[gmx-users] Umbrella Sampling on peptides

Huey Ling Tan huelyn at gmail.com
Mon Oct 15 15:56:22 CEST 2007

Hi all,

I am new in Gromacs.
I used umbrella samplings in my simulations of 2 peptide chain with 1
positive charge and 1 negative charge on each chain. However, this 2
chain is sticking together even at high force (1ooo mol*nm^2).

below is the pull.ppa file that i used:
verbose = no
runtype = umbrella
ngroups = 1
group_1 = FEFK_1
reference_group = FEFK_2
reftype =com
K1 = 1000
pulldim = Y Y Y
pos = 2 2 2

Is the .ppa file correct? Please suggest what can I do in order to
separate this 2 peptide chains.

Thanks in advance.
Best regards,
Huey Ling

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