AMBER: question about parallel simulation

From: <qlu.notes.cc.sunysb.edu>
Date: Wed, 1 Dec 2004 14:17:43 -0500

Hi AMBER

In order to run go model in AMBER8, I changed some parameters in sander.
However the results from single CPU and parallel versions are quite
different.
The radius gyration and the number of native contacts are all different.
Could anyone tell me what's wrong.

Qiang Lu


< go model
> original


< rad(1000),wel(1000),radhb(1000),welhb(1000)

---
>       rad(100),wel(100),radhb(200),welhb(200)
<    parameter (maxigr=500)
---
>    parameter (maxigr=200)
< parameter (extraboxdim=50.d0)
---
> parameter (extraboxdim=30.d0)
< _REAL_ rk(40000),req(40000),tk(7000),teq(7000),pk(10000), &
<       pn(1200),phase(1200),cn1(40000),cn2(40000),solty(1000), &
<       gamc(1000),gams(1000),fmn(1000), &
<       asol(40000),bsol(40000),hbcut(40000)
---
> _REAL_ rk(5000),req(5000),tk(900),teq(900),pk(1200), &
>       pn(1200),phase(1200),cn1(1830),cn2(1830),solty(60), &
>       gamc(1200),gams(1200),fmn(1200), &
>       asol(200),bsol(200),hbcut(200)
<          nphb > 40000 .or. natyp > 500 .or. nttyp > 40000) then
---
>          nphb > 200 .or. natyp > 60 .or. nttyp > 1830) then
< common/p14/ cn114(40000),cn214(40000)
< common/ub/rkub(40000),rub(40000)
---
> common/p14/ cn114(1830),cn214(1830)
> common/ub/rkub(900),rub(900)
<    parameter (maxpr = 10000000)
---
 >    parameter (maxpr = 5000)
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Received on Wed Dec 01 2004 - 19:53:00 PST