Re: [gmx-users] adding counter ions
OZGE ENGIN wrote: Dear Mark, I had read papers about the simulations of charged systems. You' re right. In these studies, the distance between the charged residues have been controlled during the simulation. In this respect, you suggest me not adding counter ions to the system: Providing the distance between the oppositely charged residues :-) is not far apart than the optimum which means that they are located at such a distance that they have the ability to cancel each other. If they're already 3 angstrom apart you won't want counter ions, but if they're 3nm apart you will. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: Re: [gmx-users] adding counter ions
Dear Mark, I had read papers about the simulations of charged systems. You' re right. In these studies, the distance between the charged residues have been controlled during the simulation. In this respect, you suggest me not adding counter ions to the system: Providing the distance between the oppositely charged residues :-) is not far apart than the optimum which means that they are located at such a distance that they have the ability to cancel each other. Thank you... Ozge Engin -Original Message- From: Mark Abraham <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Date: Tue, 12 Jun 2007 10:49:54 +1000 Subject: Re: [gmx-users] adding counter ions OZGE ENGIN wrote: > Hi all, > > My peptide contains two adversely charged residues. I use PME option for the > investigation of electrostatic interactions within my system. The total > charge of the box must be neutral. Since the system contains adversely > charged residues, is it still necessary to add counter ions into the system? "adversely charged" doesn't mean the same thing as "oppositely charged" :-) While overall periodic cell neutrality has been achieved here, you will still have separated charges that will attract each other, potentially distorting your equilibrium state. In a real system, each of these residues would likely have a counter-ion present closer than the other residue - but of course you know how far apart these residues are, don't you? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] adding counter ions
OZGE ENGIN wrote: Hi all, My peptide contains two adversely charged residues. I use PME option for the investigation of electrostatic interactions within my system. The total charge of the box must be neutral. Since the system contains adversely charged residues, is it still necessary to add counter ions into the system? "adversely charged" doesn't mean the same thing as "oppositely charged" :-) While overall periodic cell neutrality has been achieved here, you will still have separated charges that will attract each other, potentially distorting your equilibrium state. In a real system, each of these residues would likely have a counter-ion present closer than the other residue - but of course you know how far apart these residues are, don't you? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] adding counter ions
Not for the sake of the PME, since your system has no net charge. However, there a few papers out there discussing the need for counterions for proper folding and such. /Erik 8 jun 2007 kl. 13.11 skrev OZGE ENGIN: Hi all, My peptide contains two adversely charged residues. I use PME option for the investigation of electrostatic interactions within my system. The total charge of the box must be neutral. Since the system contains adversely charged residues, is it still necessary to add counter ions into the system? Thanks in advance! Ozge Engin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 4537 fax: +46 18 511 755 [EMAIL PROTECTED] http://xray.bmc.uu.se/molbiophys ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
