AMBER Archive (2008)

Subject: RE: AMBER: increasing temperature smoothly

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Fri Sep 19 2008 - 13:29:31 CDT

Hi Germain,

Firstly you don't have nmropt=1 in you cntrl namelist. I think the
restraints also need to come last, after the &wt namelists.

All the best
Ross

> -----Original Message-----
> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
> Of Germain Vallverdu
> Sent: Friday, September 19, 2008 8:18 AM
> To: amber_at_scripps.edu
> Subject: AMBER: increasing temperature smoothly
>
> Dear amber users
>
> I would like to know if the following input will do what I want. I would
> like to start a simulation with temp0=100K and in the first 20000 steps,
> I would like temp0 increase linearly from 100K to 300K and then keep the
> value of 300K for the remainder of the run.
>
> equilibration a volume constant thermalisation avec contrainte prot
> &cntrl
> nstlim=50000, dt=0.002,
> irest=0, ntx=1, t=0.0, ig=300708,
> ntpr=1000, ntwr=1000, ntwx=1000,
> tempi=100.0, temp0=300.0, ntt=3,
> ntb=1, ntp=0,
> ntc=2, ntf=2,
> cut=10.0
> ntr=1,
> /
> Keep protein fixed with weak restraints
> 10.0
> RES 1 227
> END
> END
> &wt
> type='TEMP0',
> istep1=1,
> istep2=20000,
> istep2=0,
> imult=0,
> iinc=0,
> value1=100,
> value2=300,
> /
> &wt
> type='END'
> /
>
> I got the following error message
>
> PGFIO-F-252/formatted read/unit=5/operation attempted after end of file.
> File name = eq_v.in formatted, sequential access record = 34
> In source file _rgroup.f, at line number 175
>
>
> Thanks
>
> Germain
>
> --
> Germain Vallverdu
> Laboratoire de Chimie Physique
> Université Paris Sud 11
> germain.vallverdu_at_lcp.u-psud.fr
> ma page perso <http://pagesperso.lcp.u-psud.fr/vallverdu/>
> 01 69 15 30 38 / 06 88 59 08 87
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