' groups. So when replacing solvent with ions it has added double the amount of ions to the topol.top file. Think I'll go back a couple of steps and try to sort out why there are two 'SOL' groups. Were there water molecules (i.e., from a crystal structure) in the initial structure passed to pdb2gmx? -Justin Thanks for the help! xxx *From:* gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Natalie Stephenson [natalie.stephen...@postgrad.manchester.ac.uk] *Sent:* 22 September 2010 13:02 *To:* Discussion list for GROMACS users *Subject:* RE: [gmx-users] Energy minimisation problems - coordinate file and topology file not matching. Thanks for your help Justin Terry I've been letting genion etc update it ... so there must be somewhere where i've missed it or something. I'll check through the files and see if I can see what's missing... xxx *From:* gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Terry [terrence...@gmail.com] *Sent:* 22 September 2010 11:55 *To:* Discussion list for GROMACS users *Subject:* Re: [gmx-users] Energy minimisation problems - coordinate file and topology file not matching. Hi, Natalie, Obviously, number of coordinates still doesn't match the topology file even you updated the topol.top *carefully*. Check the topol.top thoroughly or paste several line of your coordinate and topology files may be good ideas. Note that the topology file is lacking information for *28* atoms. Does that number remind you anything? Terry On Wed, Sep 22, 2010 at 6:42 PM, Natalie Stephenson natalie.stephen...@postgrad.manchester.ac.uk mailto:natalie.stephen...@postgrad.manchester.ac.uk wrote: Hi everyone, I was hoping you could clear up a problem I'm having when performing energy minimisation. I'm following the instructions from one of the tutorials (Justin's Umbrella Sampling) with my own protein, however, this time when I try to perform the energy minimisation it throws out this 'fatal error message' ... number of coordinates in coordinate file (nrr_solv_ions.gro, 33181) does not match topology (topol.top, 33153) I've been updating the topol.top file every time I've done something, so I'm not really sure what's happened. Can anyone throw some light on what I've gone wrong!! Thanks loads! Natalie -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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 -- 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] Energy minimisation of solvated protein - Tutorial
Hi Nayef, Can you - copy-paste the sequence of commands as you have typed them in (not as you think you typed them in or as they're given in the tutorial) - provide the output of 'tail 1qlz-water.gro' Cheers, Tsjerk On Mon, Jun 21, 2010 at 9:49 PM, Nayef Daher eltha...@ualberta.ca wrote: Hi, I have the same problem as listed below back in February. I am using the latest gromacs version (4.0.7) and tried the solution below by entering genbox -cp 1qlz-PBC.gro -cs spc216.gro -p 1qlz.top -o 1qlz-water.gro instead of making the output as pdb file. Yet the same result occurs with the same error message. One of the box lengths is smaller than twice the cut-off length. Please let me know what other options I can try. Thanks! nayef -- original message below -- Hi Anna, You should mention the version of Gromacs you're using. One of the versions did not write the box correctly to pdb files, which I think happened in your case. If you take as the solvation step genbox -cp 1qlz-PBC.gro -cs spc216.gro -p 1qlz.top -o 1qlz-water.gro instead of writing output to 1qlz-water.pdb, I think you should be fine. The reason for writing a .pdb file is the easier visualization with a multitude of programs. Thanks for your interest in the tutorial. Cheers, Tsjerk On Fri, Feb 26, 2010 at 1:27 PM, Anna Duncan anna.duncan at mrc-mbu.cam.ac.uk wrote: Hi, I've been trying to go through the 'Introduction to Molecular Dynamics Simulations and Analysis' tutorial written by Tsjerk Wassenaar, one of the tutorials listed on the GROMACS website. I've got to the stage where I am performing energy minimisation on my solvated protein but when I use grompp to create the .tpr file for mdrun, I get the error message: One of the box lengths is smaller than twice the cut-off length. Increase the box size or decrease rlist I am using the protein with pdb ID 1QLZ, one of the suggested structures for the tutorial and have so far carried out the following commands: % pdb2gmx -f 1qlz.pdb -o 1qlz.gro -p 1qlz.top -ignh % grompp -f minim.mdp -c 1qlz.gro -p 1qlz.top -o 1qlz-EM-vacuum.tpr % mdrun -v -deffnm 1qlz-EM-vacuum.tpr -c 1qlz-EM-vacuum.pdb % editconf -f 1qlz-EM-vacuum.pdb -o 1qlz-PBC.gro -bt dodecahedron -d 1.0 % genbox -cp 1qlz-PBC.gro -cs spc216.gro -p 1qlz.top -o 1qlz-water.pdb % grompp -v -f minim.mdp -c 1qlz-water.pdb -p 1qlz.top -o 1qlz-water.tpr % genion -s 1qlz-water.tpr -o 1qlz-solvated.pdb -conc 0.15 -neutral -pname NA+ -nname CL- % grompp -v -f minim_pbc.mdp -c 1qlz-solvated.pdb -p 1qlz.top -o 1qlz-EM-solvated.tpr after which I receive the error message. The minim_pbd.mdp file I use in the last grompp command is the same as minim.mdp used in previous grompp commands (the latter file I downloaded as part of the tutorial) except that the line 'pbc = no' has been replaced by 'pbc = xyz'. I have tried increasing the value of 'd' in the editconf command, to 2,3 and even 8 but this doesn't make any difference. (I have read that it is not a good idea to tamper with the cut-off values so have avoided doing that) The box vector lengths when d = 1.0 are all 7.10051, and rvdw, rcoulomb = 1.0 in mimim.mdp and minim_pbd.mdp, so I don't understand what is going wrong... Anna -- gmx-users mailing list gmx-users at gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-request at gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Energy minimisation of solvated protein - Tutorial
remember to change the pbc = xyz from pbc = no. lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Tsjerk Wassenaar [tsje...@gmail.com] Sent: Tuesday, June 22, 2010 12:04 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Energy minimisation of solvated protein - Tutorial Hi Nayef, Can you - copy-paste the sequence of commands as you have typed them in (not as you think you typed them in or as they're given in the tutorial) - provide the output of 'tail 1qlz-water.gro' Cheers, Tsjerk On Mon, Jun 21, 2010 at 9:49 PM, Nayef Daher eltha...@ualberta.ca wrote: Hi, I have the same problem as listed below back in February. I am using the latest gromacs version (4.0.7) and tried the solution below by entering genbox -cp 1qlz-PBC.gro -cs spc216.gro -p 1qlz.top -o 1qlz-water.gro instead of making the output as pdb file. Yet the same result occurs with the same error message. One of the box lengths is smaller than twice the cut-off length. Please let me know what other options I can try. Thanks! nayef -- original message below -- Hi Anna, You should mention the version of Gromacs you're using. One of the versions did not write the box correctly to pdb files, which I think happened in your case. If you take as the solvation step genbox -cp 1qlz-PBC.gro -cs spc216.gro -p 1qlz.top -o 1qlz-water.gro instead of writing output to 1qlz-water.pdb, I think you should be fine. The reason for writing a .pdb file is the easier visualization with a multitude of programs. Thanks for your interest in the tutorial. Cheers, Tsjerk On Fri, Feb 26, 2010 at 1:27 PM, Anna Duncan anna.duncan at mrc-mbu.cam.ac.uk wrote: Hi, I've been trying to go through the 'Introduction to Molecular Dynamics Simulations and Analysis' tutorial written by Tsjerk Wassenaar, one of the tutorials listed on the GROMACS website. I've got to the stage where I am performing energy minimisation on my solvated protein but when I use grompp to create the .tpr file for mdrun, I get the error message: One of the box lengths is smaller than twice the cut-off length. Increase the box size or decrease rlist I am using the protein with pdb ID 1QLZ, one of the suggested structures for the tutorial and have so far carried out the following commands: % pdb2gmx -f 1qlz.pdb -o 1qlz.gro -p 1qlz.top -ignh % grompp -f minim.mdp -c 1qlz.gro -p 1qlz.top -o 1qlz-EM-vacuum.tpr % mdrun -v -deffnm 1qlz-EM-vacuum.tpr -c 1qlz-EM-vacuum.pdb % editconf -f 1qlz-EM-vacuum.pdb -o 1qlz-PBC.gro -bt dodecahedron -d 1.0 % genbox -cp 1qlz-PBC.gro -cs spc216.gro -p 1qlz.top -o 1qlz-water.pdb % grompp -v -f minim.mdp -c 1qlz-water.pdb -p 1qlz.top -o 1qlz-water.tpr % genion -s 1qlz-water.tpr -o 1qlz-solvated.pdb -conc 0.15 -neutral -pname NA+ -nname CL- % grompp -v -f minim_pbc.mdp -c 1qlz-solvated.pdb -p 1qlz.top -o 1qlz-EM-solvated.tpr after which I receive the error message. The minim_pbd.mdp file I use in the last grompp command is the same as minim.mdp used in previous grompp commands (the latter file I downloaded as part of the tutorial) except that the line 'pbc = no' has been replaced by 'pbc = xyz'. I have tried increasing the value of 'd' in the editconf command, to 2,3 and even 8 but this doesn't make any difference. (I have read that it is not a good idea to tamper with the cut-off values so have avoided doing that) The box vector lengths when d = 1.0 are all 7.10051, and rvdw, rcoulomb = 1.0 in mimim.mdp and minim_pbd.mdp, so I don't understand what is going wrong... Anna -- gmx-users mailing listgmx-users at gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-request at gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http
Re: [gmx-users] Energy minimisation of solvated protein - Tutorial
Hi Anna, You should mention the version of Gromacs you're using. One of the versions did not write the box correctly to pdb files, which I think happened in your case. If you take as the solvation step genbox -cp 1qlz-PBC.gro -cs spc216.gro -p 1qlz.top -o 1qlz-water.gro instead of writing output to 1qlz-water.pdb, I think you should be fine. The reason for writing a .pdb file is the easier visualization with a multitude of programs. Thanks for your interest in the tutorial. Cheers, Tsjerk On Fri, Feb 26, 2010 at 1:27 PM, Anna Duncan anna.dun...@mrc-mbu.cam.ac.uk wrote: Hi, I've been trying to go through the 'Introduction to Molecular Dynamics Simulations and Analysis' tutorial written by Tsjerk Wassenaar, one of the tutorials listed on the GROMACS website. I've got to the stage where I am performing energy minimisation on my solvated protein but when I use grompp to create the .tpr file for mdrun, I get the error message: One of the box lengths is smaller than twice the cut-off length. Increase the box size or decrease rlist I am using the protein with pdb ID 1QLZ, one of the suggested structures for the tutorial and have so far carried out the following commands: % pdb2gmx -f 1qlz.pdb -o 1qlz.gro -p 1qlz.top -ignh % grompp -f minim.mdp -c 1qlz.gro -p 1qlz.top -o 1qlz-EM-vacuum.tpr % mdrun -v -deffnm 1qlz-EM-vacuum.tpr -c 1qlz-EM-vacuum.pdb % editconf -f 1qlz-EM-vacuum.pdb -o 1qlz-PBC.gro -bt dodecahedron -d 1.0 % genbox -cp 1qlz-PBC.gro -cs spc216.gro -p 1qlz.top -o 1qlz-water.pdb % grompp -v -f minim.mdp -c 1qlz-water.pdb -p 1qlz.top -o 1qlz-water.tpr % genion -s 1qlz-water.tpr -o 1qlz-solvated.pdb -conc 0.15 -neutral -pname NA+ -nname CL- % grompp -v -f minim_pbc.mdp -c 1qlz-solvated.pdb -p 1qlz.top -o 1qlz-EM-solvated.tpr after which I receive the error message. The minim_pbd.mdp file I use in the last grompp command is the same as minim.mdp used in previous grompp commands (the latter file I downloaded as part of the tutorial) except that the line 'pbc = no' has been replaced by 'pbc = xyz'. I have tried increasing the value of 'd' in the editconf command, to 2,3 and even 8 but this doesn't make any difference. (I have read that it is not a good idea to tamper with the cut-off values so have avoided doing that) The box vector lengths when d = 1.0 are all 7.10051, and rvdw, rcoulomb = 1.0 in mimim.mdp and minim_pbd.mdp, so I don't understand what is going wrong... Anna -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] energy minimisation of Si3N4 did not converge
Kothai Thiruvengadam wrote: Dear all, I am using MD simulation of a protein on Silicon nitride surface. The surface has been created using VMD and tcl script (ref. bionano tutorial).The protein+surface complex also has been generated using VMD.Using that PDB file I have done md simulation in gromacs. One itp file for silicon nitride has been developed using PRODRG server and included in the top file. But, during energy minimisation I got a message Steepest Descents did not converge to Fmax 8000 in 2001 steps. Potential Energy = -4.5347610e+06 Maximum force = 1.0913173e+05 on atom 7417 Norm of force = 2.8918979e+02 The EM ends without converging to Fmax. I put different values of Fmax and steps starts from 1000. But for Fmax 8000 and 2000 steps also I am getting the same message. What force field I can use for Silicon nitride surface? How can I rectify this error? The unmodified output of PRODRG often contains undesirable and inconsistent charges/charge groups (when compared to known functional groups in a given force field). Thus the topologies from PRODRG, while useful as a starting point, often require manual modification. In the case of something like Si3N4, you certainly have your work cut out for you. The Gromos96 force fields, like all of natively supported by Gromacs, were designed for simulations of biomolecules, so their application to other materials may or may not be straightforward. That doesn't mean you can't make it work, but you will probably have to go into the literature to see how people have come up with parameters for their materials, since Gromacs has certainly been used to simulate non-biological systems (CNT, silica, etc). -Justin - T.Kothai Centre for Biotechnology Anna University Chennai -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Energy Minimisation and Equilibration Problems
On Thursday, August 6, 2009 at 7:59:43 PM Nancy nancy5vi...@gmail.com wrote: I ran the minimisation, and mdrun gave the following last few lines of output: == Step=19990, Dmax= 7.8e-06 nm, Epot= -7.14922e+04 Fmax= 3.19585e+04, atom= 2395 Step=19992, Dmax= 4.7e-06 nm, Epot= -7.14924e+04 Fmax= 8.72456e+03, atom= 2395 Step=19993, Dmax= 5.6e-06 nm, Epot= -7.14927e+04 Fmax= 3.70693e+04, atom= 2395 Step=19994, Dmax= 6.8e-06 nm, Epot= -7.14929e+04 Fmax= 2.10513e+04, atom= 2395 Step=19995, Dmax= 8.1e-06 nm, Epot= -7.14929e+04 Fmax= 4.71234e+04, atom= 2395 Step=19996, Dmax= 9.7e-06 nm, Epot= -7.14931e+04 Fmax= 3.68827e+04, atom= 2395 Step=19998, Dmax= 5.8e-06 nm, Epot= -7.14933e+04 Fmax= 1.35461e+04, atom= 2395 Step=1, Dmax= 7.0e-06 nm, Epot= -7.14933e+04 Fmax= 4.77130e+04, atom= 2395 Step=2, Dmax= 8.4e-06 nm, Epot= -7.14936e+04 Fmax= 2.41860e+04, atom= 2395 writing lowest energy coordinates. Steepest Descents did not converge to Fmax 10 in 20001 steps. Potential Energy = -7.1493609e+04 Maximum force = 2.4185994e+04 on atom 2395 Norm of force = 8.1511212e+02 == As you can be seen, the forces still do not converge to Fmax 10, even after 20,000 steps. Does anyone know what the problem might be? The problem is my error in the specification of non-bonded interaction combination rules, FudgeLJ, and FudgeQQ for gromacs force fields. Line 7 of your file ffethanediol.itp currently reads: 1 2yes 0.5 0.83 This was taken from ambconv and is correct for amber and gaff force fields, but not for gromacs force fields, nor for OPLS-AA. Change line 7 of the file ffethanediol.itp to read: 1 1 no 1.0 1.0 The correction is in topolbuild 1.3 which is not yet released, but this error was not caught for the topolbuild 1.2 series. Quite frankly, I had forgotten that modification was made as I've been editing the set of tables needed to add OPLS-AA to the mix of force fields available. As a general note. For gromacs force field topologies generated with anything in the topolbuild 1.2 series, this edit to the itp file that specifies the defaults is required. Sincerely, -- Bruce D. Ray, Ph.D. Associate Scientist IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Energy Minimisation and Equilibration Problems
On Wednesday, August 5, 2009 at 6:03:51 PM, Nancy nancy5vi...@gmail.com wrote:
I am trying to run equilibration on my solvated ethylene glycol
(ethanediol) system. I started
with an ethanediol mol2 file from which
topolbuild generated various files. I used editconf
to enlarge to box
of the ethanediol.gro file:
$ editconf -f ethanediol.gro -o ethanediol_box.gro -box 5 5 5
and then I used genbox to solvate it:
$ genbox -cp ethanediol_box.gro -cs spc216.gro -shell 1 -o
ethanediol_solv.gro -p ethanediol.top
I ran energy minimisation on it:
$ grompp -f minim.mdp -c ethanediol_solv.gro -p ethanediol.top -o em.tpr
my minim.mdp file is:
==
define= -DFLEXIBLE
integrator= steep
emtol= 1000.0
emstep = 0.01
nsteps= 5000
nstlist= 1
ns_type= grid
rlist= 1.0
coulombtype= PME
rcoulomb= 1.0
rvdw= 1.3
pbc= xyz
pme_order= 4
constraints = none
nstxout= 1
nstvout= 1
nstenergy= 1
nstlog= 1
==
$ mdrun -v -deffnm em
and the energies converge (although I think that the values are still too
large for this system):
==
Steepest Descents converged to Fmax 1000 in 12 steps
Potential Energy = -1.1206108e+04
Maximum force = 9.4016180e+02 on atom 31
Norm of force = 3.4989252e+02
==
{remainder snipped}
The energies do seem large. What happens if you do energy minimization
with emtol = 10.0 ?
--
Bruce D. Ray, Ph.D.
Associate Scientist, and Operations Director
NMR Center
IUPUI
Physics Dept.
402 N. Blackford St.
Indianapolis, IN 46202-3273
From: Nancy nancy5vi...@gmail.com
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Wednesday, August 5, 2009 10:28:47 PM
Subject: [gmx-users] Energy Minimisation and Equilibration Problems
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Re: [gmx-users] Energy Minimisation and Equilibration Problems
The energies simply do not seem to come down any further within several
thousand steps.
I start with a .mol2 file which contains the structure of ethylene glycol
(ethanediol). These are the commands that I use to set up and run the
minimisation:
$ .../topolbuild1_2_1/src/topolbuild -n ethanediol -dir
.../topolbuild1_2_1/dat/gromacs -ff gmx53a6
the above command outputs the following files:
ethanediol.gro
ethanediol.log
ethanediolMOL.mol2
ethanediol.top
ffethanediol.itp
posreethanediol.itp
I then proceed to enlarge the box and solvate the molecule:
$ editconf -f ethanediol.gro -o ethanediol_box.gro -box 5 5 5
$ genbox -cp ethanediol_box.gro -cs spc216.gro -o ethanediol_box.gro -p
ethanediol.top -shell 1
I then use grompp to configure the minimisation:
$ grompp -f minim.mdp -c ethanediol_box.gro -p ethanediol.top -o em.tpr
This is my .mdp file for minimisation:
===
define= -DPOSRE
integrator= steep
emtol= 10.0
emstep = 0.01
nsteps= 2000
nstlist= 1
ns_type= grid
rlist= 1.0
coulombtype= PME
rcoulomb= 1.0
rvdw= 1.3
pbc= xyz
pme_order= 4
constraints = none
nstxout= 1
nstvout= 1
nstenergy= 1
nstlog= 1
nstcomm = 1
Tcoupl = no
Pcoupl = no
gen_vel = no
===
$ mdrun -v -deffnm em
the minimisation runs without error and these are the last few lines of
output:
===
Step= 1990, Dmax= 1.1e-05 nm, Epot= -1.76427e+04 Fmax= 1.25524e+04, atom=
304
Step= 1991, Dmax= 1.3e-05 nm, Epot= -1.76433e+04 Fmax= 3.13881e+04, atom=
484
Step= 1992, Dmax= 1.6e-05 nm, Epot= -1.76443e+04 Fmax= 2.11785e+04, atom=
484
Step= 1993, Dmax= 1.9e-05 nm, Epot= -1.76445e+04 Fmax= 4.22489e+04, atom=
484
Step= 1994, Dmax= 2.3e-05 nm, Epot= -1.76456e+04 Fmax= 3.33021e+04, atom=
484
Step= 1996, Dmax= 1.4e-05 nm, Epot= -1.76468e+04 Fmax= 1.26110e+04, atom=
304
Step= 1997, Dmax= 1.6e-05 nm, Epot= -1.76474e+04 Fmax= 3.81619e+04, atom=
484
Step= 1998, Dmax= 2.0e-05 nm, Epot= -1.76486e+04 Fmax= 2.68240e+04, atom=
484
Step= 2000, Dmax= 1.2e-05 nm, Epot= -1.76496e+04 Fmax= 1.26501e+04, atom=
304
writing lowest energy coordinates.
Steepest Descents did not converge to Fmax 10 in 2001 steps.
Potential Energy = -1.7649566e+04
Maximum force = 1.2650057e+04 on atom 30
Norm of force = 1.7544460e+03
===
If I proceed to equilibration after doing the above, the water molecules
simply fly apart (although not immediately). Additionally, it seems that
there are no interactions between the waters during equilibration.
I have tried to run the minimisation for a larger number of steps, but it
does not help. I have also tried to delete individual water molecules from
the structure files, but doing so simply causes the minimisation to fixate
on another two molecules. I am not sure what values of the energies are
reasonable for this system, and how to minimise it further. Please advise.
Thank you.
Nancy
On Thu, Aug 6, 2009 at 8:38 AM, Bruce D. Ray bruced...@yahoo.com wrote:
On Wednesday, August 5, 2009 at 6:03:51 PM, Nancy nancy5vi...@gmail.com
wrote:
I am trying to run equilibration on my solvated ethylene glycol
(ethanediol) system. I started
with an ethanediol mol2 file from which topolbuild generated various
files. I used editconf
to enlarge to box of the ethanediol.gro file:
$ editconf -f ethanediol.gro -o ethanediol_box.gro -box 5 5 5
and then I used genbox to solvate it:
$ genbox -cp ethanediol_box.gro -cs spc216.gro -shell 1 -o
ethanediol_solv.gro -p ethanediol.top
I ran energy minimisation on it:
$ grompp -f minim.mdp -c ethanediol_solv.gro -p ethanediol.top -o em.tpr
my minim.mdp file is:
==
define= -DFLEXIBLE
integrator= steep
emtol= 1000.0
emstep = 0.01
nsteps= 5000
nstlist= 1
ns_type= grid
rlist= 1.0
coulombtype= PME
rcoulomb= 1.0
rvdw= 1.3
pbc= xyz
pme_order= 4
constraints = none
nstxout= 1
nstvout= 1
nstenergy= 1
nstlog= 1
==
$ mdrun -v -deffnm em
and the energies converge (although I think that the values are still too
large for this system):
==
Steepest Descents converged to Fmax 1000 in 12 steps
Potential Energy = -1.1206108e+04
Maximum force = 9.4016180e+02 on atom 31
Norm of force = 3.4989252e+02
==
{remainder snipped}
The energies do seem large. What happens if you do energy minimization
with emtol = 10.0 ?
--
Bruce D. Ray, Ph.D.
Associate Scientist, and Operations Director
NMR Center
IUPUI
Physics Dept.
402 N. Blackford St.
Indianapolis, IN 46202-3273
*From:* Nancy
Re: [gmx-users] Energy Minimisation and Equilibration Problems
Nancy wrote:
snip
I then proceed to enlarge the box and solvate the molecule:
$ editconf -f ethanediol.gro -o ethanediol_box.gro -box 5 5 5
$ genbox -cp ethanediol_box.gro -cs spc216.gro -o ethanediol_box.gro -p
ethanediol.top -shell 1
So, instead of filling the box, you are simply specifying a shell of water
around your ethanediol? Have you tried just filling the box to see if this
works? I'm wondering if equilibration is failing due to vacuum space in the
cubic box you specify with edticonf. Is your ethanediol centered in the box?
You haven't used -c with editconf.
I then use grompp to configure the minimisation:
$ grompp -f minim.mdp -c ethanediol_box.gro -p ethanediol.top -o em.tpr
This is my .mdp file for minimisation:
===
define= -DPOSRE
Turn off position restraints. They don't serve much purpose in EM except to
potential interfere with the relaxation of bad geometry.
snip
If I proceed to equilibration after doing the above, the water molecules
simply fly apart (although not immediately). Additionally, it seems
that there are no interactions between the waters during equilibration.
Never plow ahead with such large forces. It is generally a waste of time. The
flying apart could be due to voids in the box, as I guessed above.
I have tried to run the minimisation for a larger number of steps, but
it does not help. I have also tried to delete individual water
molecules from the structure files, but doing so simply causes the
minimisation to fixate on another two molecules. I am not sure what
values of the energies are reasonable for this system, and how to
minimise it further. Please advise.
The potential energy will be proportional to the number of atoms in the system.
Without knowing that, we don't know what will be reasonable, either :) What
is for sure is that Fmax is far too large. Perhaps some of the above comments
will lead you in the right direction.
-Justin
Thank you.
Nancy
On Thu, Aug 6, 2009 at 8:38 AM, Bruce D. Ray bruced...@yahoo.com
mailto:bruced...@yahoo.com wrote:
On Wednesday, August 5, 2009 at 6:03:51 PM, Nancy
nancy5vi...@gmail.com mailto:nancy5vi...@gmail.com wrote:
I am trying to run equilibration on my solvated ethylene glycol
(ethanediol) system. I started
with an ethanediol mol2 file from which topolbuild generated
various files. I used editconf
to enlarge to box of the ethanediol.gro file:
$ editconf -f ethanediol.gro -o ethanediol_box.gro -box 5 5 5
and then I used genbox to solvate it:
$ genbox -cp ethanediol_box.gro -cs spc216.gro -shell 1 -o
ethanediol_solv.gro -p ethanediol.top
I ran energy minimisation on it:
$ grompp -f minim.mdp -c ethanediol_solv.gro -p ethanediol.top -o
em.tpr
my minim.mdp file is:
==
define= -DFLEXIBLE
integrator= steep
emtol= 1000.0
emstep = 0.01
nsteps= 5000
nstlist= 1
ns_type= grid
rlist= 1.0
coulombtype= PME
rcoulomb= 1.0
rvdw= 1.3
pbc= xyz
pme_order= 4
constraints = none
nstxout= 1
nstvout= 1
nstenergy= 1
nstlog= 1
==
$ mdrun -v -deffnm em
and the energies converge (although I think that the values are
still too large for this system):
==
Steepest Descents converged to Fmax 1000 in 12 steps
Potential Energy = -1.1206108e+04
Maximum force = 9.4016180e+02 on atom 31
Norm of force = 3.4989252e+02
==
{remainder snipped}
The energies do seem large. What happens if you do energy minimization
with emtol = 10.0 ?
--
Bruce D. Ray, Ph.D.
Associate Scientist, and Operations Director
NMR Center
IUPUI
Physics Dept.
402 N. Blackford St.
Indianapolis, IN 46202-3273
*From:* Nancy nancy5vi...@gmail.com mailto:nancy5vi...@gmail.com
*To:* Discussion list for GROMACS users gmx-users@gromacs.org
mailto:gmx-users@gromacs.org
*Sent:* Wednesday, August 5, 2009 10:28:47 PM
*Subject:* [gmx-users] Energy Minimisation and Equilibration
Problems
___
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Re: [gmx-users] Energy Minimisation and Equilibration Problems
On Thursday, August 6, 2009 at 11:58:20 AM, Nancy nancy5vi...@gmail.com wrote: The energies simply do not seem to come down any further within several thousand steps. I start with a .mol2 file which contains the structure of ethylene glycol (ethanediol). These are the commands that I use to set up and run the minimisation: $ .../topolbuild1_2_1/src/topolbuild -n ethanediol -dir .../topolbuild1_2_1/dat/gromacs -ff gmx53a6 the above command outputs the following files: ethanediol.gro ethanediol.log ethanediolMOL.mol2 ethanediol.top ffethanediol.itp posreethanediol.itp Those are the correct files to be generated for the topolbuild command given. Are the parameters blank in any of the lines in ethanediol.top? Are there any lines in ethanediol.log that do not involve nonpolar hydrogens that have asterisks instead of parameter values? I then proceed to enlarge the box and solvate the molecule: $ editconf -f ethanediol.gro -o ethanediol_box.gro -box 5 5 5 $ genbox -cp ethanediol_box.gro -cs spc216.gro -o ethanediol_box.gro -p ethanediol.top -shell 1 Is this a shell of solvent around the molecule rather than a box of solvent containing the molecule of interest? How is that to work with vacuum outside the shell? I then use grompp to configure the minimisation: $ grompp -f minim.mdp -c ethanediol_box.gro -p ethanediol.top -o em.tpr This is my .mdp file for minimisation: === define= -DPOSRE Why position restraints when doing energy minimization? integrator= steep emtol= 10.0 emstep = 0.01 nsteps= 2000 Why so few steps when the emtol is this small. For this emtol, I would expect to need 1 to 2 steps. nstlist= 1 ns_type= grid rlist= 1.0 coulombtype= PME rcoulomb= 1.0 rvdw= 1.3 pbc= xyz pme_order= 4 constraints = none nstxout= 1 nstvout= 1 nstenergy= 1 nstlog= 1 nstcomm = 1 Tcoupl = no Pcoupl = no gen_vel = no === I've been told that the last three lines are not needed for energy minimization. $ mdrun -v -deffnm em the minimisation runs without error and these are the last few lines of output: === Step= 1990, Dmax= 1.1e-05 nm, Epot= -1.76427e+04 Fmax= 1.25524e+04, atom= 304 Step= 1991, Dmax= 1.3e-05 nm, Epot= -1.76433e+04 Fmax= 3.13881e+04, atom= 484 Step= 1992, Dmax= 1.6e-05 nm, Epot= -1.76443e+04 Fmax= 2.11785e+04, atom= 484 Step= 1993, Dmax= 1.9e-05 nm, Epot= -1.76445e+04 Fmax= 4.22489e+04, atom= 484 Step= 1994, Dmax= 2.3e-05 nm, Epot= -1.76456e+04 Fmax= 3.33021e+04, atom= 484 Step= 1996, Dmax= 1.4e-05 nm, Epot= -1.76468e+04 Fmax= 1.26110e+04, atom= 304 Step= 1997, Dmax= 1.6e-05 nm, Epot= -1.76474e+04 Fmax= 3.81619e+04, atom= 484 Step= 1998, Dmax= 2.0e-05 nm, Epot= -1.76486e+04 Fmax= 2.68240e+04, atom= 484 Step= 2000, Dmax= 1.2e-05 nm, Epot= -1.76496e+04 Fmax= 1.26501e+04, atom= 304 writing lowest energy coordinates. Steepest Descents did not converge to Fmax 10 in 2001 steps. Potential Energy = -1.7649566e+04 Maximum force = 1.2650057e+04 on atom 30 Norm of force = 1.7544460e+03 === If I proceed to equilibration after doing the above, the water molecules simply fly apart (although not immediately). Additionally, it seems that there are no interactions between the waters during equilibration. Really no point in proceeding further until the energy minimization issues are solved. I have tried to run the minimisation for a larger number of steps, but it does not help. I have also tried to delete individual water molecules from the structure files, but doing so simply causes the minimisation to fixate on another two molecules. I am not sure what values of the energies are reasonable for this system, and how to minimise it further. Please advise. I've never used the -shell with genbox and don't know what effect that would have on energy minimization. -- Bruce D. Ray, Ph.D. Associate Scientist, and Operations Director NMR Center IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Energy Minimisation and Equilibration Problems
I have attempted to perform energy minimisation from scratch again, and these are the commands that I am using to do so: $ .../topolbuild1_2_1/src/topolbuild -n ethanediol -dir .../topolbuild1_2_1/dat/gromacs -ff gmx53a6 which generates the files: ethanediol.gro ethanediol.log ethanediolMOL.mol2 ethanediol.top ffethanediol.itp posreethanediol.itp in the ethanediol.log file I noticed the following lines with asterisks: Angles Force Field Results AngleAtomsforceangle method measured 1 H12- C1- H11 ** ** **109.403 2C2- C1- H11 ** ** **109.456 3O1- C1- H11 ** ** **109.438 4C2- C1- H12 ** ** **109.537 5O1- C1- H12 ** ** **109.468 6O1- C1- C2320.0 109.501109.526 7C1- C2- O2320.0 109.501109.526 8C1- C2- H22 ** ** **109.453 9C1- C2- H21 ** ** **109.537 10 H22- C2- O2 ** ** **109.439 11 H21- C2- O2 ** ** **109.468 12C2- O2- HO2450.0 109.501106.864 13 H21- C2- H22 ** ** **109.404 14C1- O1- HO1450.0 109.501106.864 I then enlarge the box and solvate the molecule: $ editconf -f ethanediol.gro -o ethanediol_box.gro -box 3 3 3 -c $ genbox -cp ethanediol_box.gro -cs spc216.gro -o ethanediol_solv.gro -p ethanediol.top -box 3 3 3 There are 2679 atoms (891 waters and 1 ethanediol). I then configure the minimisation with grompp: $ grompp -f minim.mdp -c ethanediol_solv.gro -p ethanediol.top -o em.tpr using the following .mdp file: define= -DFLEXIBLE integrator= steep emtol= 10.0 emstep = 0.1 nsteps= 15000 nstlist= 1 ns_type= grid rlist= 1.0 coulombtype= PME rcoulomb_switch= 1.0 rvdw_switch= 1.3 pbc= xyz pme_order= 4 constraints = none nstxout= 1 nstvout= 1 nstenergy= 1 nstlog= 1 nstcomm = 1 Tcoupl = no Pcoupl = no gen_vel = no I then run the simulation for 15,000 steps: $ mdrun -v -deffnm em the last few lines of output are as follows: Step=14991, Dmax= 5.3e-06 nm, Epot= -6.24538e+04 Fmax= 2.50258e+04, atom= 2397 Step=14992, Dmax= 6.4e-06 nm, Epot= -6.24539e+04 Fmax= 3.52982e+04, atom= 1171 Step=14993, Dmax= 7.6e-06 nm, Epot= -6.24540e+04 Fmax= 3.71731e+04, atom= 2397 Step=14994, Dmax= 9.2e-06 nm, Epot= -6.24540e+04 Fmax= 4.93409e+04, atom= 1171 Step=14995, Dmax= 1.1e-05 nm, Epot= -6.24541e+04 Fmax= 5.53109e+04, atom= 2397 Step=14997, Dmax= 6.6e-06 nm, Epot= -6.24546e+04 Fmax= 8.50832e+03, atom= 1171 Step=14998, Dmax= 7.9e-06 nm, Epot= -6.24547e+04 Fmax= 6.37691e+04, atom= 2397 Step=14999, Dmax= 9.5e-06 nm, Epot= -6.24553e+04 Fmax= 2.67488e+04, atom= 1171 Step=15000, Dmax= 1.1e-05 nm, Epot= -6.24548e+04 Fmax= 8.09451e+04, atom= 2397 writing lowest energy coordinates. Steepest Descents did not converge to Fmax 10 in 15001 steps. Potential Energy = -6.2455254e+04 Maximum force = 2.6748828e+04 on atom 1171 Norm of force = 9.5851715e+02 After viewing the trajectory with ngmx, I noticed that most of the motion of the water molecules occurs within the first 50 picoseconds. Please advise on how to further minimise this system. Thank you. Nancy On Thu, Aug 6, 2009 at 2:23 PM, Bruce D. Ray bruced...@yahoo.com wrote: On Thursday, August 6, 2009 at 11:58:20 AM, Nancy nancy5vi...@gmail.com wrote: The energies simply do not seem to come down any further within several thousand steps. I start with a .mol2 file which contains the structure of ethylene glycol (ethanediol). These are the commands that I use to set up and run the minimisation: $ .../topolbuild1_2_1/src/topolbuild -n ethanediol -dir .../topolbuild1_2_1/dat/gromacs -ff gmx53a6 the above command outputs the following files: ethanediol.gro ethanediol.log ethanediolMOL.mol2 ethanediol.top ffethanediol.itp posreethanediol.itp Those are the correct files to be generated for the topolbuild command given. Are the parameters blank in any of the lines in ethanediol.top? Are there any lines in ethanediol.log that do not involve nonpolar hydrogens that have asterisks instead of parameter values? I then proceed to enlarge the box and solvate the molecule: $ editconf -f ethanediol.gro -o ethanediol_box.gro -box 5 5 5 $ genbox -cp ethanediol_box.gro -cs spc216.gro -o ethanediol_box.gro -p ethanediol.top -shell 1 Is this a shell of solvent around the molecule
Re: [gmx-users] Energy Minimisation and Equilibration Problems
On Thursday, August 6, 2009 at 4:08:18 PM, Nancy nancy5vi...@gmail.com wrote: I have attempted to perform energy minimisation from scratch again, and these are the commands that I am using to do so: $ .../topolbuild1_2_1/src/topolbuild -n ethanediol -dir .../topolbuild1_2_1/dat/gromacs -ff gmx53a6 which generates the files: ethanediol.gro ethanediol.log ethanediolMOL.mol2 ethanediol.top ffethanediol.itp posreethanediol.itp in the ethanediol.log file I noticed the following lines with asterisks: Angles Force Field Results AngleAtomsforceangle method measured 1 H12- C1- H11 ** ** **109.403 2C2- C1- H11 ** ** **109.456 3O1- C1- H11 ** ** **109.438 4C2- C1- H12 ** ** **109.537 5O1- C1- H12 ** ** **109.468 6O1- C1- C2320.0 109.501109.526 7C1- C2- O2320.0 109.501109.526 8C1- C2- H22 ** ** **109.453 9C1- C2- H21 ** ** **109.537 10 H22- C2- O2 ** ** **109.439 11 H21- C2- O2 ** ** **109.468 12C2- O2- HO2450.0 109.501106.864 13 H21- C2- H22 ** ** **109.404 14C1- O1- HO1450.0 109.501106.864 These are fine. Only the nonpolar hydrogens lack parameters and they are removed from consideration in the final topology because this is a united atoms model force field. I then enlarge the box and solvate the molecule: $ editconf -f ethanediol.gro -o ethanediol_box.gro -box 3 3 3 -c $ genbox -cp ethanediol_box.gro -cs spc216.gro -o ethanediol_solv.gro -p ethanediol.top -box 3 3 3 There are 2679 atoms (891 waters and 1 ethanediol). I then configure the minimisation with grompp: $ grompp -f minim.mdp -c ethanediol_solv.gro -p ethanediol.top -o em.tpr using the following .mdp file: define= -DFLEXIBLE Just out of curiosity, why are you defining flexible waters at this point? integrator= steep emtol= 10.0 emstep = 0.1 nsteps= 15000 nstlist= 1 ns_type= grid rlist= 1.0 coulombtype= PME rcoulomb_switch= 1.0 rvdw_switch= 1.3 pbc= xyz pme_order= 4 constraints = none nstxout= 1 nstvout= 1 nstenergy= 1 nstlog= 1 nstcomm = 1 Tcoupl = no Pcoupl = no gen_vel = no I then run the simulation for 15,000 steps: $ mdrun -v -deffnm em the last few lines of output are as follows: Step=14991, Dmax= 5.3e-06 nm, Epot= -6.24538e+04 Fmax= 2.50258e+04, atom= 2397 Step=14992, Dmax= 6.4e-06 nm, Epot= -6.24539e+04 Fmax= 3.52982e+04, atom= 1171 Step=14993, Dmax= 7.6e-06 nm, Epot= -6.24540e+04 Fmax= 3.71731e+04, atom= 2397 Step=14994, Dmax= 9.2e-06 nm, Epot= -6.24540e+04 Fmax= 4.93409e+04, atom= 1171 Step=14995, Dmax= 1.1e-05 nm, Epot= -6.24541e+04 Fmax= 5.53109e+04, atom= 2397 Step=14997, Dmax= 6.6e-06 nm, Epot= -6.24546e+04 Fmax= 8.50832e+03, atom= 1171 Step=14998, Dmax= 7.9e-06 nm, Epot= -6.24547e+04 Fmax= 6.37691e+04, atom= 2397 Step=14999, Dmax= 9.5e-06 nm, Epot= -6.24553e+04 Fmax= 2.67488e+04, atom= 1171 Step=15000, Dmax= 1.1e-05 nm, Epot= -6.24548e+04 Fmax= 8.09451e+04, atom= 2397 writing lowest energy coordinates. Steepest Descents did not converge to Fmax 10 in 15001 steps. Potential Energy = -6.2455254e+04 Maximum force = 2.6748828e+04 on atom 1171 Norm of force = 9.5851715e+02 After viewing the trajectory with ngmx, I noticed that most of the motion of the water molecules occurs within the first 50 picoseconds. Please advise on how to further minimise this system. I downloaded NSC93876 ethylene glycol as a Sybyl (.sy2) file from NCI, processed it with dos2unix, added the missing@TRIPOS last line, and named it ethylene_glycol.mol2 Charge information is absent on this file as downloaded, and I did not do anything to account for charges. This may make my results less than useful. I then ran the following commands: /usr/bdray/bin/topolbuild1_3 -dir /usr/bdray/tables -ff gmx53a6 -n glycol/ethylene_glycol editconf -f ethylene_glycol.gro -o ethanediol_box.gro -box 3 3 3 -c genbox -cp ethanediol_box.gro -cs spc216.gro -o ethanediol_solv.gro -p ethanediol.top -box 3 3 3 grompp -f em.mdp -c ethanediol_solv.gro -p ethanediol.top -o em.tpr File em.mdp includes: constraints = none integrator = steep nsteps
Re: [gmx-users] Energy Minimisation and Equilibration Problems
I ran the minimisation, and mdrun gave the following last few lines of output: == Step=19990, Dmax= 7.8e-06 nm, Epot= -7.14922e+04 Fmax= 3.19585e+04, atom= 2395 Step=19992, Dmax= 4.7e-06 nm, Epot= -7.14924e+04 Fmax= 8.72456e+03, atom= 2395 Step=19993, Dmax= 5.6e-06 nm, Epot= -7.14927e+04 Fmax= 3.70693e+04, atom= 2395 Step=19994, Dmax= 6.8e-06 nm, Epot= -7.14929e+04 Fmax= 2.10513e+04, atom= 2395 Step=19995, Dmax= 8.1e-06 nm, Epot= -7.14929e+04 Fmax= 4.71234e+04, atom= 2395 Step=19996, Dmax= 9.7e-06 nm, Epot= -7.14931e+04 Fmax= 3.68827e+04, atom= 2395 Step=19998, Dmax= 5.8e-06 nm, Epot= -7.14933e+04 Fmax= 1.35461e+04, atom= 2395 Step=1, Dmax= 7.0e-06 nm, Epot= -7.14933e+04 Fmax= 4.77130e+04, atom= 2395 Step=2, Dmax= 8.4e-06 nm, Epot= -7.14936e+04 Fmax= 2.41860e+04, atom= 2395 writing lowest energy coordinates. Steepest Descents did not converge to Fmax 10 in 20001 steps. Potential Energy = -7.1493609e+04 Maximum force = 2.4185994e+04 on atom 2395 Norm of force = 8.1511212e+02 == As you can be seen, the forces still do not converge to Fmax 10, even after 20,000 steps. Does anyone know what the problem might be? Thanks, Nancy On Thu, Aug 6, 2009 at 6:48 PM, Bruce D. Ray bruced...@yahoo.com wrote: On Thursday, August 6, 2009 at 4:08:18 PM, Nancy nancy5vi...@gmail.com wrote: I have attempted to perform energy minimisation from scratch again, and these are the commands that I am using to do so: $ .../topolbuild1_2_1/src/topolbuild -n ethanediol -dir .../topolbuild1_2_1/dat/gromacs -ff gmx53a6 which generates the files: ethanediol.gro ethanediol.log ethanediolMOL.mol2 ethanediol.top ffethanediol.itp posreethanediol.itp in the ethanediol.log file I noticed the following lines with asterisks: Angles Force Field Results AngleAtomsforceangle method measured 1 H12- C1- H11 ** ** **109.403 2C2- C1- H11 ** ** **109.456 3O1- C1- H11 ** ** **109.438 4C2- C1- H12 ** ** **109.537 5O1- C1- H12 ** ** **109.468 6O1- C1- C2320.0 109.501109.526 7C1- C2- O2320.0 109.501109.526 8C1- C2- H22 ** ** **109.453 9C1- C2- H21 ** ** **109.537 10 H22- C2- O2 ** ** **109.439 11 H21- C2- O2 ** ** **109.468 12C2- O2- HO2450.0 109.501106.864 13 H21- C2- H22 ** ** **109.404 14C1- O1- HO1450.0 109.501106.864 These are fine. Only the nonpolar hydrogens lack parameters and they are removed from consideration in the final topology because this is a united atoms model force field. I then enlarge the box and solvate the molecule: $ editconf -f ethanediol.gro -o ethanediol_box.gro -box 3 3 3 -c $ genbox -cp ethanediol_box.gro -cs spc216.gro -o ethanediol_solv.gro -p ethanediol.top -box 3 3 3 There are 2679 atoms (891 waters and 1 ethanediol). I then configure the minimisation with grompp: $ grompp -f minim.mdp -c ethanediol_solv.gro -p ethanediol.top -o em.tpr using the following .mdp file: define= -DFLEXIBLE Just out of curiosity, why are you defining flexible waters at this point? integrator= steep emtol= 10.0 emstep = 0.1 nsteps= 15000 nstlist= 1 ns_type= grid rlist= 1.0 coulombtype= PME rcoulomb_switch= 1.0 rvdw_switch= 1.3 pbc= xyz pme_order= 4 constraints = none nstxout= 1 nstvout= 1 nstenergy= 1 nstlog= 1 nstcomm = 1 Tcoupl = no Pcoupl = no gen_vel = no I then run the simulation for 15,000 steps: $ mdrun -v -deffnm em the last few lines of output are as follows: Step=14991, Dmax= 5.3e-06 nm, Epot= -6.24538e+04 Fmax= 2.50258e+04, atom= 2397 Step=14992, Dmax= 6.4e-06 nm, Epot= -6.24539e+04 Fmax= 3.52982e+04, atom= 1171 Step=14993, Dmax= 7.6e-06 nm, Epot= -6.24540e+04 Fmax= 3.71731e+04, atom= 2397 Step=14994, Dmax= 9.2e-06 nm, Epot= -6.24540e+04 Fmax= 4.93409e+04, atom= 1171 Step=14995, Dmax= 1.1e-05 nm, Epot= -6.24541e+04 Fmax= 5.53109e+04, atom= 2397 Step=14997, Dmax= 6.6e-06 nm, Epot= -6.24546e+04 Fmax= 8.50832e+03, atom= 1171 Step=14998, Dmax= 7.9e-06 nm, Epot= -6.24547e+04 Fmax= 6.37691e+04, atom= 2397 Step=14999, Dmax= 9.5e-06 nm, Epot= -6.24553e+04 Fmax=
Re: [gmx-users] Energy Minimisation and Equilibration Problems
Nancy wrote: I ran the minimisation, and mdrun gave the following last few lines of output: == Step=19990, Dmax= 7.8e-06 nm, Epot= -7.14922e+04 Fmax= 3.19585e+04, atom= 2395 Step=19992, Dmax= 4.7e-06 nm, Epot= -7.14924e+04 Fmax= 8.72456e+03, atom= 2395 Step=19993, Dmax= 5.6e-06 nm, Epot= -7.14927e+04 Fmax= 3.70693e+04, atom= 2395 Step=19994, Dmax= 6.8e-06 nm, Epot= -7.14929e+04 Fmax= 2.10513e+04, atom= 2395 Step=19995, Dmax= 8.1e-06 nm, Epot= -7.14929e+04 Fmax= 4.71234e+04, atom= 2395 Step=19996, Dmax= 9.7e-06 nm, Epot= -7.14931e+04 Fmax= 3.68827e+04, atom= 2395 Step=19998, Dmax= 5.8e-06 nm, Epot= -7.14933e+04 Fmax= 1.35461e+04, atom= 2395 Step=1, Dmax= 7.0e-06 nm, Epot= -7.14933e+04 Fmax= 4.77130e+04, atom= 2395 Step=2, Dmax= 8.4e-06 nm, Epot= -7.14936e+04 Fmax= 2.41860e+04, atom= 2395 writing lowest energy coordinates. Steepest Descents did not converge to Fmax 10 in 20001 steps. Potential Energy = -7.1493609e+04 Maximum force = 2.4185994e+04 on atom 2395 Norm of force = 8.1511212e+02 == As you can be seen, the forces still do not converge to Fmax 10, even after 20,000 steps. Does anyone know what the problem might be? No. You have to look at the structure and the simulation box and see if there's anything unrealistic. That's tedious and time-consuming, but if you're aware there's a problem, you need to do that. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Energy Minimisation and Equilibration Problems
Have you managed to minimise a single molecule? Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Energy Minimisation Values
Nancy wrote: Hello, I was trying to run equilibration on my solvated ethylene glycol system. However, the system seems to be exploding. I believe this is due to inadequate energy minimisation, however, I am unable to minimise my system any further. I am using the following .mdp file minim.mdp for minimsation: == define= -DFLEXIBLE integrator= steep emtol= 1000.0 emstep = 0.5 nsteps= 1000 nstlist= 1 ns_type= grid rlist= 1.0 coulombtype= PME rcoulomb= 1.0 rvdw= 1.3 pbc= xyz pme_order= 4 constraints = none == I process it with grompp, where ethanediol_solv.gro is the solvated system, and ethanediol.top is the topolgy generated with topolbuild: $ grompp -f minim.mdp -c ethanediol_solv.gro -p ethanediol.top -o em.tpr I then run it: $ mdrun -v -deffnm em mdrun outputs the following information: == Steepest Descents did not converge to Fmax 1000 in 1001 steps. Potential Energy = -6.7546914e+03 Maximum force = 2.7262363e+04 on atom 34 Norm of force = 2.5032930e+03 == I have viewed the output trajectory of the minimisation and I can see that the waters do not move much. I am wondering if there is a way to let solvent water molecules move about during minimsation, and/or how to remove some of them. I am also unsure what value of emtol is reasonable for this type of small system. I think this is the root of your problem. The maximum force is far too high. Decrease your value of emstep (the default of 0.01 is generally fine), and try again. You will not likely see large changes over the course of the trajectory. EM makes small changes to optimize geometry, hydrogen bonding, etc. There are no dynamics (remember that EM is essentially conducted at 0 K). -Justin Please advise Thanks Nancy ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Energy Minimisation Values
I tried decreasing emstep, and also tried increasing the number of steps, but I still get the following output from mdrun: == Steepest Descents did not converge to Fmax 1000 in 5001 steps. Potential Energy = -6.9329155e+03 Maximum force = 2.1965221e+04 on atom 39 Norm of force = 2.1487129e+03 == Please advise on how to further decrease the forces. Thanks, Nancy On Wed, Aug 5, 2009 at 6:08 PM, Justin A. Lemkul jalem...@vt.edu wrote: Nancy wrote: Hello, I was trying to run equilibration on my solvated ethylene glycol system. However, the system seems to be exploding. I believe this is due to inadequate energy minimisation, however, I am unable to minimise my system any further. I am using the following .mdp file minim.mdp for minimsation: == define= -DFLEXIBLE integrator= steep emtol= 1000.0 emstep = 0.5 nsteps= 1000 nstlist= 1 ns_type= grid rlist= 1.0 coulombtype= PME rcoulomb= 1.0 rvdw= 1.3 pbc= xyz pme_order= 4 constraints = none == I process it with grompp, where ethanediol_solv.gro is the solvated system, and ethanediol.top is the topolgy generated with topolbuild: $ grompp -f minim.mdp -c ethanediol_solv.gro -p ethanediol.top -o em.tpr I then run it: $ mdrun -v -deffnm em mdrun outputs the following information: == Steepest Descents did not converge to Fmax 1000 in 1001 steps. Potential Energy = -6.7546914e+03 Maximum force = 2.7262363e+04 on atom 34 Norm of force = 2.5032930e+03 == I have viewed the output trajectory of the minimisation and I can see that the waters do not move much. I am wondering if there is a way to let solvent water molecules move about during minimsation, and/or how to remove some of them. I am also unsure what value of emtol is reasonable for this type of small system. I think this is the root of your problem. The maximum force is far too high. Decrease your value of emstep (the default of 0.01 is generally fine), and try again. You will not likely see large changes over the course of the trajectory. EM makes small changes to optimize geometry, hydrogen bonding, etc. There are no dynamics (remember that EM is essentially conducted at 0 K). -Justin Please advise Thanks Nancy ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Energy Minimisation Values
On Wednesday, August 5, 2009 at 6:03:51 PM, Nancy nancy5vi...@gmail.com wrote: I was trying to run equilibration on my solvated ethylene glycol system. However, the system seems to be exploding. I believe this is due to inadequate energy minimisation, however, I am unable to minimise my system any further. I am using the following .mdp file minim.mdp for minimsation: == define= -DFLEXIBLE integrator= steep emtol= 1000.0 emstep = 0.5 nsteps= 1000 I use more steps than 1000 (may want 1) with: emstep = 0.01 nstcomm= 1 Tcoupl = no Pcoupl = no gen_vel = no nstlist= 1 ns_type= grid rlist= 1.0 coulombtype= PME rcoulomb= 1.0 rvdw= 1.3 pbc= xyz pme_order= 4 constraints = none == I process it with grompp, where ethanediol_solv.gro is the solvated system, and ethanediol.top is the topolgy generated with topolbuild: $ grompp -f minim.mdp -c ethanediol_solv.gro -p ethanediol.top -o em.tpr I then run it: $ mdrun -v -deffnm em mdrun outputs the following information: == Steepest Descents did not converge to Fmax 1000 in 1001 steps. Potential Energy = -6.7546914e+03 Maximum force = 2.7262363e+04 on atom 34 Norm of force = 2.5032930e+03 == I have viewed the output trajectory of the minimisation and I can see that the waters do not move much. I am wondering if there is a way to let solvent water molecules move about during minimsation, and/or how to remove some of them. I am also unsure what value of emtol is reasonable for this type of small system. I use the same value of emtol, but that's just based on examples I've seen where others have used that value. -- Bruce D. Ray, Ph.D. Associate Scientist, and Operations Director NMR Center IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 From: Nancy nancy5vi...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, August 5, 2009 6:03:51 PM Subject: [gmx-users] Energy Minimisation Values ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Energy Minimisation Values
Nancy wrote: I tried decreasing emstep, and also tried increasing the number of steps, but I still get the following output from mdrun: == Steepest Descents did not converge to Fmax 1000 in 5001 steps. Potential Energy = -6.9329155e+03 Maximum force = 2.1965221e+04 on atom 39 Norm of force = 2.1487129e+03 == Please advise on how to further decrease the forces. Figure out what's pushing on atom 39 to generate such a huge force. How to resolve the problem depends on what's happening. If it's just a poorly-placed water molecule, you can try deleting that water molecule and trying again. Beyond that, it will depend on what you find. -Justin Thanks, Nancy On Wed, Aug 5, 2009 at 6:08 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Nancy wrote: Hello, I was trying to run equilibration on my solvated ethylene glycol system. However, the system seems to be exploding. I believe this is due to inadequate energy minimisation, however, I am unable to minimise my system any further. I am using the following .mdp file minim.mdp for minimsation: == define= -DFLEXIBLE integrator= steep emtol= 1000.0 emstep = 0.5 nsteps= 1000 nstlist= 1 ns_type= grid rlist= 1.0 coulombtype= PME rcoulomb= 1.0 rvdw= 1.3 pbc= xyz pme_order= 4 constraints = none == I process it with grompp, where ethanediol_solv.gro is the solvated system, and ethanediol.top is the topolgy generated with topolbuild: $ grompp -f minim.mdp -c ethanediol_solv.gro -p ethanediol.top -o em.tpr I then run it: $ mdrun -v -deffnm em mdrun outputs the following information: == Steepest Descents did not converge to Fmax 1000 in 1001 steps. Potential Energy = -6.7546914e+03 Maximum force = 2.7262363e+04 on atom 34 Norm of force = 2.5032930e+03 == I have viewed the output trajectory of the minimisation and I can see that the waters do not move much. I am wondering if there is a way to let solvent water molecules move about during minimsation, and/or how to remove some of them. I am also unsure what value of emtol is reasonable for this type of small system. I think this is the root of your problem. The maximum force is far too high. Decrease your value of emstep (the default of 0.01 is generally fine), and try again. You will not likely see large changes over the course of the trajectory. EM makes small changes to optimize geometry, hydrogen bonding, etc. There are no dynamics (remember that EM is essentially conducted at 0 K). -Justin Please advise Thanks Nancy ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at
Re: [gmx-users] Energy Minimisation Values
Bruce D. Ray wrote: On Wednesday, August 5, 2009 at 6:03:51 PM, Nancy nancy5vi...@gmail.com wrote: I was trying to run equilibration on my solvated ethylene glycol system. However, the system seems to be exploding. I believe this is due to inadequate energy minimisation, however, I am unable to minimise my system any further. I am using the following .mdp file minim.mdp for minimsation: == define= -DFLEXIBLE integrator= steep emtol= 1000.0 emstep = 0.5 nsteps= 1000 I use more steps than 1000 (may want 1) with: emstep = 0.01 nstcomm= 1 Tcoupl = no Pcoupl = no gen_vel = no These last three are not relevant for energy minimization. There are no velocities, so they can't be generated, and thus there's no temperature or pressure. nstcomm is probably moot or ignored. Mark nstlist= 1 ns_type= grid rlist= 1.0 coulombtype= PME rcoulomb= 1.0 rvdw= 1.3 pbc= xyz pme_order= 4 constraints = none == I process it with grompp, where ethanediol_solv.gro is the solvated system, and ethanediol.top is the topolgy generated with topolbuild: $ grompp -f minim.mdp -c ethanediol_solv.gro -p ethanediol.top -o em.tpr I then run it: $ mdrun -v -deffnm em mdrun outputs the following information: == Steepest Descents did not converge to Fmax 1000 in 1001 steps. Potential Energy = -6.7546914e+03 Maximum force = 2.7262363e+04 on atom 34 Norm of force = 2.5032930e+03 == I have viewed the output trajectory of the minimisation and I can see that the waters do not move much. I am wondering if there is a way to let solvent water molecules move about during minimsation, and/or how to remove some of them. I am also unsure what value of emtol is reasonable for this type of small system. I use the same value of emtol, but that's just based on examples I've seen where others have used that value. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Energy Minimisation and Equilibration Problems
Nancy wrote: Hello, I am trying to run equilibration on my solvated ethylene glycol (ethanediol) system. I started with an ethanediol mol2 file from which topolbuild generated various files. I used editconf to enlarge to box of the ethanediol.gro file: $ editconf -f ethanediol.gro -o ethanediol_box.gro -box 5 5 5 and then I used genbox to solvate it: $ genbox -cp ethanediol_box.gro -cs spc216.gro -shell 1 -o ethanediol_solv.gro -p ethanediol.top I ran energy minimisation on it: $ grompp -f minim.mdp -c ethanediol_solv.gro -p ethanediol.top -o em.tpr my minim.mdp file is: snip and the energies converge (although I think that the values are still too large for this system): == Steepest Descents converged to Fmax 1000 in 12 steps Potential Energy = -1.1206108e+04 Maximum force = 9.4016180e+02 on atom 31 Norm of force = 3.4989252e+02 == This all seems reasonable to me. snip nsteps= 5000 dt= 0.0002 As I said before, 1 ps is too short to be meaningful for just about every system. rvdw= 1.3 Also, if using Gromos96, this value of rvdw is not strictly correct for this force field. the system blows up. Addtionally, the structure of the solute is incorrect (all atoms are bonded to each other). Are you still getting LINCS warnings? If so, try constraints = all-bonds instead of constraints = all-angles. With respect to the bonds they are simply an artefact of whatever visualization software you are using. Bonds are not formed and broken in classical MD. Again I ask, when looking at the trajectory, are you compensating for periodic boundary conditions properly using trjconv? -Justin Please advise on how to minimise such a system further, and as to why the equilibration is so unstable. Thank you. Nancy ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Energy Minimisation and Equilibration Problems
Maximum force = 9.4016180e+02 on atom 31 As has already been suggested, have you looked at the atoms listed as having the maximum force to see why? Addtionally, the structure of the solute is incorrect (all atoms are bonded to each other). How are you visualising it? If using VMD, then it guesses the bonding based on how far things are apart. If your atoms are too close, then will appear like all bonded to each other. Sounds to me like there is something wrong with the box / molecule. Start with a box with only one molecule in it, see if you can equilibrate etc. Then build up from there so you can pin down where the issue is. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Energy minimisation problem
You should also do some MD and then look at your molecule and trajectory (bond
lengths, angles, etc.), if it becomes distorted. If that is the case, there
might be something wrong with your topology.
If everything is fine, you should use the energy minimised molecule to build
the box, EM again and then MD.
Not sure about the energies. Maybe they should be negative ?
Andreas
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
On Behalf Of Jussi Lehtola
Sent: 14 May 2008 04:28
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] Energy minimisation problem
On Tue, 2008-05-13 at 20:32 +0300, Jussi Lehtola wrote:
On Tue, 2008-05-13 at 14:34 +0100, Kukol, Andreas wrote:
First try the EM/MD of 1 molecule in vacuum ('ethanol-gas') and check,
if it looks reasonable.
Thanks, using the vacuum method I seem to get better results.
It seems I spoke too soon. Energy minimising the one-particle structure
in vacuum gives me the following potential energies:
methanol21.4
ethanol 9.4
propanol3.8
butanol 4.1
pentanol12.2
hexanol 81.0
All minimizations have converged with Fmax 1e-3. Are these energies
reasonable? The energies of methanol and hexanol are somewhat high.
Energy minimisation with a system of 4913 methanol molecules with
initial density of 500 kg/m^3 and periodic boundary conditions gives as
potential energy Epot = -1.67e5, however the forces do not converge.
Running the system with Berendsen pressure and temperature thermostats
(p = 1 bar, T = 300 K) results in a crash after 82 ps. The total energy
is positive and of the order 1e5.
--
--
Jussi Lehtola, FM, Tohtorikoulutettava
Fysiikan laitos, Helsingin Yliopisto
[EMAIL PROTECTED], p. 191 50673
--
Mr. Jussi Lehtola, M. Sc., Doctoral Student
Department of Physics, University of Helsinki, Finland
[EMAIL PROTECTED]
--
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RE: [gmx-users] Energy minimisation problem
First try the EM/MD of 1 molecule in vacuum ('ethanol-gas') and check, if it
looks reasonable.
You could also have a look at the definition of ETHH in the GROMOS96
forcefield, e.g. in ffG43a2.rtp. Although this is a united atom topology it
might give you clues, if something is wrong.
Andreas
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
On Behalf Of Jussi Lehtola
Sent: 13 May 2008 11:36
To: gmx-users@gromacs.org
Subject: [gmx-users] Energy minimisation problem
Hi,
I have constructed topologies for methanol, ethanol, propanol and butanol
using x2top with the atomic coordinates from NIST Chemistry WebBook. I have
modified the topologies by putting the CH3s, CH2s and OHs in their separate
charge groups.
Now I have run into problems when trying to minimize the energy of the
configuration. I have used a system with 5000 molecules, with the box size
chosen to give an initial mass density of the order 500 kg/m^3 (which is
less than the physical densities).
The system behaves really badly: the potential energy sticks to high
positive numbers (order of 10^6). I have tried with smaller densities with
no success. Sometimes the minimization gets energies of -10^8, but the
forces remain large. A few iterations after the potential energy attains
again positive values, and then converges to machine precision.
Increasing the step size doesn't help, neither does using another minimizer
(steep or l-bfgs): the system stays non-bonded.
Interestingly, if one generates the system using the -rot switch of genconf,
the potential increases some 10 orders of magnitude compared to the default,
-norot.
What could be the problem?
Attachments: ethanol coordinates topology
--
--
Jussi Lehtola, FM, Tohtorikoulutettava
Fysiikan laitos, Helsingin Yliopisto
[EMAIL PROTECTED], p. 191 50673
--
Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of Physics,
University of Helsinki, Finland [EMAIL PROTECTED]
--
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RE: [gmx-users] Energy minimisation problem
On Tue, 2008-05-13 at 14:34 +0100, Kukol, Andreas wrote:
First try the EM/MD of 1 molecule in vacuum ('ethanol-gas') and check, if it
looks reasonable.
You could also have a look at the definition of ETHH in the GROMOS96
forcefield, e.g. in ffG43a2.rtp. Although this is a united atom topology it
might give you clues, if something is wrong.
Thanks, using the vacuum method I seem to get better results.
--
--
Jussi Lehtola, FM, Tohtorikoulutettava
Fysiikan laitos, Helsingin Yliopisto
[EMAIL PROTECTED], p. 191 50673
--
Mr. Jussi Lehtola, M. Sc., Doctoral Student
Department of Physics, University of Helsinki, Finland
[EMAIL PROTECTED]
--
___
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RE: [gmx-users] Energy minimisation problem
On Tue, 2008-05-13 at 20:32 +0300, Jussi Lehtola wrote:
On Tue, 2008-05-13 at 14:34 +0100, Kukol, Andreas wrote:
First try the EM/MD of 1 molecule in vacuum ('ethanol-gas') and check, if
it looks reasonable.
Thanks, using the vacuum method I seem to get better results.
It seems I spoke too soon. Energy minimising the one-particle structure
in vacuum gives me the following potential energies:
methanol21.4
ethanol 9.4
propanol3.8
butanol 4.1
pentanol12.2
hexanol 81.0
All minimizations have converged with Fmax 1e-3. Are these energies
reasonable? The energies of methanol and hexanol are somewhat high.
Energy minimisation with a system of 4913 methanol molecules with
initial density of 500 kg/m^3 and periodic boundary conditions gives as
potential energy Epot = -1.67e5, however the forces do not converge.
Running the system with Berendsen pressure and temperature thermostats
(p = 1 bar, T = 300 K) results in a crash after 82 ps. The total energy
is positive and of the order 1e5.
--
--
Jussi Lehtola, FM, Tohtorikoulutettava
Fysiikan laitos, Helsingin Yliopisto
[EMAIL PROTECTED], p. 191 50673
--
Mr. Jussi Lehtola, M. Sc., Doctoral Student
Department of Physics, University of Helsinki, Finland
[EMAIL PROTECTED]
--
___
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Re: RE: [gmx-users] Energy minimisation problem
I guess you have not listed all the dihedrals in the configuration of a ethanol
molecule.
In your .top file, there are only two dihedrals, you might need to include all
others.
By the way, check the other part of your topology to avoid other incorrect
inputs.
Best regards.
Yue Shao
silvester.thu
2008-05-14
发件人： Jussi Lehtola
发送时间： 2008-05-14 11:28:31
收件人： Discussion list for GROMACS users
抄送：
主题： RE: [gmx-users] Energy minimisation problem
On Tue, 2008-05-13 at 20:32 +0300, Jussi Lehtola wrote:
On Tue, 2008-05-13 at 14:34 +0100, Kukol, Andreas wrote:
First try the EM/MD of 1 molecule in vacuum ('ethanol-gas')
and check, if it looks reasonable.
Thanks, using the vacuum method I seem to get better results.
It seems I spoke too soon. Energy minimising the one-particle
structure
in vacuum gives me the following potential energies:
methanol 21.4
ethanol 9.4
propanol 3.8
butanol 4.1
pentanol 12.2
hexanol 81.0
All minimizations have converged with Fmax 1e-3. Are these energies
reasonable? The energies of methanol and hexanol are somewhat high.
Energy minimisation with a system of 4913 methanol molecules with
initial density of 500 kg/m^3 and periodic boundary conditions gives
as
potential energy Epot = -1.67e5, however the forces do not converge.
Running the system with Berendsen pressure and temperature thermostats
(p = 1 bar, T = 300 K) results in a crash after 82 ps. The
total energy
is positive and of the order 1e5.
--
--
Jussi Lehtola, FM, Tohtorikoulutettava
Fysiikan laitos, Helsingin Yliopisto
[EMAIL PROTECTED], p. 191 50673
--
Mr. Jussi Lehtola, M. Sc., Doctoral Student
Department of Physics, University of Helsinki, Finland
[EMAIL PROTECTED]
--
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Re: Re: RE: Re: Re: [gmx-users] Energy minimisation
Hi Jestin, As I said, the last line in the .gro file codes for the box. So, you have a singular box! You probably did something wrong with editconf. Did you give it box dimensions at all (-box/-d). Have a look at the help: editconf -h Besides that, do have a look at the procedure you used to obtain the topology and such. You shouldn't have a non-integer total charge, as Justin pointed out. Cheers, Tsjerk On 4 Dec 2007 07:36:32 -, JMandumpal [EMAIL PROTECTED] wrote: Dear users, What I see the difference between the .gro file given at the examples in the tutor directory and my own .gro file is that the last lines gives 0.000 0.000 0. in my file and in the examples it is not. I assume it is the dimension of the box, isn' it? I built up the gro file using editconf -f *.pdb file. regards Jestin Mandumpal [image: Reliance Mobile]http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-home.htm/[EMAIL PROTECTED]/1960866_1953803/1960349/1?PARTNER=3OAS_QUERY=null+target=new+ ___ 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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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: Re: RE: Re: Re: [gmx-users] Energy minimisation
the last lines gives 0.000 0.000 0. in my file and in the examples it is not. I assume it is the dimension of the box, isn' it? That is correct. So that full explains what you see occuring. I built up the gro file using editconf -f *.pdb file. You need to specify the size of the box with editconf. Type editconf -h and that will tell you the various options available. You will probably need to do something like editconf -f filename.pdb -o filename.gro -box 2 2 2 Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacology Victorian College of Pharmacy, Monash University 381 Royal Parade, Parkville VIC 3010 [EMAIL PROTECTED] +61 3 9903 9524 - When the only tool you own is a hammer, every problem begins to resemble a nail. ___ 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: Re: [gmx-users] Energy minimisation
Jestin, Please don't use all capitals. As Mark has pointed out several times, that's considered shouting. You're probably frustrated that things don't work according to your expectations, but the frustration comes from you not knowing what your doing. Don't blame us for that, go read a manual. If something is not specified in the .mdp file, the default is used. One thing not specified in your .mdp file is the way to treat PBC, so grompp will want to use xyz. When using (standard) PBC, the cut-off should not be longer than half the box length, as you should be aware if you have read MD basics. Apparently, you're using a cut-off length longer than allowed for your box (says grompp). You say it's 20.1 A to all sides, which should be okay when using a 1.0 nm cut-off. I suspect the last line of your .gro file, which describes the box dimensions, says something else. You should verify that and paste us the last line of the .gro file if you can't see anything wrong with it. Cheers, Tsjerk On 3 Dec 2007 00:19:25 -, JMandumpal [EMAIL PROTECTED] wrote: Dear Justin, Thanks for the response. This is my input file (em.mdp) which contains parameters for doing energy minimisation. cpp= /lib/cpp define= -DPOSRES -DFLEX_ constraints= none morse = no integrator= steep nsteps= 2000 ; Energy minimizing emtol = 100 emstep= 0.1 nstcomm= 1 ns_type= grid rlist = 1.0 rcoulomb = 1.0 rvdw = 1.0 Tcoupl= no Pcoupl= no MY BOX DIMENSION, 20.1* 20.1* 20.1 ANGSTROM. THIS IS THE THREAD WHERE I COLLECTED THE .mdp FILE FOR ENERGY MINIMISATION. http://www.gromacs.org/component/option,com_wrapper/Itemid,84/ regards Jestin [image: Shaadi]http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-home.htm/[EMAIL PROTECTED]/1961853_1954773/1961358/1?PARTNER=3OAS_QUERY=null+target=new+ ___ 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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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: Re: Re: [gmx-users] Energy minimisation
Quoting JMandumpal [EMAIL PROTECTED]: Dear Justin, I made some changes in my .mdp file, but the result is same. My box size, as mentioned in the previous mail, is 20.1 A. The cut off I used is 8 angstrom. I attach the input file here. ** cpp= /lib/cpp define = -DPOSRES-DFLEX_SPC constraints= none morse = no integrator = steep nsteps = 2000 ; Energy minimizing emtol = 100 emstep = 0.1 nstcomm= 1 ns_type= grid rlist = 0.8 coulumbtype= pme rcoulomb = 0.8 vdw-type = cut-off rvdw = 0.8 nstenergy = 10 Tcoupl = no Pcoupl = no gen_vel= no * And the output message is : --- creating statusfile for 1 node... Back Off! I just backed up mdout.mdp to ./#mdout.mdp.5# checking input for internal consistency... calling /lib/cpp... processing topology... Generated 332520 of the 332520 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 332520 of the 332520 1-4 parameter combinations Excluding 2 bonded neighbours for SOL 258 NOTE: System has non-zero total charge: -2.58e-01 processing coordinates... double-checking input for internal consistency... ERROR: The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease rlist. --- Program grompp, VERSION 3.3.2 Source code file: grompp.c, line: Fatal error: There were 1 error(s) processing your input --- Stop Drinking My Beer ! (The Amps) -- HOW CAN I SETTLE THIS ISSUE? Did you read Tsjerk's message from this morning? His suggestions regarding PBC and verifying your box dimensions are good ones that I had not considered. Also note that you probably have a broken topology, as the net charge on your system is non-integral. This has nothing to do with the problem at hand, but it will likely be problematic later. -Justin REGARDS JESTIN Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ 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: Re: Re: [gmx-users] Energy minimisation
As noted by someone, please post the last couple of lines of the .gro file you provide to grompp. Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacology Victorian College of Pharmacy, Monash University 381 Royal Parade, Parkville VIC 3010 [EMAIL PROTECTED] +61 3 9903 9524 - When the only tool you own is a hammer, every problem begins to resemble a nail. ___ 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: Re: RE: Re: Re: [gmx-users] Energy minimisation
Dear users, What I see the difference between the .gro file given at the examples in the tutor directory and my own .gro file is that the last lines gives 0.000 0.000 0. in my file and in the examples it is not. I assume it is the dimension of the box, isn' it? I built up the gro file using editconf -f *.pdb file. regards Jestin Mandumpal___ 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: RE: Re: Re: [gmx-users] Energy minimisation
Dear Gromacs users, Thanks for the messages. Tsjerk, I was not aware that capital letters denote unpolite. I just used them to highlight the problem so others can easily pick out. Thanks for the suggestions as well. I modified the file: *** cpp= /lib/cpp define = -DPOSRES -DFLEX_SPC constraints= none morse = no integrator = steep nsteps = 2000 ; Energy minimizing emtol = 100 emstep = 0.1 nstcomm= 1 nstlist= 10 ns_type= grid pbc= xyz rlist = 0.8 coulombtype= pme rcoulomb = 0.8 vdw-type = cut-off rvdw = 0.8 nstenergy = 10 Tcoupl = no Pcoupl = no gen_vel= no * But the message is the same. As Dallas and others mentioned, I attach the last part of myt .gro file * 245SOLLP2 1225 0.977 -0.910 0.116 246SOL OW 1226 0.927 -0.946 0.484 246SOLHW1 1227 0.985 -0.880 0.447 246SOLHW2 1228 0.852 -0.950 0.425 246SOLLP1 1229 0.907 -0.928 0.549 246SOLLP2 1230 0.960 -1.008 0.487 247SOL OW 1231 0.970 -0.641 -0.228 247SOLHW1 1232 1.010 -0.704 -0.169 247SOLHW2 1233 1.006 -0.556 -0.201 247SOLLP1 1234 0.900 -0.642 -0.221 247SOLLP2 1235 0.986 -0.655 -0.295 248SOL OW 1236 0.953 -0.556 0.247 248SOLHW1 1237 1.010 -0.481 0.233 248SOLHW2 1238 1.010 -0.624 0.284 248SOLLP1 1239 0.925 -0.578 0.186 248SOLLP2 1240 0.901 -0.540 0.292 249SOL OW 1241 0.974 -0.356 -0.452 249SOLHW1 1242 1.010 -0.438 -0.485 249SOLHW2 1243 1.010 -0.347 -0.364 249SOLLP1 1244 0.904 -0.359 -0.450 249SOLLP2 1245 0.993 -0.302 -0.493 250SOL OW 1246 0.981 -0.228 0.866 250SOLHW1 1247 1.010 -0.229 0.957 250SOLHW2 1248 1.010 -0.312 0.831 250SOLLP1 1249 1.010 -0.175 0.831 250SOLLP2 1250 0.911 -0.223 0.863 251SOL OW 1251 0.979 -0.053 -0.717 251SOLHW1 1252 0.884 -0.039 -0.721 251SOLHW2 1253 1.006 -0.053 -0.809 251SOLLP1 1254 0.994 -0.114 -0.686 251SOLLP2 1255 1.010 -0.001 -0.682 252SOL OW 1256 0.981 0.286 -0.345 252SOLHW1 1257 1.010 0.289 -0.254 252SOLHW2 1258 1.010 0.369 -0.383 252SOLLP1 1259 0.911 0.281 -0.349 252SOLLP2 1260 1.010 0.232 -0.379 253SOL OW 1261 0.968 0.619 -0.698 253SOLHW1 1262 0.886 0.667 -0.704 253SOLHW2 1263 0.942 0.531 -0.672 253SOLLP1 1264 1.010 0.648 -0.649 253SOLLP2 1265 1.002 0.618 -0.759 254SOL OW 1266 0.981 0.543 -0.103 254SOLHW1 1267 1.010 0.467 -0.054 254SOLHW2 1268 1.010 0.618 -0.051 254SOLLP1 1269 0.911 0.544 -0.110 254SOLLP2 1270 1.010 0.545 -0.167 255SOL OW 1271 0.985 0.378 0.613 255SOLHW1 1272 1.010 0.327 0.690 255SOLHW2 1273 0.890 0.377 0.613 255SOLLP1 1274 1.010 0.348 0.555 255SOLLP2 1275 1.010 0.443 0.617 256SOL OW 1276 0.981 0.516 0.287 256SOLHW1 1277 1.010 0.572 0.215 256SOLHW2 1278 1.010 0.562 0.366 256SOLLP1 1279 1.010 0.453 0.283 256SOLLP2 1280 0.911 0.510 0.287 257SOL OW 1281 0.847 0.408 0.942 257SOLHW1 1282 0.841 0.466 0.866 257SOLHW2 1283 0.941 0.407 0.964 257SOLLP1 1284 0.825 0.344 0.926 257SOLLP2 1285 0.810 0.433 0.996 258SOL OW 1286 0.983 0.951 0.741 258SOLHW1 1287 0.888 0.947 0.746 258SOLHW2 1288 1.001 1.010 0.668 258SOLLP1 1289 1.010 0.888 0.728 258SOLLP2 1290 1.010 0.976 0.800 0.0 0.0 0.0 out.gro 1293L, 58138C the system is tip5p water molecule. regards, Jestin Mandumpal___ 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] Energy minimisation
Quoting JMandumpal [EMAIL PROTECTED]: Dear Gromacs users When I run Energy minimisation using the command, grompp -f em.mdp -p topol.top -c out.gro -o pr.tpr, I received the following error message. ** processing coordinates... double-checking input for internal consistency... ERROR: The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease rlist. --- Program grompp, VERSION 3.3.2 Source code file: grompp.c, line: Fatal error: There were 1 error(s) processing your input --- *** MY BOX DIMENSION IS 20.1 * 20.1 * 20.1 Angstoms or nanometers? I CHANGED THE RLIST, FOR A LOWER VALUE: STILL THE MESSAGE IS SAME. What was the initial value? What did you change it to? What are you trying to do? You need to provide explicit information to get a useful response. Note: I copied the .mdp file form the gromacs users list ( DECMEBER 2001) What is in this .mdp file? There are lots out there on the archive... -Justin regards, Jestin Mandumpal Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ 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: Re: [gmx-users] Energy minimisation
Dear Justin, Thanks for the response. This is my input file (em.mdp) which contains parameters for doing energy minimisation. cpp= /lib/cpp define = -DPOSRES -DFLEX_ constraints= none morse = no integrator = steep nsteps = 2000 ; Energy minimizing emtol = 100 emstep = 0.1 nstcomm= 1 ns_type= grid rlist = 1.0 rcoulomb = 1.0 rvdw = 1.0 Tcoupl = no Pcoupl = no MY BOX DIMENSION, 20.1* 20.1* 20.1 ANGSTROM. THIS IS THE THREAD WHERE I COLLECTED THE .mdp FILE FOR ENERGY MINIMISATION. http://www.gromacs.org/component/option,com_wrapper/Itemid,84/ regards Jestin ___ 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: Re: Re: [gmx-users] Energy minimisation
Dear Justin, It seems, the given link which was directed to a post where I got contents of ENERGY MINIMISATION FILE .mdp in my previous mail is not the right one, so I paste its content here. *** Geraudis Mustelier gera at ict.cim.sld.cu Wed Dec 12 20:00:03 CET 2001 * Previous message: [gmx-users] Merging several topology files * Next message: [gmx-users] problem with energy minimization * Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] Hi I would like to refine a model obtained with modeling by homology technique from X-ray structures. So, I am treating to do an energy minimization. The parameter values in .mdp file are: ; cpp = /lib/cpp define = -DPOSRES constraints = none morse = no integrator = steep nsteps = 2000 ; ; Energy minimizing stuff emtol = 100 emstep = 0.1 ; nstcomm = 1 ns_type= grid rlist = 1 rcoulomb = 1.0 rvdw= 1.0 Tcoupl = no Pcoupl = no gen_vel = no *** regards Jestin Mandumpal ___ 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: Re: [gmx-users] Energy minimisation
Quoting Justin A. Lemkul [EMAIL PROTECTED]: Quoting JMandumpal [EMAIL PROTECTED]: Dear Justin, Thanks for the response. This is my input file (em.mdp) which contains parameters for doing energy minimisation. cpp= /lib/cpp define = -DPOSRES -DFLEX_ constraints= none morse = no integrator = steep nsteps = 2000 ; Energy minimizing emtol = 100 emstep = 0.1 nstcomm= 1 ns_type= grid rlist = 1.0 rcoulomb = 1.0 rvdw = 1.0 Tcoupl = no Pcoupl = no MY BOX DIMENSION, 20.1* 20.1* 20.1 ANGSTROM. And that's why grompp is complaining. Your cutoff is 1.0 nm, which is half of your box size. You said you tried decreasing your cutoff? To what value? Also note that -DFLEX_ is not a valid definition, unless you've created it yourself. What you probably want (from the thread) is -DFLEX_SPC. -Justin THIS IS THE THREAD WHERE I COLLECTED THE .mdp FILE FOR ENERGY MINIMISATION. http://www.gromacs.org/component/option,com_wrapper/Itemid,84/ regards Jestin Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ 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] Energy Minimisation problem
supti mukherjee wrote: Dear all, I was minimising a protein structure. I added polar hydrogens to the protein by some program and then proceeded for the energy minimisation. I chose Conjugate Gradient of 1000 steps with emtol as 100. The mdrun came out with the following error. During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value -2147483648. It should have been within [ 0 .. 17052 ] Can anybody please help me in identifying my mistake? Try the general procedure outlined here... 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] energy minimisation in vaccum
nur avneet wrote: dear all hi, When we do energy minimisation in vaccum...what ensemble should we use... what do you mean by that? em does not create proper therrmodynamic ensembles. what is pressure or temperature during an em? and constant energy you surely don't want either. however, here's an mdp file which should be ok. no cut-offs (if you can afford that). no pbc. ; VARIOUS PREPROCESSING OPTIONS title= cpp = /lib/cpp include = define = ; RUN CONTROL PARAMETERS integrator = steep ; Start time and timestep in ps tinit= 0 dt = 0.001 nsteps = 1000 ; For exact run continuation or redoing part of a run init_step= 0 ; mode for center of mass motion removal comm-mode= angular ; 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= 0.0001 emstep = 0.01 ; Max number of iterations in relax_shells niter= 20 ; Step size (ps^2) for minimization of flexible constraints fcstep = 0 ; Frequency of steepest descents steps when doing CG nstcgsteep = 1000 nbfgscorr= 10 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 1 nstvout = 0 nstfout = 0 ; Checkpointing helps you continue after crashes nstcheckpoint= 1000 ; Output frequency for energies to log file and energy file nstlog = 1 nstenergy= 1 ; Output frequency and precision for xtc file nstxtcout= 1 xtc-precision= 1000 ; This selects the subset of atoms for the xtc file. You can ; select multiple groups. By default all atoms will be written. xtc-grps = ; Selection of energy groups energygrps = system ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 0 ; ns algorithm (simple or grid) ns-type = simple ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = no ; nblist cut-off rlist= 0 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = Cut-Off rcoulomb-switch = 0 rcoulomb = 0 ; Dielectric constant (DC) for cut-off or DC of reaction field epsilon-r= 1 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw-switch = 0 rvdw = 0 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = No ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order= 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no ; GENERALIZED BORN ELECTROSTATICS ; Algorithm for calculating Born radii gb_algorithm = Still ; Frequency of calculating the Born radii inside rlist nstgbradii = 1 ; Cutoff for Born radii calculation; the contribution from atoms ; between rlist and rgbradii is updated every nstlist steps rgbradii = 2 ; Salt concentration in M for Generalized Born models gb_saltconc = 0 ; IMPLICIT SOLVENT (for use with Generalized Born electrostatics) implicit_solvent = No ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling tcoupl = yes ; Groups to couple separately tc-grps = system ; Time constant (ps) and reference temperature (K) tau-t= 0.1 ref-t= 300 ; Pressure coupling Pcoupl = no Pcoupltype = Isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau-p= 1 compressibility = 4.5e-5 ref-p= 1 ; Random seed for Andersen thermostat andersen_seed= 815131 ; OPTIONS FOR QMMM calculations QMMM = no ; Groups treated Quantum Mechanically QMMM-grps= ; QM method QMmethod = ; QMMM scheme QMMMscheme = normal ; QM
