[gmx-users] remd in the npt ensemble: When the exchange, the temperature abruptly surge .

[杜波]

dear teacher,
i find the answer of that  letter "Subject: Re: [gmx-users] REMD: NPT being
+-Infinity or NaN",
ifind that "when the exchange, the temperature abruptly surge .",as follows,
dt=0.002ps  -replex 4000

@ s0 legend "Temperature"
@ s1 legend "Pressure"
    0.000000  546.497375   60.637791
    1.000000  556.582397  244.328201
......
   94.000000  557.564453  -17.035589
   95.000000  543.882629   57.111996
   96.000000  523.336548  -25.745819
   97.000000  555.043335  254.709778
   98.000000  555.595886  -39.830761
   99.000000  542.395325   49.084045
  100.000000  550.955261  -149.259979
  101.000000  134372.953125  4419.518066
  102.000000  156382.859375  -17109.099609
  103.000000  138660.156250  -11395.237305
  104.000000  165148.265625  20807.541016
.......

But if change the replex to 400000000,so i can not exchange.
Then the system is ok.
&& The initial conformation has been done a long time MD

thanks for your help !!
Bo Du
Department of Polymer Science and Engineering,
School of Chemical Engineering and technology,
Tianjin University, Weijin Road 92, Nankai District 300072,
Tianjin City P. R. China
Tel/Fax: +86-22-27404303 ; +8613820062885
E-mail: 2008dubo at gmail.com ; dubo2008 at tju.edu.cn





=======================================================================================================
Message: 4
Date: Sun, 27 Nov 2011 22:36:08 -0500
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Subject: Re: [gmx-users] REMD: NPT being +-Infinity or NaN
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4ED301A8.9070609 at vt.edu>
Content-Type: text/plain; charset=UTF-8; format=flowed



杜波 wrote:
> dear teacher,
> when i do remd  in the  npt ensemble.
>
> REMD: NPT -replex 4000
> dt= 0.0001
>
> step 172000, will finish Sat Dec 31 18:44:12 2011
>
> -------------------------------------------------------
> Program mdrun_mpi_4.5.5, VERSION 4.5.5
> Source code file: nsgrid.c, line: 549
>
> Range checking error:
> Explanation: During neighborsearching, we assign each particle to a grid
> based on its coordinates. If your system contains collisions or parameter
> errors that give particles very high velocities you might end up with some
> coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
> put these on a grid, so this is usually where we detect those errors.
> Make sure your system is properly energy-minimized and that the potential
> energy seems reasonable before trying again.
>
> how could  i do except using the small dt ?
>

Your system is not stable, as is often the case with NPT REMD at high
temperature.

http://www.gromacs.org/Documentation/Terminology/Blowing_Up

-Justin

--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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