[gmx-users] How to add a repulsive harmonic potential
jalemkul at vt.edu
Tue Apr 14 17:19:52 CEST 2015
On 4/14/15 3:13 AM, atsutoshi.okabe at takeda.com wrote:
>> Depending on how structurally complex the ligands are, it may be very easy to
>> define a dummy atom within the structure using a virtual site, then specifying a
>> nonbonded interaction only between these virtual sites using [nonbond_params].
>> That way, these sites will not affect ligand-water, ligand-protein, etc but will
>> repel ligands from one another.
> Thanks for your reply.
> I tried to use [virtual_sitesn] and [nonbond_params] below.
> VS1 means virtual site( dummy atoms) of center of mass of one ligand_1.
> VS2 means virtual site( dummy atoms) of center of mass of one ligand_2.
> Complex.top file
> ;name bond_type mass charge ptype sigma epsilon
> VS1 VS1 0.0000 0.0000 V 0.00000e+00 0.00000e+00
> VS2 VS2 0.0000 0.0000 V 0.00000e+00 0.00000e+00
> [ nonbond_params ]
> ;i j func V(c6) W(c12)
> VS1 VS2 1 0.00000e+00 5.8954e+03
This isn't mathematically consistent, nor do I think it will be stable. That is
a massive repulsion at just about any distance. For a bit gentler approach,
please consider what we do with hydrophobic fragments here:
> ;nr type resnr residue atom cgnr charge mass
> 100 ha 2 LIG H7 100 0.21132 1.00000
> 101 VS1 3 VIR VS1 101 0.00000 0.00000
> 102 VS2 4 VIR VS2 102 0.00000 0.00000
> [ virtual_sitesn ]
> ; Site funct from
> 101 2 25 26 27 28
> 102 2 75 76 77 78
> However, I got fatal error below.
> Fatal error:
> Number of coordinates in coordinate file(NVT_1.gro, 77111)
> Does not match topology (complex.top, 77113)
> Does it mean that I have to add coordinate information of dummy atoms(VS1, VS2) in .gro file ?
All particles require coordinates. They're virtual, but they're not magical.
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
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