<div dir="ltr">Thanks again!<br>Don't you know how to make a total charge = 0 in this case, if implicit salt concentration is not implemented currently? Or it is not critically? <br><br><div class="gmail_quote">2011/3/10 Per Larsson <span dir="ltr"><<a href="mailto:per.larsson@sbc.su.se">per.larsson@sbc.su.se</a>></span><br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div style="">Hi!<div><br></div><div>Yes, except that in point 2, I'm not sure about the effects of explicit ions in an implicit solvent. </div>
<div>Do deal with that properly one should use an implicit salt concentration, but that is not implemented currently. </div><div>The choice of water-model with pdb2gmx is not important. You can choose 'None' here.</div>
<div><br></div><div>Cheers</div><div>/Per</div><div><br><div><div>10 mar 2011 kl. 10.39 skrev Yulian Gavrilov:</div><div><div></div><div class="h5"><br><blockquote type="cite"><div dir="ltr">Thanks!
<p style="margin-bottom: 0in;">If I understand you correctly, I need
to do this (?):</p>
<ol><li><p style="margin-bottom: 0in;">pdb2gmx</p>
</li><li><p style="margin-bottom: 0in;">Adding ions (if I have no SOL,
what is better to choose on this step?)</p>
</li><li><p style="margin-bottom: 0in;">Minimization with mdp file, that
includes these lines:</p><p style="margin-bottom: 0in;">implicit_solvent = GBSA</p><p style="margin-bottom: 0in;">gb_algorithm = {Still,HCT,OBC}</p><p style="margin-bottom: 0in;">sa_algorithm=Ace-approximation</p>
</li><li><p style="margin-bottom: 0in;">Equilibration (nvt, npt) and MD
also with these lines in mdp files.</p>
</li></ol>
<br><br><div class="gmail_quote">2011/3/10 Per Larsson <span dir="ltr"><<a href="mailto:per.larsson@sbc.su.se" target="_blank">per.larsson@sbc.su.se</a>></span><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div>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><blockquote type="cite"><div><div></div><div><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></div></div>
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Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br></blockquote></div><br><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>
</blockquote></div></div></div><br></div></div></blockquote></div><br><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>