[gmx-users] Adding Urea in simulation

[bharat gupta]

Thanks Justin ... The problem was with the memory .. I ran the same
calculation on separate system and I worked perfectly fine ...



On Wed, Mar 5, 2014 at 8:11 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

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> On 3/5/14, 5:58 AM, bharat gupta wrote:
>
>> Hi,
>>
>> I am trying to add 5M urea in a box of volume 1453.73 cubic nm, which is
>> equal to 4377 molecules of urea. But while adding it using genbox command,
>> I get an error "killed" and the program stops after that. What is wrong
>> here, is my calculation correct or the size of box should need to be
>> increased ??
>>
>>
> Without your actual command(s), there's little to suggest.  genbox is
> running out of memory trying to do whatever you've asked.  Try with the
> 5.0-beta program insert-molecules; IIRC some memory leaks have been fixed
> and it is more efficient.
>
> -Justin
>
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> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
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