Re: [AMBER-Developers] slightly obscure parameter combination...

From: <>
Date: Fri, 5 Mar 2010 09:46:38 -0500 (EST)

Hi everyone,

I have a question about combining ntt=3 and ibelly (yes, I know ibelly is
an option that should normally be avoided, but it has its uses...)

The combination of these two options was prohibited by Ross citing
'issues' with MD. My question is, is there anything practically or
conceptually wrong with using ibelly and ntt=3 when we add an additional
call to zero velocities after the temperature adjustment step? It seems to
run fine for me...

Diff of runmd.f:

*** 1743,1748 ****
--- 1751,1759 ----
     end if ! ( gammai == 0.d0 )

+ ! Now zero out the non-moving velocities again if a belly is active:
+ if (belly) call bellyf(nr,ix(ibellygp),v)
     ! --- consider vlimit

     if (vlim.and.ipimd==0) then

Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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Received on Fri Mar 05 2010 - 07:00:04 PST
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