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Thank you for your reply, <br><br>Settings: <br>I am using the procedure
outline by the "speptide" tutorial (i.e. pdb2gmx, followed by editconf,
genbox, grompp, and mdrun). The ".mdp" file I've used is as follows: <br><br>;
User spoel (236)<br>; Wed Nov 3 17:12:44 1993<br>; Input file<br>;<br>cpp
= /usr/bin/cpp<br>define = -DPOSRES <br>constraints
= none<br>integrator = steep<br>nsteps = 100<br>;<br>;
Energy minimizing stuff<br>;<br>emtol = 20<br>emstep
= 0.01<br><br>nstcgsteep = 10<br>nstcomm = 1<br>ns_type
= grid<br>rlist = 1<br>rcoulomb = 1.0<br>rvdw
= 1.0<br>Tcoupl = no<br>Pcoupl = no<br>gen_vel
= no<br>coulombtype = PME<br><br>Force field: Encad all atom
force field, using full sovent charges.<br><br>Local geometry is
identical with the exception of the second charged residue, which is
replaced by Leucine in one structure. <br><br>> Date: Mon, 3 May 2010 12:11:12 -0400<br>> From: jalemkul@vt.edu<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] electrostatic interactions<br>> <br>> <br>> <br>> abdullah ahmed wrote:<br>> > Hello everyone,<br>> > <br>> > I have just started using GROMACS, and apolise if my question is naive.<br>> > <br>> > Basically, I'd like to ask if anyone has some suggestions regarding the <br>> > settings I should use for electrostatic interactions?<br>> > <br>> <br>> Well, you haven't shown us what settings you're using or what force field you're <br>> using, so it's impossible to make any specific recommendation. Your cutoffs and <br>> type of long-range electrostatics method will be largely dictated by the force <br>> field you've chosen. The primary literature will tell you a lot.<br>> <br>> > I have two protein molecules similar in everyway except, one has a <br>> > single negative charge inside the molecule, and another has two opposite <br>> > charges facing each other. The opposite charges are close enough to form <br>> > electrostatic interactions, so would expect the coloumb energy for this <br>> > molecule to be less than the other after minimization/molecular <br>> > dynamics. However, the results show that they are almost the same.<br>> > <br>> <br>> It's hard to comment on the accuracy of these results without a lot more <br>> information (see above). Other factors include the local geometry of other <br>> surrounding residues; if the structures are different (even subtly) you <br>> certainly can't make any generalizations.<br>> <br>> -Justin<br>> <br>> > Thank you in advance for your help,<br>> > Abdullah Ahmed<br>> > <br>> > ------------------------------------------------------------------------<br>> > Hotmail: Powerful Free email with security by Microsoft. Get it now. <br>> > <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 />Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. <a href='https://signup.live.com/signup.aspx?id=60969' target='_new'>Sign up now.</a></body>
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