Hello all,
To find out protein's activity change due to mutation in RNA I am
currently doing SMD with CV as COM and Umbrella Sampling. While i am
pulling RNA from bound to unbound state it goes out of my water box.
Will it affect my calculations? Should i make a bigger box ? Any kind of
suggestions would be really helpful. The input files are attached
herewith.
smd input:
&cntrl
imin=0,
irest=1,
ntx=5,
nstlim=50000000,
dt=0.002,
ntc=2, ntf=2,
cut=8.0,
ntb=2,
ntp=1, taup=2.0,
ntpr=1000,
ntwx=1000,
ntt=3, gamma_ln=2.0,
temp0=300.0,
infe=1,
&end
&smd
output_file = 'smd_COM.txt',
output_freq = 50,
cv_file = 'cv.in'
&end
&wt type='DUMPFREQ', istep1=500 /
&wt type='END' /
cv input:
cv_file
&colvar
cv_type = 'COM_DISTANCE',
cv_ni = 875,
cv_i = 5368, 5369, ....., 0, ..., 4214, 0,
npath = 3,
path = 24., 37., 50.,
path_mode = 'SPLINE',
nharm = 1,
harm = 10.,
harm_mode = 'SPLINE'
/
Regards,
Sidharth.E.K.
PhD Scholar
NACB Lab
Chemistry Department
IIT Bombay
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Received on Tue Jun 17 2025 - 06:30:03 PDT
