[gmx-users] mderror

[goldsmith]

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dear users,
I ran a simulation on a protein using gromacs 3.2.1.I ran it sucessfully for 2.5ns.then i extended it for further 2.5ns using tpbconv -f run1.trr -s run1.tpr -e run1.edr -o run1resart.tpr -extend 2500.
using run1resart.tpr I ran the md again .It ran fine for 3940ps ,then it terminated stating this error in the log file
**********************************************
Step 1970467, time 3940.93 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.000797 (between atoms 308 and 309) rms 0.000033
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
    308    311  30.8    0.1000  0.1000      0.1000

Step 1970468, time 3940.94 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.001116 (between atoms 308 and 310) rms 0.000034
bonds that rotated more than 30 degrees:
t = 3947.630 ps: Water molecule starting at atom 20960 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files with previous and current coordinates
Large VCM(group rest):  31222.23828,  2411.13110,  2129.13721, ekin-cm:  7.45159e+13

Step 1973816  Warning: pressure scaling more than 1%, mu: 2.82236e+13 2.82236e+13 2.82236e+13
******************************************************
this is my full.mdp file
title              =  enzyme
cpp                =  /lib/cpp
constraints        =  all-bonds
integrator          =  md
dt                  =  0.002     ; ps !
nsteps              =  1250000     ; total 2.5 ns.
nstxout            =  5000
nstvout            =  5000
nstfout            =  0
nstlog              =  5000
nstenergy          =  250
nstlist            =  10
ns_type            =  grid
rlist              =  0.8
coulombtype        =  cut-off
rcoulomb            =  1.4
rvdw                =  0.8
pbc                =  xyz
; Berendsen temperature coupling is on in two groups
Tcoupl              =  berendsen
tc-grps              =  Protein     SOL
tau_t              =  0.1     0.1
ref_t              =  300     300
; Energy monitoring
energygrps          =  Protein  SOL
; Isotropic pressure coupling is now on
Pcoupl              =  berendsen
tau_p              =  0.5
compressibility    =  4.5e-5
ref_p              =  1.0
gen_vel            =  yes
gen_temp            =  300.0
gen_seed            =  173529
*****************************************************
I would appreciate any help regarding this ,suggestions or how to rectify.thanks in advance-smith1