AMBER Archive (2004)

Subject: Re: AMBER: GB+LES

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Wed Jun 30 2004 - 06:26:59 CDT

you don't say what temperature you are using for
the LES region in each case. Are you coupling
to a separate both for LES? In general, the LES
region should be kept at a lower T than the non-LES
region.
carlos
----- Original Message -----
From: "Marcin Krol" <mykrol_at_cyf-kr.edu.pl>
To: <amber_at_scripps.edu>
Sent: Wednesday, June 30, 2004 5:43 AM
Subject: AMBER: GB+LES

> Dear All
>
> I would liketo run LES+GB simulations to quickly sample side chain
> coformations. I am, however, confused by the omas keyword. I think I
> should not use this keyword and scale masses of LES atoms by 1/NC to get
> corect thermal energy. On the other hand all examples in the manual
> include omas keyword. When I run LES MD with omas I got highly distorted
> structure in the area where LES copies where. Without omas I often get
> shake error. Could you please comment/give advice on the use of omas
> keyword (scaling of masses).
>
> Thank you in advance for your answer
>
> Best regards
> marcin
>
>
> Dr Marcin Krol
> Zaklad Bioinformatyki Collegium Medicum UJ
> Kopernika 7E
> 31-501 Krakow
> tel/fax (012) 422-77-64
> e-mail mykrol_at_cyf-kr.edu.pl
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