[gmx-users] Re: My problem about the job under bond constrain?

[Hanming]

>Hanming wrote: 

>Dear all,
>I have a molecule which has more than 20,000 atoms. I tried to do the
>simulation under bond constrain in order to use the long step. Firstly I
>minimised the initial model by em and md under low temperature. Then I
>did
>the md without constrain, it can run smoothly. But when I add the
> bond-constrain the LINCS-WARNING always comes out and the job crashed. >
>How can I do then?

>Ming
Can you do an EM with all bonds constrained? 

Can you do MD with all bonds constrained at a normal timestep (2fs)? 

Can you do MD without constraints at a timestep of 3 or 4 fs? 

(Are you sure you only changed the option for bond constraints?
You can use gmxcheck -s1 topol1.tpr -s2 topol2.tpr to check.)
 

I did the steep EM with all-bonds constrained,get LINCS WARNING.
MD without constrains at a timestep of 2fs is OK, but MD with constrains at
2fs get LINCS WARNING.
MD without constrains at a timestep of 3 or 4fs get a lot of nan in the
md.log and confout.gro files. 

The following is my grompp.mdp file. When use constrains What I changed  is
just change the last term constrains = none to constrains= all-bonds. Where
is the problem? 

Thx a lot, 

Ming 

title                    = Yo
cpp                      = /lib/cpp
include                  = -I../top
define                   =
integrator               = md
dt                       = 0.002
comm_mode                =  none
pbc                      = no
nsteps                   = 500
nstxout                  = 50
nstvout                  = 50
nstlog                   = 50
nstenergy                = 50
nstxtcout                = 50
xtc_grps                 = COR     G1   TAI
energygrps               = COR     G1   TAI
nstlist                  = 0
ns_type                  = simple
rlist                    = 0
rcoulomb                 = 0
rvdw                     = 0
tcoupl                   = Berendsen
tc-grps		    = COR     G1   TAI
tau_t               =  0.1    0.1   0.1
ref_t               =  300    300   300
Pcoupl                   = no
tau_p                    = 1.0
compressibility          = 4.5e-5
ref_p                    = 1.0
gen_vel                  = yes
gen_temp                 = 300
gen_seed                 = 173529
bd-temp                  = 300
bd-fric                  = 5000
ld-seed                  = 1993
constraints              = all-bonds 

 

-- 
Groetjes, 

Anton
_____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________| 

 

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