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Thank you for your reply, <br><br>However, I can not use MD. <br>I would simply like to ask whether I am correct in assuming that the minimized energies of the two structures should be very different. <br><br>> Date: Tue, 4 May 2010 08:41:15 -0400<br>> From: jalemkul@vt.edu<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] electro-static potential energy after minimization<br>> <br>> <br>> <br>> abdullah ahmed wrote:<br>> > Hello everyone,<br>> > <br>> > I have two protein structures, and the insides of both are not exposed <br>> > to water.<br>> > One structure contains two oppositely charges residues (GLU and LYS) <br>> > facing each other. The second structure contains a GLU residue only.<br>> > Upon minimization I had expected the coloumb energies of the first <br>> > structure to be lower than that of the second. However, this was not the <br>> > case, they are both very similar.<br>> > Does anyone have an idea as to why this has happened?<br>> > (The only explaination I can come up with is that perhaps the effect is <br>> > so small that it can not be seen)<br>> > <br>> <br>> We discussed this at length yesterday. By doing a simple energy minimization <br>> (in which, if I recall, you are applying position restraints), you stand to <br>> prove very little. By doing MD and obtaining an ensemble of energies, you stand <br>> a better chance of calculating a relevant energy.<br>> <br>> > I was not sure if providing PDB and .mdp files would be helpful, but I <br>> > can send then in my next mail if neccesary.<br>> > <br>> <br>> The .pdb file is unnecessary. Only post the .mdp file if it has changed since <br>> the one you posted yesterday.<br>> <br>> -Justin<br>> <br>> > Thank you in advance!<br>> > Abdullah Ahmed<br>> > <br>> > ------------------------------------------------------------------------<br>> > Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. Sign up <br>> > now. <https://signup.live.com/signup.aspx?id=60969><br>> > <br>> <br>> -- <br>> ========================================<br>> <br>> Justin A. Lemkul<br>> Ph.D. Candidate<br>> ICTAS Doctoral Scholar<br>> MILES-IGERT Trainee<br>> Department of Biochemistry<br>> Virginia Tech<br>> Blacksburg, VA<br>> jalemkul[at]vt.edu | (540) 231-9080<br>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<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 />Hotmail: Trusted email with Microsoft’s powerful SPAM protection. <a href='https://signup.live.com/signup.aspx?id=60969' target='_new'>Sign up now.</a></body>
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