[gmx-developers] modifying mdrun for non-pairwise-additive potentials

[Graham Smith]

Hi - 

I want to do a simulation of a simple lipid model consisting of just
hydrophilic and hydrophobic particles, with no water in the system. (based
on Noguchi and Takasu PRE v64 041913 (2001), if anyone's read that). There
are coulomb, soft-core repulsion, and hydrophobic attraction terms, which
I've implemented in an xvg file that is read with -table. The hydrophobic
attraction is in the h and h'' columns corresponding to C12.  By making
suitable topology files with explicit C6_ab and C12_ab parameters I've got
this to work at a pairwise-additive way. So far so good. 

What I now need to do is to modify the potential so that the hydrophobic
part "saturates". 

 ie instead of v_hb[i] = s 
                       = sum_j v_hb[i][j]
 
 I want v_hb'[i] = u ( s )
 where u (s) ~ s at small s and tends to a constant c at large s. 

 In practise I think I'll have to implement this by altering the forces, 
 multiplying by du/ds. 

I hoped at first that f_coul, f_lj6 and f_lj12 would be accumulated
separately for each particle, then summed, so I could get at them there,
but instead it seems that they are added up in the inner loops. I don't
have the godlike programming powers needed to alter these, so I'm thinking
instead of changing function force in force.c to call do_fnbf twice :

  do_fnbf(...forcerec fr, ... rvec f[], .. 
  do_fnbf(...forcerec fr0, ... rvec f0[], .. 

where fr0 has all the c12_ab parameters set to 0, so will get zero for
all the hydrophobic forces. Thus f[i] - f0[i] is the hydrophobic force,
which I can fix and add back to f0. 

Is there any reason why this won't work? I don't mind the big performance
hit. 

Also, could somebody help me with what exactly to I have to do in forcerec
fr0? I guess should be an almost exact copy of fr, (so I'll copy the ints,
reals etc, and set internal pointers to point to the corresponding parts
of fr). The exception is c12 parameters; are these fr->vdwtab or
fr->coulvdwtab or something else?  

Thanks, 

-Graham 

########################################################################

Dr. Graham R. Smith, 		       Department of Biological Sciences,  
Biomolecular Modelling Laboratory,     Biochemistry Building,              	
Cancer Research UK, 		       Imperial College of Science,        	
44 Lincoln's Inn Fields, 	        Technology & Medicine,             	
London WC2A 3PX,		       London SW7 2AZ,                     	
U.K. 				       U.K.                                	
Tel: +44-(0)20 7269 3348 	       Tel: +44-(0)20 7594 5734            	
email: graham.smith at cancer.org.uk	
URL: http://www.bmm.icnet.uk/~smithgr