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
------------------------------------------------------------------------
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
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: [EMAIL PROTECTED]
Web: http://www.bph.rub.de
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
