On Apr 9, 2014, at 4:22 AM, Urszula Uciechowska <urszula.uciechowska.biotech.ug.edu.pl> wrote:
> 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,
> /
#try adding this line
&wt type=‘DUMPFREQ’,istep1=50 /
> &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/
>
>
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Received on Wed Apr 09 2014 - 04:00:02 PDT
