<P>
dear users,<BR>
I ran a simulation on a protein using gromacs 3.2.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.<BR>
using run1resart.tpr I ran the md .It ran fine for 3650ps ,then it terminated stating this error<BR>
**********************************************<BR>
Step 1970467, time 3940.93 (ps) LINCS WARNING<BR>
relative constraint deviation after LINCS:<BR>
max 0.000797 (between atoms 308 and 309) rms 0.000033<BR>
bonds that rotated more than 30 degrees:<BR>
atom 1 atom 2 angle previous, current, constraint length<BR>
308 311 30.8 0.1000 0.1000 0.1000<BR>
<BR>
Step 1970468, time 3940.94 (ps) LINCS WARNING<BR>
relative constraint deviation after LINCS:<BR>
max 0.001116 (between atoms 308 and 310) rms 0.000034<BR>
bonds that rotated more than 30 degrees:<BR>
t = 3947.630 ps: Water molecule starting at atom 20960 can not be settled.<BR>
Check for bad contacts and/or reduce the timestep.Wrote pdb files with previous and current coordinates<BR>
Large VCM(group rest): 31222.23828, 2411.13110, 2129.13721, ekin-cm: 7.45159e+13<BR>
<BR>
Step 1973816 Warning: pressure scaling more than 1%, mu: 2.82236e+13 2.82236e+13 2.82236e+13<BR>
******************************************************<BR>
this is my full.mdp file<BR>
title = rnaseh2Mj<BR>
cpp = /lib/cpp<BR>
constraints = all-bonds<BR>
integrator = md<BR>
dt = 0.002 ; ps !<BR>
nsteps = 1250000 ; total 2.5 ns.<BR>
nstxout = 5000<BR>
nstvout = 5000<BR>
nstfout = 0<BR>
nstlog = 5000<BR>
nstenergy = 250<BR>
nstlist = 10<BR>
ns_type = grid<BR>
rlist = 0.8<BR>
coulombtype = cut-off<BR>
rcoulomb = 1.4<BR>
rvdw = 0.8<BR>
pbc = xyz<BR>
; Berendsen temperature coupling is on in two groups<BR>
Tcoupl = berendsen<BR>
tc-grps = Protein SOL<BR>
tau_t = 0.1 0.1<BR>
ref_t = 300 300<BR>
; Energy monitoring<BR>
energygrps = Protein SOL<BR>
; Isotropic pressure coupling is now on<BR>
Pcoupl = berendsen<BR>
tau_p = 0.5<BR>
compressibility = 4.5e-5<BR>
ref_p = 1.0<BR>
gen_vel = yes<BR>
gen_temp = 300.0<BR>
gen_seed = 173529<BR>
*****************************************************<BR>
I would appreciate any help regarding this ,suggestions or remedy.thanks in advance-gsmith<BR>
<BR>
</P>
<br><br>
<A target="_blank" HREF="http://clients.rediff.com/signature/track_sig.asp"><IMG SRC="http://ads.rediff.com/RealMedia/ads/adstream_nx.cgi/www.rediffmail.com/inbox.htm@Bottom" BORDER=0 VSPACE=0 HSPACE=0></a>