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<div style="font-family: times new roman,new york,times,serif; font-size: 10pt;"><span style="font-family: tahoma,new york,times,serif;">On </span><font style="font-family: tahoma,new york,times,serif;" face="Tahoma" size="2">Thursday, August 6, 2009 at 7:59:43 PM </font><font face="Tahoma" size="2"><span style="font-family: tahoma,new york,times,serif;">Nancy <nancy5villa@gmail.com> wrote:</span><br></font><div> <br>> I ran the minimisation, and mdrun gave the following last few lines of output:<br>> <br>> ==================================<br>> Step=19990, Dmax= 7.8e-06 nm, Epot= -7.14922e+04 Fmax= 3.19585e+04, atom= 2395<br>> Step=19992, Dmax= 4.7e-06 nm, Epot= -7.14924e+04 Fmax= 8.72456e+03, atom= 2395<br>>
Step=19993, Dmax= 5.6e-06 nm, Epot= -7.14927e+04 Fmax= 3.70693e+04, atom= 2395<br>> Step=19994, Dmax= 6.8e-06 nm, Epot= -7.14929e+04 Fmax= 2.10513e+04, atom= 2395<br>> Step=19995, Dmax= 8.1e-06 nm, Epot= -7.14929e+04 Fmax= 4.71234e+04, atom= 2395<br>>
Step=19996, Dmax= 9.7e-06 nm, Epot= -7.14931e+04 Fmax= 3.68827e+04, atom= 2395<br>> Step=19998, Dmax= 5.8e-06 nm, Epot= -7.14933e+04 Fmax= 1.35461e+04, atom= 2395<br>> Step=19999, Dmax= 7.0e-06 nm, Epot= -7.14933e+04 Fmax= 4.77130e+04, atom= 2395<br>>
Step=20000, Dmax= 8.4e-06 nm, Epot= -7.14936e+04 Fmax= 2.41860e+04, atom= 2395<br>> <br>> writing lowest energy coordinates.<br>> <br>> Steepest Descents did not converge to Fmax < 10 in 20001 steps.<br>> Potential Energy = -7.1493609e+04<br>>
Maximum force = 2.4185994e+04 on atom 2395<br>> Norm of force = 8.1511212e+02<br>> ==================================<br>> <br>> As you can be seen, the forces still do not converge to Fmax < 10, even after 20,000 steps.<br>
> <br>> Does anyone know what the problem might be?<br><br>The problem is my error in the specification of non-bonded interaction combination rules,<br>FudgeLJ, and FudgeQQ for gromacs force fields.<br><br>Line 7 of your file ffethanediol.itp currently reads:<br> 1 2 yes 0.5 0.833333<br><br>This was taken from ambconv and is correct for amber and gaff force fields, but not<br>for gromacs force fields, nor for OPLS-AA.<br><br>Change line 7 of the file ffethanediol.itp to read:<br> 1 1
no 1.0 1.0<br><br>The correction is in topolbuild 1.3 which is not yet released, but this error was not caught<br>for the topolbuild 1.2 series. Quite frankly, I had forgotten that modification was made as<br>I've been editing the set of tables needed to add OPLS-AA to the mix of force fields available.<br><br>As a general note. For gromacs force field topologies generated with anything in the<br>topolbuild 1.2 series, this edit to the itp file that specifies the defaults is required.<br><br><br>Sincerely,<br><br><br></div>-- <br>Bruce D. Ray, Ph.D.<br>Associate Scientist<br>IUPUI<br>Physics Dept.<br>402 N. Blackford St.<br>Indianapolis, IN 46202-3273<div><br></div></div></div><br>
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