[gmx-users] unexpected trajectory

[Vivek Raut]

At 07:18 PM 6/10/2003 -0700, you wrote:
>yes, i added that condition in .mdp file. but am not able to keep the 
>water box intact.
>
>David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>>Subject: Re: [gmx-users] unexpected trajectory
>>From: David van der Spoel
>>To: gmx-users at gromacs.org
>>Date: 10 Jun 2003 16:43:23 +0200
>>
>>On Mon, 2003-06-09 at 16:08, Vivek Raut wrote:
>> > i loaded the .trr file in VMD. My system has middle layer of molecules
>> > fixed, & molecules in upper/ lower layer are free to move. All the
>> > molecules are in cubical box.
>> >
>> > the trajectory shows that lower half molecules maintained the box shape &
>> > were shown moving within the shape, but the molecules in upper half 
>> wander
>> > off & disperse in all directions, not following the periodic boundary
>> > conditions.
>>are you sure you have pbc=xyz in your mdp file?
>> >
>> > what maybe the reason ?
>> >
>> > 
>> -------------------------------------------------------------------------------------------------------------------------------------------
>> > Vivek Raut
>> > Graduate Research Assistant
>> > Department of Bioengineering
>> > Clemson University
>> > Clemson, SC- 29631. USA
>> > Email: vraut at clemson.edu
>> > Phone: 864-650-1431
>> > 
>> --------------------------------------------------------------------------------------------------------------------------------------------
>> >
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>> >
>>--
>>Groeten, David.
>>________________________________________________________________________
>>Dr. David van der Spoel, Dept. of Cell & Mol. Biology
>>Husargatan 3, Box 596, 75124 Uppsala, Sweden
>>phone: 46 18 471 4205 fax: 46 18 511 755
>>spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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>
>  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
>Vivek Raut
>Graduate Research Assistant
>Dept. of Bioengineering
>Clemson University, SC- 29631.
>Email:vraut at clemson.edu
>Phone: 864-650-1431
>
>
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-------------------------------------------------------------------------------------------------------------------------------------------
Vivek Raut
Graduate Research Assistant
Department of Bioengineering
Clemson University
Clemson, SC- 29631. USA
Email: vraut at clemson.edu
Phone: 864-650-1431
--------------------------------------------------------------------------------------------------------------------------------------------