[gmx-users] Weird structure after minimization (membrane protein simulation)

Alok alokjain at iitk.ac.in
Mon Jan 28 15:35:20 CET 2008

Dear All,

I am doing the simulation of POPE lipid + Protein, I did my system setup using mdrun_hole program. It looks fine to me  http://i269.photobucket.com/albums/jj58/gromacs/all-three_final.gif (Figure-A). When I was doing energy minimization (using steepest decent and conjugant gradient algorithm), water molecules diffuse a lot, structure looks very weird (Figure-B). But only after 1ps mdrun (NVT ensemble) it comes back to its normal (Figure-C). But during this 1ps I got lots of LINCE warning, all for water molecules. If I continue my simulation (till now ~5ns production run) I do not get any problem/warning.

So I just want to know should I proceed further, or I have to come back to my initial state and resolve this problem?
Previously I tried different options by changing value of emtol but I could not resolve this problem. So I proceeded. By this mail, I am requesting expert comments from you people. Is it normal to Membrane simulation or there is some problem in my system? Till now I have not encountered any problems/warning.

Eagerly waiting for your reply,

Best regards,
Alok Jain

Thanks a lot for your reply/comments and time. I am using TIP4P water model, and I really could not understand why it happens, Some of the bonds of the water molecules are broken down, and after 1ps MD  they make bonds again. Is it not very strange? I have tried to visualize in different visualization tool but still problem was persisting. I was not able to implement your suggestion regarding tolerance limit of the visualization software, I used rasmol, chimera, insightII but could not found any such option. I am still trying for that, if I could found it, I will inform you the result after that.  I am really worried about temporary LINCE warning
which I was getting. Is there any way to resolve this issue?

I am pasting the em.mdp and my top file below.

@chris: Thanks for your time spent on investigating on my problem. Thanks for creating the public album. I am sorry to say I could not get your statement "In the worst case scenario that I can imagine, temporary lincs warning could represent a chiral inversion that will never be resolved and never give you any more warning messages, but would definitely give you the wrong answer." could you please explain it a little more (in layman term) because as I think there is no Chiral center in water so what it
means by chiral inversion.
I have also plotted the two plots to validate my final structure of mdrun_hole program and uploaded these plots at http://i269.photobucket.com/albums/jj58/gromacs/hole-depth-atom1.jpg  As I pasted below my em.mdp file. I was using FLEXIBLE TIP4P water molecules.


define              =  -DFLEXIBLE
constraints         =  none
integrator          =  steep
nsteps              =  10000
;       Energy minimizing stuff
emtol                    =  100
emstep                 =  0.001
nstcgsteep           =  1000

comm_mode      =  Linear
nstcomm             =  1
comm_grps        =  Protein_POP SOL
ns_type               =  grid
rlist                       =  0.9
coulombtype       =  PME
rcoulomb             =  0.9
vdw-type              =  Cut-off
rvdw                     =  1.2
fourierspacing     =  0.12
pme_order          =  4
ewald_rtol            =  1e-5
optimize_fft         =  yes
Tcoupl                 =  no
Pcoupl                 =  no
gen_vel               =  no

top file:

; Include forcefield parameters
#include "/home/lysine/ffoplsaa.itp"

; Include chain topologies
#include "Protein_A.itp"
#include "Protein_B.itp"
#include "Protein_C.itp"
#include "Protein_D.itp"

#include "pope_opls.itp"

; Include water topology
#include "tip4p.itp"

; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       10000      10000       10000

; Include generic topology for ions
#include "ions.itp"

[ system ]
; Name
protein + POPE +  TIP4P water molecules

[ molecules ]
; Compound        #mols
Protein_A           1
Protein_B           1
Protein_C           1
Protein_D           1
POPE               269
SOL              13800

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