[gmx-users] CG-MD simulation of protein, always crash with protein

[Trang]

On Fri, Apr 16, 2010 at 5:17 PM, Martti Louhivuori <m.j.louhivuori at rug.nl>wrote:

> On 15 Apr 2010, at 18:06, Trang wrote:
>
>> My target system is a protein with lipid molecules added randomly (using
>> GENBOX). Running MD, I expect to
>>
>
> I hope you're using a larger van der Waals distance (0.24nm or so) when
> inserting the lipids.


I tried 0.3 - 0.5. It looked fine, but didn't work.

>
>
>  broke down the problem, that is, to run md simulation for the protein
>> molecule only, and in vacuum. Still no improvement. Although all the
>> distances in the minimized structure are visually proper, the system
>> exploded.
>>
>
> If you can't run the protein even in vacuum, then the problem is either in
> your MD parameters, starting co-ordinates or some simple mistake somewhere.
> Since the .mdp files you posted seem ok, my bet is on the starting
> co-ordinates, just as Xavier proposed.
>
> Could you post the system topology (.top) and the protein topology (.itp),
> so we can rule out any mistakes in those?


The protein topo is too large, so I put it here. http://pastie.org/926617
Here is the system topology.

----------------------------
#include "../martini_v2.1.itp"
#include "../martini_v2.1_aminoacids.itp"
#include "11BHSD1.itp"

; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif


[ system ]
11BHSD1

[ molecules ]
11BHSD1               1
----------------------------



> You should also double check whether you have close contacts between some
> atoms in the protein; e.g. in VMD this is easily done using the "dynamic
> bonds" representation.


> -martti-
>

Minimized structure showed no close contact (with distance cutoff 1.6, even
to 1.9). Production run stopped at step 175552 (5266.56 ps) with
Segmentation fault, preceeded with a lot of Lincs warnings (I set ring_bonds
= "constraints").  This is the mdp file, this file goes along with the
system in vaccuum that crashed. I'm not sure if too long simulation time can
be the cause. The strange thing is that the system seemed to be relatively
stable at the time of crash. rmds.xvg is below, in case you want to see the
graph first-hand.

-------------------------MD---------------------------
integrator               = md
tinit                    = 0.0
dt                       = 0.030
nsteps                   = 900000
nstcomm                  = 1
comm-grps        =
nstxout                  = 5000
nstvout                  = 5000
nstfout                  = 0
nstlog                   = 2000
nstenergy                = 2000
nstxtcout                = 1000
xtc_precision            = 100
xtc-grps                 =
energygrps               =
nstlist                  = 10
ns_type                  = grid
pbc                      = xyz
rlist                    = 1.2
coulombtype              = Shift
rcoulomb_switch          = 0.0
rcoulomb                 = 1.2
epsilon_r                = 15
vdw_type                 = Shift
rvdw_switch              = 0.9
rvdw                     = 1.2
DispCorr                 = No
tcoupl                   = Berendsen
tc-grps                  = Protein
tau_t                    = 0.3
ref_t                    = 323
Pcoupl                   = berendsen
Pcoupltype               = isotropic
tau_p                    = 3.0
compressibility          = 3e-5
ref_p                    = 1.0
gen_vel                  = no
gen_temp                 = 323
gen_seed                 = 666
constraints              = none
constraint_algorithm     = Lincs
unconstrained_start      = no
lincs_order              = 4
lincs_warnangle          = 30
----------------------------------------------------------

-------------rmsd.xvg-------------------------------
@    title "RMSD"
@    xaxis  label "Time (ps)"
@    yaxis  label "RMSD (nm)"
@TYPE xy
@ subtitle "Protein after lsq fit to Protein"
   0.0000000    0.0001400
 150.0000000    0.6150032
 300.0000000    0.6162945
 450.0000000    0.6451609
 600.0000000    0.6317724
 750.0000000    0.6501579
 900.0000000    0.6642945
1050.0000000    0.6742513
1200.0000000    0.6651280
1350.0000000    0.6965100
1500.0000000    0.6856629
1650.0000000    0.7271055
1800.0000000    0.7174531
1950.0000000    0.7088170
2100.0000000    0.7492073
2250.0000000    0.7352809
2400.0000000    0.7196461
2550.0000000    0.7162255
2700.0000000    0.7277457
2850.0000000    0.7121301
3000.0000000    0.7084662
3150.0000000    0.7153199
3300.0000000    0.7209989
3450.0000000    0.7342823
3600.0000000    0.7297466
3750.0000000    0.7254455
3900.0000000    0.7175814
4050.0000000    0.7134616
4200.0000000    0.7212958
4350.0000000    0.7258847
4500.0000000    0.7201833
4650.0000000    0.7286560
4800.0000000    0.7188574
4950.0000000    0.7177775
5100.0000000    0.7247230
5250.0000000    0.7153631
-----------------------------------------------------------
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