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TYR on graphene

An example for conformers of tyrosine on a graphene cutout.


Conformational sampling of tyrosine on a graphene surface

To sample a tyrosine molecule at a graphene surface, the graphene sheet has to be constrained. All atoms in the graphene layer are constrained and removed from the metadynamics list. For a detailed guide on how to fix substructure parts see Example 4.

Tyrosine on graphene
Tyrosine on a graphene cutout.

In order for the caluculation to be stable, some of the MD settings have to be adjusted. The SHAKE constraint is turned off (--shake 0), the timestep is reduced to 1 fs (--tstep 1), and only the unconstrained atoms are included in the metadynamics bias and structure comparisons in CREGEN (--subrmsd).

crest coord --subrmsd --shake 0 --tstep 1 --cinp constraints.inp
$coord
    25.57030991921202   -1.29059115296523   -0.00598160501741      C
    25.57044241258889    1.28341269512943   -0.00397025649369      C
    23.26056590790795    2.70217665940709   -0.00029100251731      C
    23.24029402398585    5.32779404644931    0.00100734191172      C
    20.94157103860908    6.71653777403401    0.00350095166658      C
    20.91152361664611    9.36664222799565    0.00390218154564      C
    18.62125921494789   10.73533662251798    0.00644642379287      C
    18.58134086796354   13.40310199790359    0.00577252431633      C
    16.30144187186615   14.75441822463413    0.00911453357094      C
    16.24838174294015   17.43954219647988    0.00645557179198      C
    13.98481323267349   18.77014376357869    0.00996412506652      C
    13.91132086532623   21.47993962309619    0.00398308521361      C
    11.68223395792687   22.76705405593083    0.00667868517840      C
    23.23975279130400   -5.33474095446540   -0.00731302769541      C
    23.26029458648507   -2.70912180306862   -0.00467349937707      C
    20.93174016704535   -1.33727196043975   -0.00133108922934      C
    20.93188342707722    1.33055529046503    0.00081585427198      C
    18.61221093462830    2.68271748197896    0.00282646704916      C
    18.60800793365893    5.36022077189572    0.00464910445605      C
    16.29058723267624    6.70694827919018    0.00657403025646      C
    16.28436011426403    9.38628406493185    0.00875170443409      C
    13.96723583506467   10.73158318782874    0.01208246556117      C
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    22.64102523397671  -10.38177606637344   -0.01282653219870      H
    -2.30271237654611  -24.78134786444018   -0.00066468432950      H
    -24.92242630623978  -6.35644775444972    0.02400571974929      H
    -22.59910878260334  10.37717801353707    0.02571014278132      H
    -27.24448188791929   2.33134552584358    0.01877626642906      H
    4.27571474378505    -1.92854948200207    9.94745802440185      N
    4.85863257632589    -1.86976812841619   11.77386435287947      H
    2.41997661925239    -2.42173187608252    9.97254129755107      H
    4.53188129867197     0.54201882289930    8.80305477310553      C
    3.10180400437508     2.58147803262171   10.25033240656862      C
    1.70252284002797     2.17538275447565   11.99395863899712      O
    3.59502480456652     4.91081582322646    9.40273172353399      O
    2.64101197107364     6.15144169604561   10.36051515045620      H
    6.53940694073007     1.05972961089276    8.80707208579245      H
    3.60684313919014     0.48755395354171    6.03553367623200      C
    0.79623558975634     0.11581314423023    5.88366583446487      C
    -0.24093223813749   -2.29403771457139    5.84928985318257      C
    -2.83094211079699   -2.64168158463332    5.81583719831421      C
    -4.43914545143533   -0.56757465165303    5.80885193908835      C
    -3.41896413800189    1.85508153404960    5.82002566936256      C
    -0.83164012890154    2.17804731008809    5.85479160455166      C
    -0.06058114066044    4.06926172450655    5.83858398852997      H
    -4.68432097650001    3.45280350209968    5.79576231758199      H
    -6.99839493428426   -0.81481618645066    5.77227418763592      O
    -7.44727356719986   -2.58190479542918    5.74085372355529      H
    -3.61086295708159   -4.53297500622820    5.78522163995966      H
    0.99207739459520    -3.92144387056497    5.83721740609899      H
    4.58691246909114    -1.06321033030212    5.09739729211277      H
    4.13984012793008     2.26724282543661    5.14389351386854      H
$end
$constrain
    atoms: 1-252
    force constant=0.5
    reference=coord.ref
$metadyn
    atoms: 253-276
$end

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Copyright © 2022-2023 Philipp Pracht.

CREST is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.