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At the beginning of your md.mdp file you will see the following:<br><br>; RUN CONTROL PARAMETERS<br>integrator = steep<br><br>With this command you ask GROMACS to energy minimize your system by steepest descent. <br>If you want to run a md simulation you will have to change the intergrator to md.<br>You can read this, and more, in details in the manual.<br><br>Good luck<br>Antonia<br><br><hr id="stopSpelling">Date: Tue, 7 Apr 2009 17:16:03 +0530<br>From: bissoyi.akalabya@gmail.com<br>To: gmx-users@gromacs.org<br>Subject: [gmx-users] md.mdp query<br><br>hello gromacs,<br>i want to know the changes to be done in md.mdp files for 10 ns.<br>i am trying to run it but it's showing the following message.<br><br>Steepest Descents:<br> Tolerance (Fmax) = 1.00000e+01<br> Number of steps = 10000000<br>
Step= 0, Dmax= 1.0e-02 nm, Epot= -5.01412e+06 Fmax= 3.66197e+03, atom= 4032<br>Step= 2, Dmax= 5.0e-03 nm, Epot= -5.01438e+06 Fmax= 2.17491e+04, atom= 4032<br>Step= 3, Dmax= 6.0e-03 nm, Epot= -5.01456e+06 Fmax= 9.13099e+03, atom= 4032<br>
Step= 5, Dmax= 3.6e-03 nm, Epot= -5.01468e+06 Fmax= 9.44298e+03, atom= 4032<br>Step= 10, Dmax= 2.7e-04 nm, Epot= -5.01470e+06 Fmax= 8.04093e+03, atom= 4032<br>Step= 11, Dmax= 3.2e-04 nm, Epot= -5.01472e+06 Fmax= 6.36864e+03, atom= 4032<br>
Step= 12, Dmax= 3.9e-04 nm, Epot= -5.01474e+06 Fmax= 4.35105e+03, atom= 4032<br>Step= 14, Dmax= 2.3e-04 nm, Epot= -5.01476e+06 Fmax= 3.13319e+03, atom= 4032<br>Step= 16, Dmax= 1.4e-04 nm, Epot= -5.01478e+06 Fmax= 2.39737e+03, atom= 4032<br>
Step= 18, Dmax= 8.4e-05 nm, Epot= -5.01478e+06 Fmax= 1.98224e+03, atom= 4032<br>Step= 21, Dmax= 2.5e-05 nm, Epot= -5.01479e+06 Fmax= 1.88313e+03, atom= 4034<br>Step= 22, Dmax= 3.0e-05 nm, Epot= -5.01479e+06 Fmax= 1.68824e+03, atom= 4032<br>
Step= 23, Dmax= 3.6e-05 nm, Epot= -5.01479e+06 Fmax= 1.50693e+03, atom= 4032<br>Step= 25, Dmax= 2.2e-05 nm, Epot= -5.01479e+06 Fmax= 1.39532e+03, atom= 4032<br>Step= 26, Dmax= 2.6e-05 nm, Epot= -5.01480e+06 Fmax= 1.30313e+03, atom= 4032<br>
Step= 27, Dmax= 3.1e-05 nm, Epot= -5.01481e+06 Fmax= 1.12668e+03, atom= 4034<br>Step= 28, Dmax= 3.8e-05 nm, Epot= -5.01482e+06 Fmax= 9.41676e+02, atom= 4034<br>Step= 30, Dmax= 2.3e-05 nm, Epot= -5.01483e+06 Fmax= 8.67996e+02, atom= 4032<br>
Step= 31, Dmax= 2.7e-05 nm, Epot= -5.01483e+06 Fmax= 6.80316e+02, atom= 4034<br>Step= 32, Dmax= 3.2e-05 nm, Epot= -5.01484e+06 Fmax= 5.66923e+02, atom= 4034<br>Step= 33, Dmax= 3.9e-05 nm, Epot= -5.01485e+06 Fmax= 3.30411e+02, atom= 1881<br>
Step= 35, Dmax= 2.3e-05 nm, Epot= -5.01487e+06 Fmax= 3.12606e+02, atom= 1881<br>Step= 37, Dmax= 1.4e-05 nm, Epot= -5.01488e+06 Fmax= 3.86990e+02, atom= 92925<br>Step= 38, Dmax= 1.7e-05 nm, Epot= -5.01489e+06 Fmax= 3.70596e+02, atom= 286823<br>
Step= 40, Dmax= 1.0e-05 nm, Epot= -5.01489e+06 Fmax= 4.65471e+02, atom= 142601<br>Step= 41, Dmax= 1.2e-05 nm, Epot= -5.01490e+06 Fmax= 4.51394e+02, atom= 155810<br>Step= 43, Dmax= 7.3e-06 nm, Epot= -5.01490e+06 Fmax= 6.46500e+02, atom= 167601<br>
Step= 47, Dmax= 1.1e-06 nm, Epot= -5.01490e+06 Fmax= 4.30994e+03, atom= 214498<br>Stepsize too small, or no change in energy.<br>Converged to machine precision,<br>but not to the requested precision Fmax < 10<br><br>
Double precision normally gives you higher accuracy.<br>You might need to increase your constraint accuracy, or turn<br>off constraints alltogether (set constraints = none in mdp file)<br><br>writing lowest energy coordinates.<br>
<br>Back Off! I just backed up traj.trr to ./#traj.trr.12#<br><br>Back Off! I just backed up md.pdb to ./#md.pdb.8#<br><br>Steepest Descents converged to machine precision in 48 steps,<br>but did not reach the requested Fmax < 10.<br>
Potential Energy = -5.0149030e+06<br>Maximum force = 6.4650037e+02 on atom 167601<br>Norm of force = 7.3590344e+04<br><br><br>Kindly help me in this regard.I am attaching md.mdp file in which i have made the changes.<br>
<br clear="all"><br>-- <br>akalabya<br>N.I.T.Rourkela<br><br /><hr />See all the ways you can stay connected <a href='http://www.microsoft.com/windows/windowslive/default.aspx' target='_new'>to friends and family</a></body>
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