The thing is, I'm working with literally thousands of proteins, and running some basic simulations on them. Therefore I need to run these simulations using scripts, so I guess u can't expect me to know every charge distribution... These simulations may well be worthless and bogus, but I try to do my best to make them meaningful...
<br><br><div><span class="gmail_quote">On 12/21/05, <b class="gmail_sendername">Mark Abraham</b> <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Tamas Horvath wrote:<br>> I have a protein in water system. The protein has some charge, which I<br>> want to neutralise, introducing stochastic ammount of K+ or Cl-. As far<br>> as I figured out, the best way to do it is to use genion. Only I don't
<br>> know beforehand what the protein's charge would be, so I'm wondering if<br>> it's possible to tell genion to neutralise the system?<br><br>Not knowing the pattern of charge distribution in your protein, and thus
<br>the net charge, sounds to me like a great way to run the risk of doing<br>some worthless simulations and/or bogus science for want of a few<br>minutes of observation and thought. I'd call the gromacs utility<br>programs' inability to automatically neutralise a system a feature, not
<br>a bug!<br><br>Cheers,<br><br>Mark Abraham<br>_______________________________________________<br>gmx-users mailing list<br><a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">
http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please don't post (un)subscribe requests to the list. Use the<br>www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org
</a>.<br></blockquote></div><br>