HI, all:
I met a problem in running steered MD , I couldn't figure it out. Can
anyone tells me what is the problem?
Thank you very much
Li
*Below are the fies:*
SMD2.in:
#steer MD2
&cntrl
imin=0, irest=1, ntx=5,
nstlim=5000, dt=0.002,
ntt=1, ntc=2, ntf=2, ntb=1, ntp=0,
tempi=50.0, temp0=50.0,dielc=80.0,
ntpr=500, ntwx=500, ntwr=5000,
ntr=1, restraint_wt=50, restraintmask=':1-469,509&!.H=', ntrx=1,
jar=1,
/
&wt
type='DUMPFREQ', istep1=1,
/
&wt
type='END',
/
DISANG=SMD2.rst
DUMPAVE=dist_vs_t_threepull2
LISTIN=POUT
LISTOUT=POUT
SMD2.rst:
#
# 470 U O2 39 ASP O 46.3504
&rst
ixpk= 0, nxpk= 0, iat=7755, 661, r1= 1.30, r2= 1.80, r3=46.35, r4=46.85,
rk2=20.0, rk3=20.0, ir6=1, ialtd=0,
&end
~
*I run with command:*
$AMBERHOME/bin/pmemd -O -i SMD2.in -o rna_13a_new_pull2.out -p
rna_13a_new.prmtop -c rna_13a_new_pull1.rst -ref rna_13a_new_pull1.rst -r
rna_13a_new_pull2.rst -x rna_13a_new_pull2.mdcrd
*The error message is at below:*
| APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION
| with 50.0 points per unit in tabled values
| Relative Error Limit not exceeded for r .gt. 2.48
| APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION
| with 50.0 points per unit in tabled values
| Relative Error Limit not exceeded for r .gt. 2.91
|---------------------------------------------------
vlimit exceeded for step 4; vmax = 24.3464
vlimit exceeded for step 8; vmax = 467.0439
Coordinate resetting cannot be accomplished,
deviation is too large
iter_cnt, my_bond_idx, i and j are : 2 367 705 706
--
Li Xiao
University of California, Irvine
Email: xiaoli19871216.gmail.com
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Received on Sun Apr 19 2015 - 18:30:02 PDT
