AMBER Archive (2007)

Subject: RE: AMBER: Time step & non-bonded interactions updating

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Sat Dec 15 2007 - 19:32:08 CST

Hi Francesco,

Amber 9 updates the pair list automatically as needed - there is no need to
change it unless you specifically want backwards compatibility with earlier
versions of Amber. Without seeing some output around the region where you
describe "having problems of protein stability" it is hard to offer specific
advise.

However, I would try reducing the restraint weight to something like 5.0.
You might also want to increase the value of taup to 5.0 or so. Also I have
no experience with membrane simulations but I think you may need anisotropic
pressure control. Perhaps other can chime in here.

A time step of 1.8 to 1.5 fs may also help.

All the best
Ross

/\
\/
|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.

> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of Francesco Pietra
> Sent: Saturday, December 15, 2007 10:40
> To: Amber
> Subject: AMBER: Time step & non-bonded interactions updating
>
> I am having problems of protein stability (in a POPC membrane) during
> equilibration and MD although the min heat density equil
> analyses imitated from
> tutorial A3 were OK.
>
> I suspect that the time-step 0.002 (see for example the in
> file below) is
> giving the problems (Minimization was carried out without
> shake and heating
> along the method of tutorial A3)
>
> density equilibration
> &cntrl
> imin=0, irest=1, ntx=5,
> nstlim=25000, dt=0.002,
> cut=10, ntb=2, ntp=1, taup=1.0,
> ntc=2, ntf=2,
> ntpr=500, ntwx=500,
> ntt=3, gamma_ln=2.0,
> temp0=300.0,
> ntr=1,
> restraintmask=":77-521 | :POP_at_O2, P1, O3, O4, O1, C15, C11,
> N, C12, C13, C14"
> restraint_wt=32,
> /
>
> Before changing to dt=0.001, may I ask about updating
> non-bonded interactions,
> which might also be relevant. As far as I understand from the
> manual of Amber9,
> updating non-bonded interactions with a *.in file like above
> occurs by default
> to security values. In descriptions from Amber8 non-bonded
> interactions were
> set to be updated every 10 time steps. I would like to have
> this precise
> condition. Much obliged for instructing me how to set that in Amber9.
>
> francesco pietra
>
>
>
> ______________________________________________________________
> ______________________
> Be a better friend, newshound, and
> know-it-all with Yahoo! Mobile. Try it now.
> http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ
>
> --------------------------------------------------------------
> ---------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>

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