<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi!<div><br></div><div>Starting an implicit solvent simulation works just as starting a "normal", explicit solvent simulation, except there is no solvent molecules.</div><div>You should use version 4.5.3 for this though (4.0.5 will not work). </div><div><br></div><div>Then you specify in the mdp-file implicit_solvent = GBSA and use pdb2gmx, grompp, mdrun etc... as you otherwise would do.</div><div>The choice of the Born radii model is set by gb_algorithm = {Still,HCT,OBC} and the non-polar solvation is calculated using sa_algorithm=Ace-approximation.</div><div><br></div><div>Cheers</div><div>/Per</div><div><br></div><div><div><div>10 mar 2011 kl. 10.10 skrev Yulian Gavrilov:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div dir="ltr">Dear, all<br>I just begin to work in gromacs.<br>I would like to run on a protein with amber99. <br>Is there someone here that successfully did a protein simulation in<br>GROMACS with implicit solvent and willing to explain the procedure and<br>
share the parameters used (especially force field). <br><br>In mdout.mdp (gromacs 4.0.5) I found this lines. Can I add them to md.mdp? How to change this parameters correctly? <br>What changes should be done on the previous steps? I mean, how to start a simulation with implicit solvent model from the very beginning?<br>
Sorry for primitive question, but I did not found any useful information about it for the begginers. <br><br>; IMPLICIT SOLVENT ALGORITHM<br>implicit_solvent = No<br><br>; GENERALIZED BORN ELECTROSTATICS<br>; Algorithm for calculating Born radii<br>
gb_algorithm = Still<br>; Frequency of calculating the Born radii inside rlist<br>nstgbradii = 1<br>; Cutoff for Born radii calculation; the contribution from atoms<br>; between rlist and rgbradii is updated every nstlist steps<br>
rgbradii = 2<br>; Dielectric coefficient of the implicit solvent<br>gb_epsilon_solvent = 80<br>; Salt concentration in M for Generalized Born models<br>gb_saltconc = 0<br>; Scaling factors used in the OBC GB model. Default values are OBC(II)<br>
gb_obc_alpha = 1<br>gb_obc_beta = 0.8<br>gb_obc_gamma = 4.85<br>; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA<br>; The default value (2.092) corresponds to 0.005 kcal/mol/Angstrom^2.<br>
sa_surface_tension = 2.092<br clear="all"><br>-- <br><div dir="ltr"><p style="margin-bottom: 0in;">Sincerely,</p><p style="margin-bottom: 0in;">Yulian Gavrilov
</p></div><br>
</div>
-- <br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to gmx-users-request@gromacs.org.<br>Can't post? Read http://www.gromacs.org/Support/Mailing_Lists</blockquote></div><br></div></body></html>