[gmx-users] rerun forces

[Attilio]

Hi all,
I have a little problem with the rerun of the trajectories to get out 
forces acting on atoms.
To calculate the forces I followed the instructions I read in the 
mailing list.
I changed the mdp file, as below, to get the forces every frame, without 
re-calculating the neighbor list....

-----------------
mdp ORIGINAL
....
;  OUTPUT CONTROL
nstcheckpoint       =  1000     ; checkpointing helps you continue after 
crashes
nstxtcout           =  1000              ; output frequency and 
precisionfor xtc file
nstxout             =  1000           ; write coords
nstvout             =  1000
nstfout             =  1000
nstlog              =  1000     ; print to logfile
nstenergy           =  1000            ; print energies
; NEIGHBOR SEARCHING
nstlist             =  15                       ; update pairlist
ns_type             =  grid                     ; pairlist method
pbc                 =  xyz
rlist               =  1.2                      ; cut-off for ns

-----------------------
mdp RERUN
....
;  OUTPUT CONTROL
nstcheckpoint       =  1000000000     ; checkpointing helps you continue 
after crashes
nstxtcout           =  1000000000              ; output frequency and 
precisionfor xtc file
nstxout             =  1000000000           ; write coords
nstvout             =  1000000000
nstfout             =  1
nstlog              =  1000000000     ; print to logfile
nstenergy           =  1000000000     ; print energies
;  NEIGHBOR SEARCHING
nstlist             =  0                       ; update pairlist
ns_type             =  grid                     ; pairlist method
pbc                 =  xyz
rlist               =  1.2                      ; cut-off for ns

I obtain forces of the order of 10e+30 Kj mol-1 nm-1 (are these the 
correct units, to divide by f~139 to get forces in (e/nm)^2 ?), that 
sounds quite strange.
In fact I run a new short (100ps) simulation in which forces are printed 
out, and I obtain much smaller forces, between 10e+0 and 10e+5.
Then I tried putting _nstlist = 1_, updating the forces each step during 
the rerun (yes?) of the trajectory, and I obtain values of the same 
order of magnitude, but with different values of the forces.
I would expect to find the same forces at least for the frame number 0. 
What's wrong?  I need to do some imaging of the trajectory, or to leave 
unchanged also the nslist flag? In my case, the results do not vary by 
changing neither the flag nstfout from 1 to 1000, neither the nstlist 
from 1 to 1000.
Can somebody tell me how to set correctly the flags in my mdp????
Any help is greatly appreciated!!!

Thanks in advance,
Attilio

-- 
Attilio Vittorio Vargiu
PhD Student in Statistical and Biological Physics
SISSA/ISAS, via Beirut 4 I-34014 Trieste, Italy
tel +390403787335   fax +390403787528