[gmx-users] "Too many LINCS warnings" in a minimization after solvation with coarse-grained waters

[Fotis Baltoumas]

Hello Cheng,

The lines at the end of this mail are the extra parameters we usually 
define in our lab whenever we need to use soft potentials.

They are based on the parameters given by CHARMM-GUI for the Martini 
Maker.  However, you *may* need to make alterations if there are 
conflicts with your existing parameters.

Just remember to also run an additional, standard minimization after the 
"soft" one.


As for  constraints, you can control them through the relevant mdp options:

http://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html#mdp-constraints


;soft-core-minimization so that single precision GROMACS works here
; Free energy parameters
free-energy              = yes
init-lambda              = 0.01
sc-alpha                 = 4
sc-power                 = 2
sc-coul                  = yes
nstdhdl                  = 0
couple-moltype           = system
; we are changing both the vdw and the charge. In the initial state, 
both are on
couple-lambda0           = vdw-q
; in the final state, both are off.
couple-lambda1           = none
couple-intramol          = yes


Good luck,

Fotis

-- 
Fotis A. Baltoumas, Bsc, Msc
Phd Candidate, Bioinformatics Postgraduate Programme
Section of Cell Biology and Biophysics
Department of Biology
National & Kapodistrian University of Athens
Panepistimiopolis, Athens 157 01, GREECE
    --------------------------------------

email : fbaltoumas at biol.uoa.gr
http://biophysics.biol.uoa.gr
http://bioinformatics.biol.uoa.gr
Tel.: +30 2107274876
Mob.: +30 6979258570


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