[gmx-users] the relationship between mdp file and the force field
brettliu123 at 163.com
Mon Apr 27 15:01:26 CEST 2015
I have read some of the force fields original paper, but my purpose is to use MD to settle some biological issues, thus I am afraid I do not have such deep understanding what explained in the original force field papers.
For Force field 6, here I mean AMBER99SB_ILDNprotein. For the MDP files, I think AMBER99SB_ILDNprotein force field, AMBER99SB protein, AMBER 99 protein, AMBER 96 protein can have the same mdp files, GROMOS96 43a1, 43a2, 45a3, 53a3, 53a5,53a6,54a7 can have the same MDP files, am I right? If we modified based on the on-line lysozyme tutorial, what items should we modify based on the original lysozyme mdp diles?
In addition, for biological research, can we definetely say GROMOS96 54a7 is better than the other versions of GROMOS96? In comparision with the GROMOS series, what is the advantages and disavantages of OPLS-AA/L all-atom force field?
I am looking forward to getting a reply from you.
At 2015-04-27 19:41:17, "Justin Lemkul" <jalemkul at vt.edu> wrote:
>On 4/26/15 10:17 PM, Brett wrote:
>> Dear All,
>> In the on-line Justin tutorial on lysozyme, the several mdp files are for the specific force field OPLS-AA force field. It specifically mentioned "Settings, particularly nonbonded interaction settings, will be different for other force fields".
>> Will you please introduce to me how to modify mdp files based on the difference of the force fields? For example, if I use force field 6, what should I modify based on the mdps of the lysozyme tutorial?
>> I am looking forward to getting your reply.
>"Force field 6" is not very precise, because the numbering in the pdb2gmx list
>varies between GROMACS versions. What force field (exactly) are you using?
>Have you read the primary literature for the force field? Settings are given in
>the parametrization/validation papers and that's what you should use.
>Justin A. Lemkul, Ph.D.
>Ruth L. Kirschstein NRSA Postdoctoral Fellow
>Department of Pharmaceutical Sciences
>School of Pharmacy
>Health Sciences Facility II, Room 629
>University of Maryland, Baltimore
>20 Penn St.
>Baltimore, MD 21201
>jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>Gromacs Users mailing list
>* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>* For (un)subscribe requests visit
>https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users