Dear Amber users,
I changed a bit my input file, please see below. After that the MD seems
to run but my DISTout.RST.4 is empty at the end of the simulations. What
is wrong now? How could I change the input file.
Heating
&cntrl
imin = 0,
irest = 0,
ntx = 1,
cut = 9,
ntb = 1,
iwrap = 1,
nmropt = 1,
ntc = 2,
ntf = 2,
tempi = 0.0,
temp0 = 300.0,
ntt = 3,
gamma_ln = 1.0,
nstlim = 200, dt = 0.002,
ntpr = 10, ntwx = 10, ntwr = 10,
/
&wt TYPE='END'
/
DISANG=dist.RST
LISTOUT=POUT
DUMPAVE=DISTout.RST.4
/
&end
my dist.RST
&rst iat=3457,4153
r1=0,r2=13.8,r3=13.8,r4=100.0,rk2=10.0,rk3=10.0, /
&end
In my out file I have:
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
begin time read from input coords = 0.000 ps
Begin reading energy term weight changes/NMR restraints
WEIGHT CHANGES:
** No weight changes given **
RESTRAINTS:
Requested file redirections:
DISANG = dist.RST
LISTOUT = POUT
DUMPAVE = DISTout.RST.4
Restraints will be read from file: dist.RST
Here are comments from the DISANG input file:
Number of restraints read = 1
Done reading weight changes/NMR restraints
Number of triangulated 3-point waters found: 24092
Sum of charges from parm topology file = 0.00000017
Forcing neutrality...
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
| # of SOLUTE degrees of freedom (RNDFP): 158552.
| # of SOLVENT degrees of freedom (RNDFS): 0.
| NDFMIN = 158552. NUM_NOSHAKE = 0 CORRECTED RNDFP = 158552.
| TOTAL # of degrees of freedom (RNDF) = 158552.
---------------------------------------------------
APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
using 5000.0 points per unit in tabled values
TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
| CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
| CHECK d/dx switch(x): max rel err = 0.8314E-11 at 2.736960
---------------------------------------------------
| Local SIZE OF NONBOND LIST = 19312266
| TOTAL SIZE OF NONBOND LIST = 19312266
Is that correct?
Please guide me.
Thanks
Urszula
-----------------------------------------
Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego
http://www.ug.edu.pl/
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Apr 09 2014 - 01:30:02 PDT
