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

[Mark Abraham]

On 28/11/2011 10:37 PM, ?? wrote:
> 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

If this is the same system as previously reported, then you're probably 
observing the system velocities exploding on one replica then being 
exchanged to a new replica.

Mark

>
> 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 <mailto:2008dubo at gmail.com> ; 
> dubo2008 at tju.edu.cn <mailto:dubo2008 at tju.edu.cn>
>
>
>
>
>
> =======================================================================================================
> Message: 4
> Date: Sun, 27 Nov 2011 22:36:08 -0500
> From: "Justin A. Lemkul" <jalemkul at vt.edu <mailto: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 
> <mailto:gmx-users at gromacs.org>>
> Message-ID: <4ED301A8.9070609 at vt.edu <mailto:4ED301A8.9070609 at vt.edu>>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
>
>
> ?? 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 <http://vt.edu/> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>

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