[gmx-users] Normal mode analysis of pure water
Hi, I encountered the following remarks during normal mode analysis of pure water. Can someone please suggest a solution. mdrun_d -v -s water.tpr -o traj.trr -c confout.gro -e ener.edr -g md.log -mtx nm.mtx Getting Loaded... Reading file water.tpr, VERSION 4.0.4 (double precision) Loaded with Money Non-cutoff electrostatics used, forcing full Hessian format. Allocating Hessian memory... starting normal mode calculation 'Pure Water' 648 steps. Maximum force: 2.74758e+03 Maximum force probably not small enough to ensure that you are in an energy well. Be aware that negative eigenvalues may occur when the resulting matrix is diagonalized. Finished step 648 out of 648 Writing Hessian... gcq#258: In the End Science Comes Down to Praying (P. v.d. Berg) g_nmeig_d -f nm.mtx -s water.tpr -of eigenfreq.xvg -ol eigenval.xvg -v eigenvec.trr Reading file water.tpr, VERSION 4.0.4 (double precision) Reading file water.tpr, VERSION 4.0.4 (double precision) Reading double precision matrix generated by Gromacs VERSION 4.0.4 Full matrix storage format, nrow=1944, ncols=1944 Diagonalizing to find vectors 1 through 50... One of the lowest 6 eigenvalues has a non-zero value. This could mean that the reference structure was not properly energy minimized. Writing eigenvalues... Writing eigenfrequencies - negative eigenvalues will be set to zero. Writing average structure eigenvectors 1--50 to eigenvec.trr gcq#132: Shit Happens (Pulp Fiction) The eigenfreq is 0 which is the problem The .mdp file used was; ; User spoel (236) ; Wed Nov 3 17:12:44 1993 ; Input file ; cpp = define = -DFLEXIBLE constraints = none integrator = nm nsteps = 1 ; ; Energy minimizing stuff ; emtol = 0.01 emstep = 0.01 coulombtype = PME nstcomm = 1 ns_type = grid rlist = 0.9 rcoulomb= 0.9 rvdw= 0.9 Tcoupl = no Pcoupl = no gen_vel = no ___ 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] Normal mode analysis of pure water
simon sangma wrote: Hi, I encountered the following remarks during normal mode analysis of pure water. Can someone please suggest a solution. You've been told twice already what the likely solution is: snip Maximum force: 2.74758e+03 Maximum force probably not small enough to ensure that you are in an energy well. Be aware that negative eigenvalues may occur when the resulting matrix is diagonalized. snip One of the lowest 6 eigenvalues has a non-zero value. This could mean that the reference structure was not properly energy minimized. -Justin -- 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] Normal mode analysis of pure water
Hi Justin, I tried altering the .mdp file (integrator = steep instead of nm) for energy minimization. But in that case the mdrun did not generate the Hessian matrix (nm.mtx) inspite of using the command twice. ___ 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] Normal mode analysis of pure water
simon sangma wrote: Hi Justin, I tried altering the .mdp file (integrator = steep instead of nm) for energy minimization. But in that case the mdrun did not generate the Hessian matrix (nm.mtx) inspite of using the command twice. Energy minimization is not the same thing as Normal Mode Analysis. You have to energy minimize your system (thoroughly!) first, then run NMA. -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 -- 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] Normal mode analysis of pure water
This is wasting a large amount of CPU time. Water is solid (ice) at 0 K. A plain normal mode analysis would give you the normal modes of ice. You can do a normal mode analysis of liquid water without minimization, but the standard NMA techniques will not work. Berk Date: Tue, 20 Oct 2009 18:33:43 +0530 From: simoniitc...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] Normal mode analysis of pure water Hi, I encountered the following remarks during normal mode analysis of pure water. Can someone please suggest a solution. mdrun_d -v -s water.tpr -o traj.trr -c confout.gro -e ener.edr -g md.log -mtx nm.mtx Getting Loaded... Reading file water.tpr, VERSION 4.0.4 (double precision) Loaded with Money Non-cutoff electrostatics used, forcing full Hessian format. Allocating Hessian memory... starting normal mode calculation 'Pure Water' 648 steps. Maximum force: 2.74758e+03 Maximum force probably not small enough to ensure that you are in an energy well. Be aware that negative eigenvalues may occur when the resulting matrix is diagonalized. Finished step 648 out of 648 Writing Hessian... gcq#258: In the End Science Comes Down to Praying (P. v.d. Berg) g_nmeig_d -f nm.mtx -s water.tpr -of eigenfreq.xvg -ol eigenval.xvg -v eigenvec.trr Reading file water.tpr, VERSION 4.0.4 (double precision) Reading file water.tpr, VERSION 4.0.4 (double precision) Reading double precision matrix generated by Gromacs VERSION 4.0.4 Full matrix storage format, nrow=1944, ncols=1944 Diagonalizing to find vectors 1 through 50... One of the lowest 6 eigenvalues has a non-zero value. This could mean that the reference structure was not properly energy minimized. Writing eigenvalues... Writing eigenfrequencies - negative eigenvalues will be set to zero. Writing average structure eigenvectors 1--50 to eigenvec.trr gcq#132: Shit Happens (Pulp Fiction) The eigenfreq is 0 which is the problem The .mdp file used was; ; User spoel (236) ; Wed Nov 3 17:12:44 1993 ; Input file ; cpp = define = -DFLEXIBLE constraints = none integrator = nm nsteps = 1 ; ; Energy minimizing stuff ; emtol = 0.01 emstep = 0.01 coulombtype = PME nstcomm = 1 ns_type = grid rlist = 0.9 rcoulomb= 0.9 rvdw= 0.9 Tcoupl = no Pcoupl = no gen_vel = no _ What can you do with the new Windows Live? Find out http://www.microsoft.com/windows/windowslive/default.aspx___ 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] Normal mode analysis of pure water
Hi Berk, You mentioned that standard NMA techniques will not work for the liquid water system. Could you suggest the alternatives then? ___ 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] Normal mode analysis of pure water
You could get better help if you tell us what information you want to get out of this analysis. NMA gives you a harmonic description of the potential energy around a minimum of the system. For water the minimum is ice, so you would get the modes of a certain ice state. Berk Date: Tue, 20 Oct 2009 19:20:19 +0530 From: simoniitc...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] Normal mode analysis of pure water Hi Berk, You mentioned that standard NMA techniques will not work for the liquid water system. Could you suggest the alternatives then? _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ 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] Normal mode analysis of pure water
Hi Justin, Are you suggesting that after thorough energy minimization, seperate .mdp file is to be used for NMA? In that case how would that output file (energy minimised file) be taken as an input file for the grompp and mdrun command (for NMA)? What extension would the file have (.what) ? ___ 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] Normal mode analysis of pure water
simon sangma wrote: Hi Justin, Are you suggesting that after thorough energy minimization, seperate .mdp file is to be used for NMA? In that case how would that output file (energy minimised file) be taken as an input file for the grompp and mdrun command (for NMA)? What extension would the file have (.what) ? Yes, they are done in separate steps. I think you need to do some tutorial material on the workflow of a GROMACS procedure. Run energy minimization (in double precision), and the output of EM is your input for NMA (the minimized structure). -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 -- 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
