[gmx-users] Re: how to write the correct top file for membrane protein
Hi Mark, i indeed checked some publications about how to choose lipid force field, please check this reference: Journal of Physics: Condensed Matter 18(2006) S1221-S1234, Tieleman and his coworkers tested two combinations: Berger+ffgmx+SPC, Berger+OPLS+TIP4P, and they recommended that using OPLS together with united-atom lipid force field. So, i would like to know whether it is reasonable or not, and how should i modify them in top file? Thanks for your reply. Liang - Original Message - From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Sent: Monday, November 26, 2007 5:28 PM Subject: gmx-users Digest, Vol 43, Issue 96 Message: 4 Date: Mon, 26 Nov 2007 12:24:31 +0800 From: Mark Abraham [EMAIL PROTECTED] Subject: Re: [gmx-users] Re: how to write the correct top file for membrane protein To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1; format=flowed liang wrote: Dear Mark, Thanks for your advice, but from my understanding, Berger's force field is based on OPLS/Amber. Lipid itp files from Tieleman's website just use the atom type definitions from GROMOS87. And GROMOS87 is out of fashion now. So thats why i think it would be better to use OPLS for protein and ffgmx.itp for lipid. Fine, but you can't use them both at the same time (unless you want to produce indefensible gibberish), and ffgmx is deprecated anyway. I am not sure whether I misunderstand the usage of Berger's force field, if i am wrong, please give me further instruction. See my advice last time. Don't mix forcefields unless you already have hard evidence that this combination works - and I'm not aware of any. The link Justin provided warns you about that. You need to find a force field that has parameters optimized that suit your system. Mixing anything else is about 99% likely to make an expensive (and poor) random number generator. Look in the literature for systems similar to yours and see if their ideas on force fields are suitable for you to use. Making it up based on stuff you found on the web is for high school students doing assignments :-) 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] Re: how to write the correct top file for membrane protein
Dear Mark, Thanks for your advice, but from my understanding, Berger's force field is based on OPLS/Amber. Lipid itp files from Tieleman's website just use the atom type definitions from GROMOS87. And GROMOS87 is out of fashion now. So thats why i think it would be better to use OPLS for protein and ffgmx.itp for lipids. I am not sure whether I misunderstand the usage of Berger's force field, if i am wrong, please give me further instruction. I hope it would not be bothering you. Thanks so much! Liang Dear Justin, Thanks for you quickly reply. I have tried before to comment out the section of [ defaults ] in the next itp file, but still too many warnings and final crashed. And i think it would not be the best method to solve this problem, because i have to use ffgmx.itp to deal with DPPC. Is there any other method i can try? Don't mix forcefields unless you already have hard evidence that this combination works - and I'm not aware of any. The link Justin provided warns you about that. You need to find a force field that has parameters optimized that suit your system. Mixing anything else is about 99% likely to make an expensive (and poor) random number generator. 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] Re: how to write the correct top file for membrane protein
liang wrote: Dear Mark, Thanks for your advice, but from my understanding, Berger's force field is based on OPLS/Amber. Lipid itp files from Tieleman's website just use the atom type definitions from GROMOS87. And GROMOS87 is out of fashion now. So thats why i think it would be better to use OPLS for protein and ffgmx.itp for lipid. Fine, but you can't use them both at the same time (unless you want to produce indefensible gibberish), and ffgmx is deprecated anyway. I am not sure whether I misunderstand the usage of Berger's force field, if i am wrong, please give me further instruction. See my advice last time. Don't mix forcefields unless you already have hard evidence that this combination works - and I'm not aware of any. The link Justin provided warns you about that. You need to find a force field that has parameters optimized that suit your system. Mixing anything else is about 99% likely to make an expensive (and poor) random number generator. Look in the literature for systems similar to yours and see if their ideas on force fields are suitable for you to use. Making it up based on stuff you found on the web is for high school students doing assignments :-) 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
