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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fn:Nicolas SAPAY
n:SAPAY;Nicolas
org:University of Calgary;Biological Sciences
adr:;;2500 University drive NW;Calgary;AB;T2N 1N4;Canada
email;internet:[EMAIL PROTECTED]
title:PhD
tel;work:(403) 220-6869
tel;fax:(403) 289-9311
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version:2.1
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