Quoting Payman Pirzadeh <[email protected]>: > Dear Mark, > I think I know the problem! I have simulated homogeneous systems (liquid > water) without any problems. Problem is with the order of particles in the > PDB or gro file which I use as my input. As the order of oxygen changes in > the input, when I 'settle' the oxygen, then the corresponding Hs are not > after my oxygen. So, settle takes sth else for constraining the system. Now,
Didn't grompp warn you that atom names did not match the topology? > I need a smart advice on how to convert the order of particles in PDB or gro > file in way that it matches the OHH format, not sth else. > Probably could be done with a simple Perl script to sort the atoms based on name, for each residue number. -Justin > Payman > > -----Original Message----- > From: [email protected] [mailto:[email protected]] > On Behalf Of Mark Abraham > Sent: Thursday, July 16, 2009 8:40 PM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] minimzation problem with a heterogeneous system > > Payman Pirzadeh wrote: > > Hello, > > I have a configuration in which half of the box is liquid water and the > > other half is ice. This configuration is the output of another simulation > in > > which the mentioned config worked (and still works fine). But when I start > > minimizing it (I started minimization since my first round of MD run > crashed > > due to messages indicative of clashes). But minimation ends with the > > following message: > > > > Steepest Descents: > > Tolerance (Fmax) = 1.00000e-06 > > Number of steps = 500000 > > Step= 1, Dmax= 1.0e-01 nm, Epot= 6.09464e+11 Fmax= 1.31718e+14, atom= > > 2938 > > Step= 2, Dmax= 1.2e-01 nm, Epot= 1.15027e+09 Fmax= 2.00242e+11, atom= > > 2576 > > Step= 3, Dmax= 1.4e-01 nm, Epot= 1.56529e+08 Fmax= 2.20702e+09, atom= > > 11062 > > > > t = 0.004 ps: Water molecule starting at atom 16078 can not be settled. > > Check for bad contacts and/or reduce the timestep. > > Wrote pdb files with previous and current coordinates > > Step= 4, Dmax= 1.7e-01 nm, Epot= 2.11002e+10 Fmax= 5.75671e+13, atom= > > 14986 > > t = 0.005 ps: Water molecule starting at atom 14902 can not be settled. > > Check for bad contacts and/or reduce the timestep. > > Wrote pdb files with previous and current coordinates > > Step= 5, Dmax= 8.6e-02 nm, Epot= 1.22915e+07 Fmax= 4.57843e+07, atom= > > 6280 > > > > t = 0.006 ps: Water molecule starting at atom 15952 can not be settled. > > Check for bad contacts and/or reduce the timestep. > > Wrote pdb files with previous and current coordinates > > Step= 7, Dmax= 5.2e-02 nm, Epot= 5.50887e+06 Fmax= 1.19611e+08, atom= > > 7348 > > Step= 8, Dmax= 6.2e-02 nm, Epot= 4.29974e+06 Fmax= 1.39548e+07, atom= > > 12066 > > Step= 9, Dmax= 7.5e-02 nm, Epot= 1.93270e+06 Fmax= 2.81542e+07, atom= > > 7204 > > > > t = 0.010 ps: Water molecule starting at atom 7300 can not be settled. > > Check for bad contacts and/or reduce the timestep. > > Wrote pdb files with previous and current coordinates > > Step= 26, Dmax= 1.4e-06 nm, Epot= 2.53306e+06 Fmax= 8.74996e+06, atom= > > 15953 > > Stepsize too small, or no change in energy. > > Converged to machine precision, > > but not to the requested precision Fmax < 1e-06 > > > > Double precision normally gives you higher accuracy. > > You might need to increase your constraint accuracy, or turn > > off constraints alltogether (set constraints = none in mdp file) > > > > writing lowest energy coordinates. > > > > Steepest Descents converged to machine precision in 27 steps, > > but did not reach the requested Fmax < 1e-06. > > Potential Energy = 1.9327006e+06 > > Maximum force = 2.8154184e+07 on atom 7204 > > Norm of force = 4.1820662e+05 > > > > I checked the output .pdb files, and they show box is cracking from the > > position of the ice-water interface! Also, the ice part looks like a > > complete mess! (like it's not going to be ice anymore). I checked the .itp > > file to make sure are the variables are correct. Nothing looked wrong to > me. > > I checked the mailing list about minimization. Just remember this water > > model is not flexible. > > All we can say is the something is broken with your model or initial > configuration. Simplify it into small, homogeneous systems until you can > diagnose the source of the problem. > > Mark > _______________________________________________ > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > _______________________________________________ > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > ======================================== 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 list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
