AMBER Archive (2004)

Subject: AMBER: question about parallel simulation

From: qlu_at_notes.cc.sunysb.edu
Date: Wed Dec 01 2004 - 13:17:43 CST

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)

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu