[gmx-users] calculation the force of interaction

[Nicolas Sapay]

  Hello,

In the same context that my question of yesterday (see the post at the 
end of this message), I'm interested in calculating the force of the 
interaction between lipids and solvent. More precisely, I want to 
calculate the norm of the force vector related to all non-bonded 
interactions (LJ+Coulomb). Is it possible to do that in Gromacs without 
severely hacking the code? I have searched in the mailing-list but have 
found only few posts about that, all on the developer mailing-list.

thanks

Nicolas

Nicolas Sapay wrote:
> Hello everybody,
>
> I have a system made of lipid and water and I want to calculate the 
> components of the lipid-lipid, lipid-water and water solvent 
> interactions (LJ+electrostatics).  I know there is already a lot of 
> explanations about that kind of stuff on the mailing-list. I have 
> carefully read all of them. Probably too carefully because I'm pretty 
> confused now :(. Can someone tell me if my protocol is correct or not?
>
> 0. As a preliminary remark, I may need to specify my MD parameters:
> vdwtype = Cut-off
> rvdw = 1.4
> coulombtype = PME
> rcoulomd = 1.0
> rlist=1.0
>
> 1. For the LJ interactions:
> There is not much to do except running g_energy. For the Lipid-Water 
> LJ interactions, I just have to sum LJ-SR:DOPC-SOL + LJ-LR:DOPC-SOL. 
> Same thing for Lipid-Lipid and Water-Water interactions
>
> 2. For the Electrostatic interactions:
> Still with g_energy, I can get the Coul-SR interactions. But Coul-LR 
> need additional calculations because of the PME. I need to rerun my 
> trajectory with
>    - a. charge set to 0.00 on water molecules
>    - b. charge set to 0.00 on POPC molecules
> Then, the Coul-LR:DOPC-DOPC term is equal to the Coul.-recip. in run 
> 'a' and the Coul-LR:SOL-SOL term is equal to the Coul.-recip. in run 
> 'b'. The Coul-LR:DOPC-SOL is equal to the Coul.-recip. of the initial 
> run. Now, I just have to sum Coul-SR and Coul-LR
>
> 3. Now, what if I want to measure the head group-water interactions 
> (supposing the group is correctly defined in my .ndx)? For the LJ and 
> the short range electrostatic interactions, it is the same thing than 
> previously. For the long range electrostatic interactions, I need to 
> do more rerun with :
>  - c.  charge set to 0.00 on everything except lipid head groups
>  - d.  charge set to 0.00 on everything except water molecules
>  - e.  charge set to 0.00 on everything except head groups and water
>  - f.  charge set to 0.00 on everything except acyl chains and water
>  - g.  charge set to 0.00 on everything except acyl chains and head 
> groups
>  - h.  charge set to 0.00 on everything except acyl chains
> Then, Coul-LR:headgroup-headgroup=Coul.-recip. of  '1' - 
> ('c'+'d'+'f'+'g'+'h')... At least that the value I'm looking for is 
> simply the one calculated in 'e'?
>
> I know the question has been asked many times. But I am still confused 
> after have read all the answers... A tutorial about that would be great!
>
> Thanks in advance for your comments
>
> Nicolas 

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