[gmx-users] Doubt regarding membrane protein in POPC bilayer

[Pawan Kumar]

Respected Sir,

Greetings from Pawan.
I have used force constants of 100000 in position restraint .itp files for
proteins as suggested in Dr. Tieleman' s webisite for Inflategro.
The mdp files are :

*For energy minimization:*
title               =  Protein in DPPC Bilayer
cpp                 =  /usr/bin/cpp
define              =  -DPOSRES
integrator          =  steep
dt                  =  0.002
nsteps              =  50000

; Constrain control
constraints         =  none

; Output frequency for coords (x), velocities (v) and forces (f)
nstxout             =  0
nstvout             =  0
nstfout             =  0
nstxtcout           =  0
nstenergy           =  0

; nblist update frequency
nstlist             =  10

; ns algorithm
ns_type             =  grid
rlist               =  1.8

; Method for doing VdW
vdw-type            =  Cut-off
rvdw                =  1.8

; Method for doing electrostatics
coulombtype            =  PME
rcoulomb            =  1.8

; Center of mass control
nstcomm              =  1

; Periodic boundary conditions
pbc                  =  xyz

; Mode for center of mass motion removal
comm-mode            =  Linear

tcoupl               =  no
pcoupl               =  no
;       Energy minimizing stuff
emtol                =  1000
emstep               =  0.001

*For position restraint mdrun:*
title               =  Protein in DPPC Bilayer
cpp                 =  /usr/bin/cpp
define              =  -DPOSRES
constraints         =  all-bonds
constraint-algorithm=  Lincs
integrator          =  md
dt                  =  0.002
nsteps              =  5000
nstcomm             =  1
nstxout             =  50
nstvout             =  1000
nstfout             =  0
nstlog              =  10
nstenergy           =  10
nstlist             =  10
ns_type             =  grid
rlist               =  1.0
coulombtype         =  PME
rcoulomb            =  1.0
vdw-type            =  Cut-off
rvdw                =  1.0
; Berendsen temperature coupling is on in two groups
Tcoupl              =  berendsen
tc-grps          =  Protein  DPPC
tau_t               =  0.1    0.1
ref_t               =  300    300
; Energy monitoring
energygrps        =  Protein DPPC
;Pressure coupling is on
Pcoupl              =  berendsen
tau_p               =  2.0 2.0
compressibility     =  4.5e-5 4.5e-5
ref_p               =  1.0 1.0
Pcoupl_type         =  semiisotropic
; Generate velocites is on at 300 K.
gen_vel             =  no
gen_temp            =  300.0
gen_seed            =  173529

*Topology file :*
; Include forcefield parameters
#include "ffoplsaa.itp"
#include "lipid.itp"
#include "dppc.itp"

; Include chain topologies
#include "topol_A.itp"
#include "topol_B.itp"
#include "topol_C.itp"

;#ifdef POSRES
;#include "lipid_posre.itp"
;#endif

; Include water topology
#ifdef FLEX_SPC
#include "flexspc.itp"
#else
#include "spc.itp"
#endif

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000
#endif

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

[ system ]
; Name
PROTEIN IN DPPC BILAYER

[ molecules ]
; Compound      #mols
Protein_A           1
Protein_B           1
Protein_C           1
DPPC              926
;SOL             23552

Please help with some suggestions.

Thanking you,

Yours sincerely,
Pawan

On Mon, Mar 30, 2009 at 6:22 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:


> Pawan Kumar wrote:
>
>> Respected Sir,
>>
>> Greetings from Pawan.
>> I did the Inflategro procedure for the POPC bilayer generated using
>> genconf.
>> It took around 26 compressions for coming near the initial area (just
>> above it).
>> The minimization were all converged to Fmax < 1350.
>> If I decrease the Fmax less than this I am getting machine precision.
>> But when I proceeded with the final compressed structure for pr mdrun it
>> gave lincs warnings and ended with segmentation fault.
>> As an alternative to this bilayer I used the DPPC bilayer
>> (pre-equilibrated) which is given in GMX-Benchmark distribution.
>> I carried out the same steps of Inflategro. I used the cutoff of 14 A in
>> the inflation and compression step also.
>> In this case the the Steepest Descents converged to Fmax < 1000 in all the
>> steps. The maximum force war never above 850.
>> But when I did position restraint mdrun with the last compressed file I
>> got Lincs warnings and Segementation fault after few steps (30 - 40 steps).
>> Can you please help how to proceed ?
>>
>>
> If the minimization procedure is adequately finishing, then the problem
> comes from something you are doing.  If you post your .mdp file, we may be
> able to see if there are any obvious mistakes.
>
> -Justin
>
>  Thanking you,
>>
>> Yours sincerely,
>> Pawan
>>
>>
>> Justin A. Lemkul
>> Graduate Research Assistant
>> ICTAS Doctoral Scholar
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
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