[gmx-users] g_density and g_potential for DMPC bilayer

[Andrei Gurtovenko]

Dear David,

David wrote:

>>
>>You are right, it's possible to re-center bilayer using trjconv,
>>the problem is that one needs to do that for EVERY frame of simulation
>>because COM position of bilayer fluctuates in time.
>>It seems to me that this needs extra coding.
>>    
>>
>you may consider using center of mass groups for your next simulation.
>You can then stop the com motion of different groups in your simulation.
>
Yes, that's right but my current simulations are over, now I'm analyzing 
trajectories


>
>
>  
>
>>As for the program for determining PN vector of a PC-head,
>>it would be nice to have it, if possible.
>>    
>>
>I'm not sure what you're after. Have you checked g_order and g_rotacf
>anf g_bond?
>
Actually, I want to calculate the orientation of PC groups (angles with 
bilayer normal)
for DMPC bilayer. Not sure that the programs you mentioned help.


Also, I have a question addressed to GROMOCS crew:
Could you tell me whether g_density explicitly takes into account
masses of united-atom carbons supplied in .tpr file
(i.e. it knows whether a carbon is C, CH, CH2 or CH3) .
I heard an opinion that g_density uses atom names instead
and it is necessary to add masses of hydrogens "by hand"?

Thanks in advance,


Andrei

-- 
Dr. A. Gurtovenko

Biophysics and Soft Matter Group
Laboratory of Physics
Helsinki University of Technology
P.O.Box 1100
FIN-02015 HUT
Finland
Tel.: +358-9-4515803
e-mail: agu at fyslab.hut.fi