[gmx-users] Hbond Shake and Gromacs Version Related

Sapna Sarupria sapna.sarupria at gmail.com
Tue Aug 21 00:45:43 CEST 2012

Hello All,

I have been having rather bizarre experience with Gromacs and was
wondering if any one can shed some light on what is happening. I am
running simulations of a hydrate + water system (think of hydrate as
ice if you are not familiar with them). So basically I have a simple
solid+liquid system. The system is minimized. The water model I am
using is TIP4P/2005. Now when I run the simulation using grompp and
mdrun both from Gromacs 4.5.5, my system crashes and writes out
step*.pdb files. This I know happens when the system is exploding or
something however, I do not see an obvious reason for this.
However, if I compile the tpr file with older Gromacs version 4.0.5
and then use mdrun from 4.5.5 to run the simulation, my simulation
proceeds just fine....the way I expect it to.

Can anyone tell me what might be happening here. I have pasted my mdp
file below.  I think this might be related to the constraint algorithm
but I have no idea how to fix it. I have tried using Lincs instead of
Shake and that also gives the same outcome. Runs with Gromacs 4.0.5
(i.e. grompp using 4.0.5 and mdrun using 4.5.5) and fails with 4.5.5
(both grompp and mdrun using 4.5.5).

Please let me know if you need any further information and thanks a
lot for your help. Any insight will be helpful.

#### BEGIN MDP FILE #######
title               =  s1-Hydrate melting simulation
dt                  =  0.002                    ; time step
nsteps              =  5000                    ; number of steps
nstcomm             =  10                       ; reset c.o.m. motion
nstxout             =  7500                     ; write coords
nstvout             =  7500                     ; write velocities
nstlog              =  25000                    ; print to logfile
nstenergy           =  250                      ; print energies
xtc_grps            =  System
nstxtcout           =  25
nstlist             =  10                       ; update pairlist
ns_type             =  grid                     ; pairlist method
coulombtype         =  PME
rvdw                =  1.20                     ; cut-off for vdw
rcoulomb            =  1.20                     ; cut-off for coulomb
rlist               =  1.20                     ; cut-off for coulomb
Tcoupl              =  Nose-Hoover
ref_t               =  200.0
tc-grps             =  System
tau_t               =  0.5
Pcoupl              =  Parrinello-Rahman
Pcoupltype          =  semiisotropic            ; pressure geometry
tau_p               =  1.0   1.0                ; p-coupoling time
compressibility     =  4.5e-5  4.5e-5           ; compressibility
ref_p               =  100.0   100.0            ; ref pressure
DispCorr            =  EnerPres                 ; long range correction
gen_vel             =  yes                      ; generate init. vel
gen_temp            =  200                      ; init. temp.
gen_seed            =  98247                    ; random seed
constraints         =  hbonds                ; constraining bonds with H
constraint_algorithm = shake

#### END MDP FILE #######

Thanks very much,


Sapna Sarupria
Assistant Professor
Department of Chemical and
Biomolecular Engineering
128 Earle Hall
Clemson University
Clemson, SC 29634

Life isn't about finding yourself. Life is about creating yourself. --
George Bernard Shaw.
Dare to Dream

More information about the gromacs.org_gmx-users mailing list