Hi everyone,
I am trying to replicate an MD protocol that has been done previously
using NAMD 2.9 using AMBER.
After the initial minimisation steps (water and ions, then backbone of
protein and so on), I am trying to do the following:
"380 ps initial MD run with consecutively weaker restraints on protein
atoms and gradually heat up the system to 300K"
Usually in my minimisation input file I keep the restraints constant
like this:
> Stage 1 - 1000 step minimisation of water and ions
> &cntrl
> imin=1, maxcyc=1000, ncyc=500,
> cut=12.,ntb=1,ntr=1,
> ntpr=100
> /
> Hold protein fixed
> 500.0
> RES 1 422
> END
> END
And to heat up a system I do it like this (after the &cntrl section):
> &wt type='TEMP0', istep1=0, istep2=50000,
> value1=0.0, value2=300.0 /
> &wt type='END' /
> Hold protein fixed
> 10.0
> RES 1 422
> END
> END
Does anyone have an idea of how could I change two variables at a time?
I've looked into section 18.8 of the Manual, but I am not sure if I
should change the BOND option or the REST one, or how to proceed to
change one of the two as well as the TEMP0 option.
Looking forward to hear any suggestion on this matter,
Juan
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Received on Mon May 18 2015 - 05:30:05 PDT
