| This is part of the colvar module |
An alias to the MULTI-RMSD function.
- Compulsory keywords
| REFERENCE | a file in pdb format containing the reference structure and the atoms involved in the CV. |
| TYPE | ( default=MULTI-SIMPLE ) the manner in which RMSD alignment is performed. Should be MULTI-OPTIMAL, MULTI-OPTIMAL-FAST, MULTI-SIMPLE or MULTI-DRMSD. |
- Options
| NUMERICAL_DERIVATIVES | ( default=off ) calculate the derivatives for these quantities numerically |
| NOPBC | ( default=off ) ignore the periodic boundary conditions when calculating distances |
| SQUARED | ( default=off ) This should be set if you want the mean squared displacement instead of the root mean squared displacement
|
- Examples
Just replace MULTI-RMSD with MULTI_RMSD
MULTI_RMSD REFERENCE=file.pdb TYPE=MULTI-DRMSD
and remember to use a pdb file like the one below to define the reference structure
ATOM 2 O ALA 2 -0.926 -2.447 -0.497 1.00 1.00 DIA O
ATOM 4 HNT ALA 2 0.533 -0.396 1.184 1.00 1.00 DIA H
ATOM 6 HT1 ALA 2 -0.216 -2.590 1.371 1.00 1.00 DIA H
ATOM 7 HT2 ALA 2 -0.309 -1.255 2.315 1.00 1.00 DIA H
ATOM 8 HT3 ALA 2 -1.480 -1.560 1.212 1.00 1.00 DIA H
ATOM 9 CAY ALA 2 -0.096 2.144 -0.669 1.00 1.00 DIA C
ATOM 10 HY1 ALA 2 0.871 2.385 -0.588 1.00 1.00 DIA H
TER
ATOM 12 HY3 ALA 2 -0.520 2.679 -1.400 1.00 1.00 DIA H
ATOM 14 OY ALA 2 -1.139 0.931 -0.973 1.00 1.00 DIA O
ATOM 16 HN ALA 2 1.713 1.021 -0.873 1.00 1.00 DIA H
ATOM 18 HA ALA 2 0.099 -0.774 -2.218 1.00 1.00 DIA H
ATOM 19 CB ALA 2 2.063 -1.223 -1.276 1.00 1.00 DIA C
ATOM 20 HB1 ALA 2 2.670 -0.716 -2.057 1.00 1.00 DIA H
ATOM 21 HB2 ALA 2 2.556 -1.051 -0.295 1.00 1.00 DIA H
ATOM 22 HB3 ALA 2 2.070 -2.314 -1.490 1.00 1.00 DIA H
END
1.8.14