Hi Daniel
Thanks so much for the reply.
what about the other question that shows the pressure equal to zero for the first two equilibration steps?
Regards
Ramin
________________________________
From: Daniel Roe <daniel.r.roe.gmail.com>
Sent: Wednesday, May 31, 2017 2:09:44 PM
To: AMBER Mailing List
Subject: Re: [AMBER] High pressure fluctuation in isothermal-isobaric ensemble
With regards to large pressure fluctuations, this has been brought up
on the list several times before, see e.g.:
https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Farchive.ambermd.org%2F201406%2F0026.html&data=02%7C01%7Cramin.salimi01%40utrgv.edu%7C21a3d4c148ed4dc301e308d4a858a652%7C990436a687df491c91249afa91f88827%7C0%7C0%7C636318546081583888&sdata=R25G5oyz4C7OXxSZ2%2BG1NLltIVjiAcs30kHulLUcdYA%3D&reserved=0
Hope this helps,
-Dan
On Wed, May 31, 2017 at 12:12 PM, Ramin Salimi <ramin.salimi01.utrgv.edu> wrote:
> Dear All
>
> I have done heating, and equilibration steps to prepare my system for the production run; however, in equilibration, I have set ntb=2 for all equilibration steps but when I look at the output file, for the first two equilibration, the pressure is zero, and for the other equilibration steps, there is so much irregularity in pressure such that in each of the output files for equilibration steps, RMS is very big for the pressure while I thought that I have tuned the equilibration to be done in constant-pressure, and constant temperature.
>
> The order is min1, min2, equil1, heat, equil2, equil3, equil4, ......, equil8.
>
> I have two questions: first, why do I see such a high RMS for pressure in equilibrium steps? second, why is the pressure zero in the first two steps of equilibration?
>
> The link to the output files for the equilibration steps along with the parameter file is provided:
>
> https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Futrgv-my.sharepoint.com%2Fpersonal%2Framin_salimi01_utrgv_edu%2F_layouts%2F15%2Fguestaccess.aspx%3Fdocid%3D15fcf7137428340b68ec739c19d5f92e0%26authkey%3DAXHIB0P6hK1PeSiI3NBJzpg&data=02%7C01%7Cramin.salimi01%40utrgv.edu%7C21a3d4c148ed4dc301e308d4a858a652%7C990436a687df491c91249afa91f88827%7C0%7C0%7C636318546081583888&sdata=nvtHSdiHUAeHT7FhntfstCtXr73d%2BQ8fd1CRfPvYlro%3D&reserved=0
>
>
> I would appreciate if you give me insight on what I have done wrong.
>
> Regards
>
> Ramin
>
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.lobos.nih.gov%2Flcb&data=02%7C01%7Cramin.salimi01%40utrgv.edu%7C21a3d4c148ed4dc301e308d4a858a652%7C990436a687df491c91249afa91f88827%7C0%7C0%7C636318546081583888&sdata=6VOBfMas7yKv3MuAeLB04u3%2BzwGEgMZKO3VHXA545zk%3D&reserved=0
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Received on Thu Jun 01 2017 - 08:00:02 PDT
