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Hi,<br><br>I would say that it is very uncommon to form a bond during free energy calculations.<br><br>To make this work easily we would need to introduce a pair interaction with all parameters explicit<br>that can be perturbed.<br><br>For the moment you should be able to get it to work using tabulated bonded interactions.<br>The only thing that is not supported through that are soft-core interactions, but I guess<br>those will not be necessary for 1-4 interactions.<br><br>Berk<br><br>> Date: Fri, 20 Nov 2009 14:01:28 +0100<br>> From: jochen@xray.bmc.uu.se<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] Disulfide bridge formation between A and B state<br>> <br>> Hi,<br>> <br>> I have yesterday already started a topic, but I think I was a bit <br>> unclear about what is the problem.<br>> <br>> I want to have a disulfide bridge in the B state, but not in the A <br>> state. And I have not found a way to get the Coulomb interaction between <br>> the two sulfurs (and other nearby atoms) right in the A and in the B state.<br>> <br>> A-state:<br>> ...C-S-H H-S-C...<br>> <br>> B-state:<br>> ... C-S-S-C<br>> | |<br>> H H (where these two H are dummies in B)<br>> <br>> To close the S-S bond smoothly by going from lambda=0 to 1, I have added <br>> a bond type 6 (harmonic potential)<br>> [ bonds ]<br>> S-nr S-nr 6 b0 k<br>> and, a bond type 5 (connection without interaction)<br>> S-nr Snr 5<br>> That is required since otherwise, I will have full LJ interaction in B <br>> state between, e.g. between the two sulfurs. To have correct LJ <br>> interaction in A, I have added pairs between all required atoms, so the <br>> LJ should be fine.<br>> <br>> But what about the charges? If I have a connection between, e.g., <br>> sulfur1 and sulfur2, I will never have a coulomb interaction. The <br>> problem seems that there is no way to scale a coulomb interaction <br>> between two atoms between A and B. There is a pair type 2, that <br>> apparently allows to add 1-4 charge interactions, but the parameters <br>> cannot be scaled between state A and B (manual table 5.4).<br>> <br>> I feel that forming a bond with the FEP should be more or less common <br>> thing, that's why I am surprised that there seems to be no solution for <br>> that. Or am I missing something here?<br>> <br>> Any ideas?<br>> <br>> Thanks a lot,<br>> <br>> Jochen<br>> <br>> <br>> <br>> -- <br>> ---------------------------------------------------<br>> Dr. Jochen Hub<br>> Molecular Biophysics group<br>> Dept. of Cell & Molecular Biology<br>> Uppsala University. Box 596, 75124 Uppsala, Sweden.<br>> Phone: +46-18-4714451 Fax: +46-18-511755<br>> ---------------------------------------------------<br>> <br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php<br> <br /><hr />New Windows 7: Find the right PC for you. <a href='http://windows.microsoft.com/shop' target='_new'>Learn more.</a></body>
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