Hi, all:
I run targeted MD with the .in file shown as below,
"
#regular vacuum md, backbone restrained
&cntrl
imin = 0, ntx = 1, nstlim = 50000, irest=0,
dt = 0.002, ntc = 2, ntf = 2,
temp0 = 50.0,
ntpr = 500, ntwx = 500, ntwr = 50000,
ntb = 2, ntt = 3, ntp=1,
nscm = 0, nmropt = 1,
ntr = 1, restraint_wt=50,
restraintmask=":1-94,163-469&!.H=",
itgtmd = 1, tgtrmsd = 6.1919, tgtmdfrc = 5,
tgtrmsmask="(:470,471,487&!.H=)|:498-499.P
,OP1,OP2,O5',C5',O4',C4',O3',C3',C2',C1'",
/
&wt
TYPE='TGTRMSD', istep1=1, istep2=25000,
value1 = 6.1919, value2 = 0.0,
/
&wt
TYPE='TGTRMSD', istep1=25000, istep2=50000,
value1 = 0.0, value2 = 0.0,
/
&wt
type="END",
/
"
However, it gives me the error as :
"
vlimit exceeded for step 48; vmax = 235.5863
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 0 3905 7743 7744
Note: This is usually a symptom of some deeper
problem with the energetics of the system."
Could anyone tell me what's wrong with it and how to run it correctly?
Thank you very much!
--
Li Xiao
University of California, Irvine
Email: xiaoli19871216.gmail.com
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Apr 17 2015 - 00:00:03 PDT
