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Hi,<br><br>You seem to be trying to decouple a 9 residue peptide from the rest of the system.<br>This "brute-force" approach will only work when you have an enormous amount<br>of computer power and you will have to tune all your parameters carefully.<br>You should consider if this approach is feasible.<br><br>You crashes are probably due to the fact that you turn off all non-bonded interactions<br>in the protein. That leads to a strange state which will be difficult to integrate.<br>If you really want to pursue this approach, you should not decouple the intra-molecular<br>interactions.<br>This is far simpler in 4.0 than what you have down now.<br>Simply use the original itp file and set couple-moltype in the mdp file.<br>You should also use an intermediate state with zero charges but full LJ interactions,<br>that will make the path much smoother.<br><br>Berk<br><br><hr id="stopSpelling">From: ecino@uwo.ca<br>To: gmx-users@gromacs.org<br>Date: Thu, 17 Sep 2009 11:11:55 -0400<br>Subject: [gmx-users] free energy problem<br><br><span class="ecxApple-style-span" style="font-family: 'PrimaSans BT,Verdana,sans-serif',helvetica,sans-serif; font-size: 12px;">Hello. I am trying to run free energy calculations on a protein - protein complex. I believe that I have made all of the necessary changes to my topology, and the nonbonded parameters are set to 0 for state B. I am using the GROMOS96 53a6 ff. My system runs fine with free energy turned off, but gives many lincs warnings when it is turned on, and lambda = 0 to 0.5. Ultimately, the run crashes. One thing that I can think of that may be a problem is that state B has a nonzero charge, while A is 0. I have attached my run input, and topology. Any help is very much appreciated. Thanks. </span><br><br> Elio Cino<br>                                            <br /><hr />See all the ways you can stay connected <a href='http://www.microsoft.com/windows/windowslive/default.aspx' target='_new'>to friends and family</a></body>
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