[gmx-users] Tabulated potential, derivative errors and interpolation

ms devicerandom at gmail.com
Thu Jan 7 20:49:42 CET 2010

David van der Spoel ha scritto:
> On 1/7/10 8:02 PM, ms wrote:
>> David van der Spoel ha scritto:
>>> ms wrote:
>>>> David van der Spoel ha scritto:
>>>>> ms wrote:
>> I sent another mail where I attached a table input file I use and the
>> corresponding full rtab.xvg -it is currently waiting mod approval
>> because of the size :)
> Let's try to see what's going on without it...

I hoped *you* were the mod! :)

>> I noticed that in the rtab14 (which should be the default LJ potential)
>> the values are, instead, apparently all negative, as expected.
> This is what I saw. Could it be that you specify the table with the
> wrong sign for the derivative?

The input table has the right signs (all negative for repulsion). I just
fixed an error in the signs of the attractive part -could that be the
culprit? Are repulsion and attraction interpolated *after* being summed?

The rtab14.xvg I have in output by the way has a slight oddity at the
very beginning:

3.6480002105e-02  0.0000000000e+00  0.0000000000e+00
3.6800000817e-02  0.0000000000e+00  0.0000000000e+00
3.7120003253e-02  0.0000000000e+00  0.0000000000e+00
3.7440001965e-02  0.0000000000e+00  0.0000000000e+00
3.7760000676e-02  0.0000000000e+00  0.0000000000e+00
3.8079999387e-02  3.3338824642e+14  8.2109411802e+18 <-positive values
3.8400001824e-02  7.3433434198e+15  3.3617108423e+19
3.8720004261e-02  2.0579002939e+16  4.7121167299e+19
3.9040002972e-02  3.6231459346e+16  4.8723151343e+19
3.9360001683e-02  5.0492120863e+16  3.8423506956e+19
3.9680000395e-02  5.9552762396e+16  1.6221962559e+19
3.9999999106e-02  5.9604645601e+16  -1.7881392787e+19 <-negative values
4.0320001543e-02  5.4162767418e+16  -1.6154702134e+19
4.0640003979e-02  4.9250029206e+16  -1.4573871595e+19
4.0960002691e-02  4.4819873519e+16  -1.3138938552e+19
4.1280001402e-02  4.0825553934e+16  -1.1849885413e+19
4.1600000113e-02  3.7220435695e+16  -1.0706720975e+19

The input table is like that:
0.324   0       0       0       0       19.057170805    -4903.66757218
0.325   0       0       0       0       14.5544681537   -4122.12982071
0.326   0       0       0       0       10.7761004826   -3452.22019522
0.327   0       0       0       0       7.61823859882   -2878.71133959
0.328   0       0       0       0       4.99123976902   -2388.40876887
0.329   0       0       0       0       2.81775232212   -1969.88234765
0.33    0       0       0       0       1.03107071308   -1613.23304761

and the rtab.xvg is like this:
3.2873699069e-01  3.0300402641e+00  -2.9821022949e+03
3.2893705368e-01  2.7424881458e+00  4.5555401611e+02
3.2913714647e-01  2.9011108875e+00  -6.1965881348e+02
3.2933723927e-01  2.5153810978e+00  -2.9490820312e+03
3.2953730226e-01  1.8357653618e+00  -3.5592436523e+03
3.2973739505e-01  1.2058072090e+00  -2.4505161133e+03
3.2993748784e-01  9.6973133087e-01  3.7754727173e+02
3.3013758063e-01  1.1429694891e+00  8.3080635071e+01
3.3033764362e-01  9.9677509069e-01  -1.3973664551e+03
3.3053773642e-01  6.4262789488e-01  -1.9951014404e+03
3.3073782921e-01  2.5727045536e-01  -1.7099414062e+03
3.3093789220e-01  1.7271757126e-02  -5.4204510498e+02
3.3113798499e-01  0.0000000000e+00  0.0000000000e+00
3.3133807778e-01  0.0000000000e+00  0.0000000000e+00
3.3153814077e-01  0.0000000000e+00  0.0000000000e+00
3.3173823357e-01  0.0000000000e+00  0.0000000000e+00


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