[gmx-users] lipid-drug simulation question

Krapnik krapnik at gmail.com
Tue Aug 31 20:07:28 CEST 2010

Hi all,
I am simulating drugs in water/lipid bilayer environment.
And I have noticed that when I put drug into the middle of the box, it is
moving rather quickly around until it finds a x or y boundary. Then it stays
there moving not much on both sides of the box.
In the first time it looked fine to me as I was supposing to be normal.
But then I realized, that it stays there much longer, then it was moving
before in the middle of the box.

I have looked into the other simulations and i found, that it makes the same
behaviour - if it goes to the box boundary, then it stays there. I was
thinking that it means, that the membrane is not ok in this region, but nay
by eye, the periodic image of membrane in VMD is ok and the boundary is

Do you have any idea what might be wrong? If it is wrong?

I use DOPC membrane in G56a6 from 1. Siu, S. et al. Biomolecular simulations
of membranes: Physical properties from different force fields. JCP *128*,
and my mdp is here.
coulombtype = PME ; see 8.4.1
rcoulomb = 1.0 ; see 8.4.1
rvdw = 1.1 ; see 8.4.1
fourierspacing = 0.15 ; see 8.4.1
ewald_rtol = 1e-5 ; see 8.4.1
pme_order = 4 ; interpolation order for PME
optimize_fft = yes ; see 8.4.1

; Couplings
; Berendsen temperature coupling given by equation (1.12) of five
molecular groups to ref_t with relaxation time tau_t.
Tcoupl = V-rescale ;
tc-grps =       System
tau_t =         0.1
ref_t =         300
; Energy monitoring of groups:
energygrps = DRG DOPC SOL
; Berendsen pressure coupling given by equation (1.13) is on
pcoupl = berendsen
pcoupltype = anisotropic ; box remains rectangular
tau_p = 10 ; pressure coupling time parameter
compressibility = 4.5e-5 4.5e-5 4.5e-5 0 0 0 ; compresibility
ref_p = 1.0 1.0 1.0 0.0 0.0 0.0  ;reference pressure
Zdraví skoro zdravý
Karel "Krápník" Berka

RNDr. Karel Berka, Ph.D.
Palacký University in Olomouc
Faculty of Science
Department of Physical Chemistry
tř. 17. listopadu 1192/12
771 46 Olomouc
tel: +420-585634769
fax: +420-585634769
e-mail: karel.berka at upol.cz

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