[gmx-users] No group in index file?
Xu Dong Huang
xudonghmath at gmail.com
Thu Oct 31 21:44:35 CET 2013
I did not define [angles] in the topology but I do have the angles result from All-atom run using OPLS forcefield. The reason for me not to include it in MARTINI forcefield topology is because I wanted to see if it will produce similar angle result of atom 1&2, 1&3 and 2&3 in martini water since the behavior of particle types I chose for my 3 atoms are well defined by martini at this point. My interest is to find for which force constant K value will the martini model match the all-atom model using OPLS.
And you’re right, sorry, I got confused about the angles, there should only be 1. However, even the angle value I received doesn’t match the traditional all-atom result.
What will happen if I define the [angles] part with the angles I received from traditional simulation? Because ultimately I am trying to find the k value parameter that will make the 3 particle display an angle similar to traditional run.
On Oct 31, 2013, at 4:26 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 10/31/13 4:22 PM, Xu Dong Huang wrote:
>> @ Justin,
>> That doesn’t sound very good. I tried it as he suggested using make_ndx, it
>> seems to work, but it’s not reporting the result I want. When I use g_angle
>> using the index i created, I chose the group I want to assess (My compound is
>> very simple in Martini, it’s only represented by 3 atoms) and it reports back
>> to me 1 angle value. However, I wish to assess the angle between atom 1 & 2,
>> 2&3 and 1&3. How should I go about achieving that?
> If you have 3 atoms/particles, there can be only one angle, by definition.
> Do you have an [angles] directive in the topology? That's how mk_angndx parses the .tpr file - by creating groups of similar angles based on theta and ktheta. If your model doesn't specify any angle potential, then mk_angndx will bail out and return nothing, though it should probably do that in a more elegant way than producing an empty file.
> 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
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