[gmx-users] Understanding of OPLS-all atomic FF

minnale minnale_gnos at rediffmail.com
Wed Jun 4 20:02:31 CEST 2008

Thanks for your reply Justin and I cleared my doubt.
Yes I am using POPC parameters from Tielemen's website.

On Wed, 04 Jun 2008 Justin A.Lemkul wrote :
>Are you referring to the POPC structure available from Tieleman's site, and thus the parameters found in lipid.itp and popc.itp?  Those are united-atom structures.  The parameters for them were based in part on OPLS parameters, hence the argument can be made that the OPLS-AA force field can be used in conjunction with these parameters, if one is careful to keep the force fields consistent (i.e., Chris Neale's procedure).
>minnale wrote:
>>  Hi all,
>>this may be a trivial question to you that, I am using OPLS-all atomic  FF for both protein and lipids. When I do protein simulations I can say that simulating protein with OPLS-all atomic FF by noticing protein.gro contain all atoms(N,H,C-alpha,HA1,HA2,C,O for Glycine etc...) for each amino acid residue, but I have doubt that how can you say that popc type lipids are simulating with OPLS-all atomic FF? if I open popc.gro files,couldnt able to find difference between atom types of opls-FF or gromos96 43a1 or some other FF.
>>Thanks in advance. 
>>gmx-users mailing list    gmx-users at gromacs.org
>>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 gmx-users-request at gromacs.org.
>>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>-- ========================================
>Justin A. Lemkul
>Graduate Research Assistant
>Department of Biochemistry
>Virginia Tech
>Blacksburg, VA
>jalemkul[at]vt.edu | (540) 231-9080
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080604/00ae08c4/attachment.html>

More information about the gromacs.org_gmx-users mailing list