[gmx-users] cholesterol distortion

[Steffen Wolf]

Hi Jian,
seems like there's something seriously wrong with the topology of the 
cholesterols - check if the angles & impropers are set and reasonable.
Cheers
Steffen
> Hi, all:
> I got the initial structure of a DPPC bilayer from Dr. Karttunen's 
> website, use the parameters (hopefully) from their paper: Patra, 
> Karttunen, Hyvönen, Falck, Lindqvist, Vattulainen, Biophys. J. *84*, 
> 3636-3645 (2003) to run for 100ns then replace some DPPC molecules 
> with cholesterols, do the energy minimization, run for 20ns and the 
> cholesterols are distorted as shown in the attached file.
>
> Here are parameters for the pure DPPC run which I deem important:
>
> nstcomm                  = 1
> comm_grps                = DPPC SOL
> nstlist                  = 10
> ns_type                  = grid
> pbc                      = xyz
> rlist                    = 1.0            
> coulombtype              = PME
> rcoulomb                 = 1.0
> vdwtype                  = Cutoff
> rvdw                     = 1.0
> ewald_rtol               = 1e-5
> optimize_fft             = yes
> tcoupl                   = Berendsen
> tau_t                    = 0.1   0.1
> tc_grps                  = DPPC  SOL
> ref_t                    = 323   323
> pcoupl                   = Berendsen
> pcoupltype               = semiisotropic
> tau_p                    = 1          1  
> compressibility          = 4.5e-5     4.5e-5
> ref_p                    = 1.0        1.0  
> gen_vel                  = yes
> gen_temp                 = 325
> gen_seed                 = 173529
> constraints              = all-bonds
> constraint_algorithm     = LINCS
> lincs_order              = 4
>
> For the DPPC-CHOL combined system I only changed corresponding 
> sections to:
>
> comm_grps                = DPPC CHOL  SOL
> tau_t                    = 0.1   0.1   0.1
> tc_grps                  = DPPC  CHOL  SOL
> ref_t                    = 323   323   323
>
> Any suggestion is appreciated. Thank you.
>
> Jian
>
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-- 
Dipl.-Chem. Steffen Wolf
Fellow of the Ruhr-University Research School
Department of Biophysics
University of Bochum
ND 04/67
44780 Bochum
Germany
Tel: +49 (0)234 32 28363
Fax: +49 (0)234 32 14626
E-Mail: swolf at bph.rub.de
Web: http://www.bph.rub.de