[gmx-users] forcefield problems - advice needed

[Lubos Vrbka]

hi guys,

for quite a long time i am trying to 'create' a forcefield for aliphatic 
alcohols (right now, for ethanol) to use with a water potential we 
employ in our simulations.

there is a problem - the water potential uses combination rule 2, so i 
thought i would just try to use FFGMX and OPLS and change it a bit. it 
didn't seem to work. i also tried the FFAMBER, that uses exactly this 
combination rule. unfortunately, it fails as well.

i'm getting all sorts of errors - segfaults, lincs failures, ... in most 
cases, the whole simulation 'freezes' (kinetic energy of order of 1e-5, 
for example) and nothing happens. i am also quite frequently getting 
close contacts between atoms (within one molecule, or between two 
different molecules).

it seems i am missing something in the forcefield, but i am not able to 
identify what is it... i would be very grateful if anyone of you could 
help me and shed more light in this.

if anyone has working alcohol potential (united or all atom type) with 
comb. rule 2, i would be more than happy, if you could share it with me...

also a 'side question' - when using FFAMBER, there are dihedrals defined 
with all atom names specified (e.g., CT CT CT CT), and also dihedrals 
with wildcards (X  CT CT X). for a CT-CT-CT-CT dihedrals, both of these 
would be applicable - are they both used in the simulation, or does the 
latter (X CT CT X) override the former definition (CT CT CT CT)?

once again, i would be very glad if anyone of you could help me. i went 
through the manual many times, but i am becoming more and more confused...

i attach the files for a simulation that is failing for me. it's 2+2 
pentanol molecules in a prismatic simulation box (i have it setup like 
this because we are normally doing slab simulations). all necessary 
files are included.

thanks. with best regards,
lubos


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