I used a vacuum equilibration and get the vlimit exceeded again in the
first heating step. My solvated molecules simulations are still running
the minimization step :
minimization with restraint
&cntrl
imin=1,
ntb=1,
cut=10.0,
maxcyc=10000, ncyc=1000,
ntt=0, ntr=1,
&end
Hold the RNA fixed
1.0
RES 1 343
END
END
minimization solutes
&cntrl
imin=1,
ntb=1,
cut=10.0,
maxcyc=10000, ncyc=1000,
ntt=0,
&end
heat/dynamics at constant volume
&cntrl
imin=0,
ntxo=1, ntrx=1,
cut=10.0,tempi=0.1,
ntpr=500, ntwx=500, ntwe=500,
nstlim=100000, temp0=100.0,
dt=0.0005,
ntc=2, ntf=2, tol=0.00001,
ntx=1, irest=0,
ntb=1,tautp=1,
ntt=1,
nmropt=1,ntr=1
/
&wt
type='TEMP0', istep1=0, istep2=40000, value1=0.1, value2=100.0,
/
&wt
type='TEMP0', istep1=40001,istep2=100000,value1=100.0, value2=100.0,
/
&wt type='END',
/
GROUP FOR CONSTRAINTS
10.0
RES 1 343
END
END
The output files have
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.01 PRESS =
0.0
Etot = -40689.5667 EKtot = 0.0998 EPtot =
-40689.6665
BOND = 54.3348 ANGLE = 1395.1889 DIHED =
281.6251
1-4 NB = 285.5361 1-4 EEL = 7286.8467 VDWAALS =
2993.9594
EELEC = -52987.1576 EHBOND = 0.0000 RESTRAINT =
0.0000
Ewald error estimate: 0.8777E-04
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
vlimit exceeded for step 6; vmax = 36.5222
vlimit exceeded for step 7; vmax = 56.0527
vlimit exceeded for step 8; vmax = 58.2767
vlimit exceeded for step 9; vmax = 52.0658
vlimit exceeded for step 10; vmax = 56.1929
Thanks for your time
Kirtana
On Sun, Dec 4, 2011 at 11:10 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> > Dear Prof. Ross , if I understood correctly I make the changes for the
> no
> > shake ntc=1 ntf=1 (for the warming step and also for equilibration )
> with
> > time step dt=0.001
>
> I think with dt=1fs, ntc=2 is indicated.
>
> > and after heating I used ntx=5 with irest=1 .
>
> Correct.
>
> Bill
>
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Received on Sun Dec 04 2011 - 20:30:03 PST
