[gmx-users] (no subject)

prithvi raj pandey pandeyprithviraj at gmail.com
Thu Oct 3 08:42:22 CEST 2013

Dear gmx-users,

We intend to perform free energy calculations by pulling a polypeptide
along water-hexane interface. We need to pull the polypypeptide from the
water layer towards the hexane layer (crossing the interface). For this we
position restrained one hexane molecule in the bulk of hexane (pull_group0)
and trying to pull the polypeptide (pull_group1) towards it. But though the
polypeptide is getting pulled, the hexane layer is breaking in the process.

The pulling options used are as follows,

pull            = umbrella
pull_geometry   = distance  ; simple distance increase
pull_dim        = N Y N
pull_start      = yes       ; define initial COM distance > 0
pull_ngroups    = 1
pull_group0     = 3
pull_group1     = Protein
pull_rate1      = 0.01      ; 0.01 nm per ps = 10 nm per ns
pull_k1         = 1000

We have also played a bit with the pull rate and pull constant, but same
thing happens. Are we doing something wrong? Can you please help?

Prithvi Raj Pandey
National Chemical Laboratory,
Pune 411008.

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