Well. It actually isn't dead but becomes very slow for large proteins. dawei<br><br><div class="gmail_quote">On Mon, Feb 7, 2011 at 11:44 AM, Da-Wei Li <span dir="ltr"><<a href="mailto:lidawei@gmail.com">lidawei@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">hi,<div><br></div><div>I did more test and found that it depended on size of the protein. Grompp will die when number of atoms of the protein is larger than about 200. Is it possible the source code limit the size of the protein that can be decoupled?</div>
<div><br></div><div>thanks.</div><div><br></div><div><br></div><div>dawei<div><div></div><div class="h5"><br><br><div class="gmail_quote">On Mon, Feb 7, 2011 at 10:34 AM, Da-Wei Li <span dir="ltr"><<a href="mailto:lidawei@gmail.com" target="_blank">lidawei@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear users<div><br></div><div>I tried free energy calculation but grompp couldn't go through. It stops after</div>
<div><br></div><div>*******************</div><div><div>Generated 2278 of the 2278 non-bonded parameter combinations</div>
<div>Generating 1-4 interactions: fudge = 0.5</div><div>Generated 2278 of the 2278 1-4 parameter combinations</div><div>Excluding 3 bonded neighbours molecule type 'Protein'</div><div>turning H bonds into constraints...</div>
<div>Excluding 2 bonded neighbours molecule type 'SOL'</div><div>turning H bonds into constraints...</div><div>Excluding 1 bonded neighbours molecule type 'CL'</div><div>turning H bonds into constraints...</div>
<div>Coupling 1 copies of molecule type 'Protein'</div></div><div>*******************</div><div><br></div><div>The CPU usage is 100%. </div><div><br></div><div>I just add following into the mdp file:</div><div><div>
<br></div><div>***************</div><div>free_energy = yes </div><div>init_lambda = 0.0</div><div>delta_lambda = 0</div><div>sc_alpha =0.5</div><div>sc-power =1.0</div>
<div>sc-sigma = 0.3 </div><div>couple-moltype = Protein </div><div>couple-lambda0 = vdw-q</div><div>couple-lambda1 = none</div></div><div>***************</div><div><br></div>
<div>Does anyone have some idea about this problem? thanks.</div><div><br></div><div>Another question is whether I can switch off "two molecules" (such as protein+ligand) in free energy calculation? I searched this list and got that 4.0.7 did support this. how about 4.5.4?</div>
<div><br></div><div>dawei</div><div><br></div><div><br></div><div><br></div>
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