[gmx-users] Gromos54a7 electrostatics interactions ?

Sim gmx simgmx at gmail.com
Tue Sep 26 14:04:30 CEST 2017


I tried to reply yesterday, but apparently my message was too big to be
sent (probably because I replied within your own reply ?). I try a second

Thanks for checking! Exactly, this temperature is for sure above the phase
transition temperature of the lipid I'm studying. Except for the potential
use of sterols discussed further, I will only use PC lipids. However, some
of my molecules do have an alkyl chain. One point of using gromos54a7 is
that those alkyl chains will interact with PC's alkyl chains as PC's alkyl
chains interact between each other. What I mean is that atomtypes used for
both lipids and molecules' alkyl chains will be identical (CH2, CH3...).
Berger lipids use different atomtypes for the alkyl chains (LP2, LP3...).
>From what I think I know, Berger lipids is pretty compatible with gromos'
forcefields. So my first intention was to use berger lipids' PC together
with gromos53a6's molecules. However, it might be better to change the
atomtypes from the alkyl chains of my molecules so that they match the
berger lipids alkyl chains atomtypes. It seems that they did so in this
paper http://pubs.acs.org/doi/abs/10.1021/jp501622d
I would be very interested in getting your opinion about this.

About the removal of leaflets COM movements, I'm not sure to know how to do
that ? "Simply" with trjconv ?

I also think that Berger setup will give the fastest simulations!

Thanks for the info about the condensing effect of Holtje sterol on berger
lipids. Still not sure if I will run simulations with sterols but this will
for sure be taken into account whenever needed.

I used a shortcut, but it is true that I should try to understand why both
forcefields don't give similar results (if it is the case).

Thanks for your clear and detailed reply !

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