it might not resolve the problem, but you should check your pressure
coupling if you have trouble getting the density right (ntp, not ntt). Of
course ntt might also be related, but since you didn't say whether
you have checked ntp and/or taup, I wasn't sure if you did since at some
point in your mail you mention constant volume calculations.
On 3/21/07, Therese Malliavin <terez.pasteur.fr> wrote:
> Dear AMBER users,
>
> I have a couple of questions about the parameters ntt. I have seen that
> several questions have been asked in the past, for versions 7 and 8 of
> AMBER, but there are some changes in the documentation of AMBER9, and I
> have some trouble with them. So I apologize if the question was already
> asked for AMBER 9 (I checked on the archive of the mailing list and did
> not find anything).
>
> In documentation of AMBER 8, one finds that ntt=1 and tautp=0.2 are
> proposed for the example (p. 103) of usual MD in the NTP ensemble.
>
> In documentation of AMBE 9, the user is told not to use ntt=1: "Unless
> you are sure you know what you are doing, please don't use ntt=1!" (p.
> 103) , and ntt=3 and gamma_ln=1.0 are proposed in the example (p. 96)
> for usual MD in the NTP ensemble.
>
> So, I decided to switch from ntt=1 to ntt=3 for running an usual MD
> simulation in the NTP ensemble (without QMMM). Before that, I was
> heating the system using ntt=1 and a constant volume ensemble.
>
> But, the equilibration simulation has a problem with the water density
> which is about 0.84 in place of slightly larger than 1. Also, the
> pressure is switched to negative values (mean pressure calculated over
> 20 ps is about -100 atm, whereas I always found it around 0 in the past
> when I was using ntt=1).
>
> So, I would greatly appreciate to have some explanation about the setup
> of thermostats in AMBER 9, and about the input values recommended for
> the different uses of sander.
>
> Best regards,
>
> Thérèse Malliavin
> CNRS research fellow
> Unité de Bioinformatique Structurale
> Institut Pasteur de Paris
>
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>
--
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
CMM Bldg, Room G80
Stony Brook University E-mail: carlos.simmerling.gmail.com
Stony Brook, NY 11794-5115
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Received on Sun Mar 25 2007 - 06:07:14 PDT
