Dear Amber users
I am trying to perform steered molecular dynamics simulation where I want
to change the distance between two atoms (or better if it is COM between a
group of atoms) as well as changing the angle between three atoms (or COM
again). I have used the following input file:
SMD
&cntrl
imin = 0, ntx = 5, irest = 1,
ntpr = 1000, ntwx = 1000, ntwe = 0, ntwprt=0,
ntc = 2, ntf = 2, iwrap = 1, ioutfm = 1,
nstlim = 50001, dt =0.002,
tempi=300.0, temp0 = 300.0, ntt =1, tautp =2.0,
ntb = 2, ntp = 1, taup = 2.0, pres0 =1.0, cut = 12.0,
jar=1,
/
&wt type='DUMPFREQ', istep1=1, /
&wt type='END', /
DISANG=dist.RST
DUMPAVE=dist_vs_t
LISTIN=POUT
LISTOUT=POUT
And my dist.RST file is:
# Change distance between atoms 1496 and 3647 from 32 A to 5.0 A
&rst iat=1496,3647, r2=32., rk2 = 50., r2a=5.0, /
# Change angle between atoms 1496, 3647 and 4199 from 0 to 360 degree
&rst iat=1496,3647,4199, r2=0., rk2 = 50., r2a=360.0, /
However from the output, it seems that only the first distance restraint is
being applied. How can I solve this?
Thanks in advance
Suchetana Gupta
IIT Madras
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Received on Fri Apr 07 2017 - 21:30:02 PDT
