FGMD annealing parameter

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jaxjaxjax
Posts: 1
Joined: Tue Feb 22, 2022 10:27 am

FGMD annealing parameter

Post by jaxjaxjax »

Hi, our bioinfo-team made a python implementation of the FGMD protocol. This implementation was tested on your benchmark tests and provides more or less the same final results. Despite this achivement we have problems to reproduce the structure that comes out from your web-server implementation, so i was wondering if you can give me the specific setup of your system for the simulation (type of solvent, temperature curve, pbc yes/no ecc..)

Thanks,
jacopo
jlspzw
Posts: 97
Joined: Tue May 04, 2021 5:04 pm

Re: FGMD annealing parameter

Post by jlspzw »

Dear user,

FG-MD use lamp simulation, and here is the setting what we found in FG-MD refinement.

units real
neigh_modify every 10
atom_style full
bond_style harmonic
angle_style harmonic
dihedral_style hybrid harmonic multi/harmonic
pair_style lj/cut/coul/cut/$hbmod 10.0 10.0
pair_modify mix arithmetic
boundary p p p
read_data $datafile
special_bonds amber
thermo 1
thermo_style multi
timestep 2.0
minimize 1.0e-3 1.0e-6 100 1000
fix 1 all nvt 100.0 1.0 1000.0
dump 1 all xyz 10 $xyz
run 10000
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