Hi

I tried using the imm1 implicit membrane model to conduct a helix dimerization experiment (input files generated by charmm gui) but some definitely went wrong as the helices quickly became beta sheets within the membrane. I already forwarded this question to charmm-gui but I'm wondering if anyone has heard of a similar experience with imm1 or might know what is going on.

Thanks!

inp:
stream toppar.str

! Read PSF
open read unit 10 card name step1_pdbreader.psf
read psf unit 10 card

! Read COOR
open read unit 10 card name step1_pdbreader.pdb
read coor unit 10 pdb resid

!
! EEF1/IMM1 Setup
!
! width : membrane thickness
! anfr : the fraction of anionic lipids [0-1]
! conc : salt concentration [in M]
! volt : transmembrane voltage
!

eef1 setup temp 298 unit 93 name toppar/solvpar.inp -
membrane slvt water slv2 chex nsmth 10 width 25.4 aemp 0.85 -
gouy anfr 0.2 area 70. offset 3.0 conc 0.15 valence 1 -
volt 0

nbond ctonnb 7.0 ctofnb 9.0 cutnb 11.0 group rdie

ENERGY

!
! short minimization and Langevin dynamics
! NOTE: CHANGE ISEED EACH TIME FOR RESTART IN LANGEVIN DYNAMICS
!

mini sd nstep 50 nprint 10 step 0.005 inbfrq -1
mini abnr nstep 50 nprint 10 step 0.005 inbfrq -1

set fbeta = 5.0
set temp = 300.0

scalar fbeta set @fbeta
scalar fbeta set 0.0 select type H* end

SHAKE BONH PARAm

open write unit 12 card name run.rst
open write unit 13 file name run.dcd

DYNAMICS LANGEVIN start nstep 5000000 timestp 0.002 -
nprint 100 iprfrq 5000 isvfrq 5000 ntrfrq 500 -
inbfrq -1 imgfrq -1 ihbfrq 0 ilbfrq 0 -
firstt @temp finalt @temp iseed 47858436 -
tbath @temp rbuf 0.0 -
iunread -1 iunwrite 12 iuncrd 13 iunvelo -1 -
nsavcrd 500 nsavvelo 0 -
iasvel 1



ENERGY

open write card unit 10 name step2_implicit_membrane.pdb
write coor pdb unit 10


stop

stream:
* GENERATED BY CHARMM-GUI (http://www.charmm-gui.org) on Oct, 27. 2011.
* Stream file for topology and parameter reading
*

! Read topology and parameter files
open read card unit 10 name toppar/toph19_eef1.1.inp
read rtf card unit 10

open read card unit 20 name toppar/param19_eef1.1.inp
read para card unit 20