[gmx-users] How to add a repulsive harmonic potential

[Justin Lemkul]

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
>
> [atomtypes]
> ;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:

http://pubs.acs.org/doi/abs/10.1021/ci100462t

> [atoms]
> ;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

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

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