[gmx-users] use g_mindist to generate restraints

Weingarth, M.H. M.H.Weingarth at uu.nl
Sun May 15 17:41:15 CEST 2011

Dear gromacs users,

I wonder if it would be possible to generate restraints in the following manner:

I do simulations of a peptide embedded in a lipid bilayer and I have experimental NMR data which reflect the number of water molecules within a radius of ~ 0.9 - 1.0 nm for several carbons of my peptide.

I could use these data to preorient my peptide to the membrane. I did a run of ~ 100 ns and back-calculated the experimental data 
with g_mindist with the -on and -d 0.9 flags. This gives me the number of water molecules around a certain carbon within a radius of 0.9 nm and the MD matches the NMR data rather well actually. 

My question would be if it would be possible to exploit these data as restraints :

for instance :

Carbon C1 has ~ 100 - 300 water molecules within a radius of 0.9 nm
Carbon C5 has ~ 50  - 150 water .............................0.9 nm
Carbon C8 ......10  - 50 water ..............................0.9 nm

Once this would not be given, I woud like to apply a penalty function. In this manner, I might be possible to place a peptide on the bilayer surface and to use the number of sourrunding H20 as a driving force to insert it in in the membrane without any preorientation.

Unfortunaly, I do not know how to generate such restraints - to create .itp files with g_sas is not an option for what I calculate is very different from the solvant accessible surface.

Thank a lot for any help & suggestions.



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