[gmx-users] question about OPLS-AA force field -required bond constraints
mrshirts at gmail.com
Thu Oct 10 19:01:52 CEST 2013
OPLS-AA was generally derived with Monte Carlo, which means that all
bonds were exactly constrained. But read the papers!
On Thu, Oct 10, 2013 at 12:27 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 10/10/13 12:17 PM, Martin, Erik W wrote:
>> Hi, I'm new to both Gromacs and OPLS. I have always used CHARMM or AMBER
>> before so am a bit confused about some idiosyncrasies.
>> When I go to a production run on my system (a protein in a truncated
>> octahedron box of Tip4 water) I have removed all constraints. When I run
>> grompp, I get an error telling me that a bond between a HG proton and OG
>> oxygen of protein has an oscillation period of 9e-3 ps and is incompatible
>> with my 1 fs time step. I am used to being able to run a completely
>> unconstrained simulation with a 1 fs time step… so I'm assuming this is a
>> property of OPLS-AA?
> No, it's not. It's a property of the bonds. Nearly all force fields (if
> not all of them) constrain X-H bonds at minimum, to remove the fastest
> motions in the system and allow for a longer time step. Using dt on the
> same order as the fastest frequencies leads to instability. See manual
> section 6.7.
>> Could someone please let me know what the bond constraint requirements are
>> for OPLS-AA and GROMOS forcefields (I'm going to need to use that next).
>> can't seem to find this information by searching but imagine its on a
> Information like this should be in the primary literature for the parameter
> sets. I don't know of any sort of database online that tracks such things,
> and moreover there are no absolute rules AFAIK. I generally follow the
> methods of the paper that derived the parameter set. Unfortunately,
> sometimes they don't say. For Gromos96 53A5/53A6, validation simulations
> were carried out with all bonds constrained.
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> gmx-users mailing list gmx-users at gromacs.org
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
More information about the gromacs.org_gmx-users